Schema 47 documentation

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfections ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <vectorPop ... /> ]
| [ <vectorTrap ... /> ]
| [ <nonHumanHostsModifications ... /> ]
| [ <addNonHumanHosts ... /> ]
| [ <human ... /> ]
</interventions>

Documentation (element)

List of interventions. Generally these are either point-time distributions of something to some subset of the population, or continuous-time distribution targetting individuals when they reach a certain age.

Attributes

Name of intervention set

name=string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeHS>

timedDeployment

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeHS → timedDeployment

<timedDeployment
    time=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timedDeployment>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Time at which this replacement occurs. See doc on intervention period and on monitoring/startDate for details of how times work. Can be specified in steps, days, years, or as a date (examples: 15t, 75d, 0.2y, 2000-03-16).

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</uncomplicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

multiple

→ scenario → interventions → human → component → decisionTree → multiple

<multiple
  [ name=string ]
  >
EXACTLY ONE OF:
| ( <caseType ... /> )*
| ( <diagnostic ... /> )*
| ( <uncomplicated ... /> )*
| ( <severe ... /> )*
| ( <random ... /> )*
| ( <age ... /> )*
| ( <treatPKPD ... /> )*
| [ <treatSimple ... /> ]
| ( <deploy ... /> )*
| ( <report ... /> )*
| ( <cohort ... /> )*
</multiple>

Documentation (type)

A special node allowing multiple sub-trees to be evaluated.

This is different from an ordinary decision tree node in that:

a) multiple types of child can occur simultaneously (e.g. multiple types of treatment or treatment plus a 'random' sub-tree)

b) the 'noTreatment' and 'treatFailure' nodes are not allowed

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → multiple → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

firstLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → firstLine

<firstLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</firstLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

secondLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → secondLine

<secondLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</secondLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

positive

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

uncomplicated

→ scenario → interventions → human → component → decisionTree → uncomplicated

<uncomplicated
  [ name=string ]
  [ memory=string ] DEFAULT VALUE 1
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</uncomplicated>

Documentation (type)

A switch which choses a branch deterministically, based on whether the host has an uncomplicated case. This could be a Malaria fever or a non-Malaria fever. If non-Malaria fevers are enable, it is possible to add a node.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Number of days to look back for fevers. This must be less than or equal to the healthsystem memory parameter. In general, this should be less than or equal to the repeatStep in MSAT with contiuous deployment

memory=string

Units: User-defined (defaults to steps)

Default value: 1

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

positive

→ scenario → interventions → human → component → decisionTree → multiple → uncomplicated → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

severe

→ scenario → interventions → human → component → decisionTree → severe

<severe
  [ name=string ]
  [ memory=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</severe>

Documentation (type)

A switch which choses a branch deterministically, based on whether the host has a severe case or not. Note that this include severe cases due to comorbidities.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Number of days to look back for fevers. This must be less than or equal to the healthsystem memory parameter. In general, this should be less than or equal to the repeatStep in MSAT with contiuous deployment

memory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

positive

→ scenario → interventions → human → component → decisionTree → multiple → severe → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

outcome

→ scenario → interventions → human → component → decisionTree → multiple → random → outcome

<outcome
  [ name=string ]
    p=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</outcome>

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Probability

p=double

Units: None Min: 0 Max: 1

Probability of selecting this outcome. The sum of probabilities across all outcomes must be 1.

age

→ scenario → interventions → human → component → decisionTree → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Categories must uniquely cover all ages from birth, with no upper bound. Categories must be listed in order of age, increasing; the first must have lower bound 0. Upper bounds are equal to the lower bound of the next category, (but are exclusive where lower bounds are inclusive); the last category has no upper bound.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Age range

→ scenario → interventions → human → component → decisionTree → multiple → age → age

<age
  [ name=string ]
    lb=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</age>

Documentation (element)

Describes a branch, selected for patients of a certain age.

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Lower bound (inclusive)

lb=double

Min: 0

noTreatment

→ scenario → interventions → human → component → decisionTree → noTreatment

<noTreatment
  [ name=string ]
  />

Documentation (type)

An end node doing nothing. This exists to explicitly state that no treatment happens and to prevent trees from accidentally being left incomplete.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

report

→ scenario → interventions → human → component → decisionTree → report

<report
  [ name=string ]
  [ outputNumber=int ] DEFAULT VALUE 0
  />

Documentation (type)

This increments measure 80 (nCMDTReport) by one every time this node is visited. This can be useful to report the results of mass test and treat interventions using the decision tree.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Delay (hours)

outputNumber=int

Default value: 0

Optionally, this can be given to delay the start of treatment by a given number of hours. If not specified, treatment is not delayed. If a delay is given, all medications within the treatment schedule used are delayed by this number of hours.

treatFailure

→ scenario → interventions → human → component → decisionTree → treatFailure

<treatFailure
  [ name=string ]
  />

Documentation (type)

An end node which reports treatment but does not change parasitalogical status. This allows correct labelling of second-line cases.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Simple treatment model, targetting liver- and/or blood-stage infections. This is all-or-nothing treatment which, when deploymed, completely clears all infections of the targetted stages. This makes it unsuitable for modeling resistance, but suitable for use with simple infection models.

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Controls action on liver-stage infections. 0 means no action, -1 step is a compatibility option to act like treatment before schema version 32 (which removed infections retrospectively), 1 step or any duration which equals some whole number of steps n>0 means to clear all liver-stage infections found on the next 1 or n steps. Note on -1 compatibility option: the main difference to 1 step (clearing on the next timestep) is that parasite densities will be reduced immediately, and thus from the point of view of surveys and mass screen and treat interventions a peak in density which is immediately treated through case management will not be seen. Can be specified in steps (e.g. 1t, -1t) or days (e.g. 5d).

Length of blood-stage effect

durationBlood=string

Units: User defined

Controls action on blood-stage infections. 0 means no action, -1 step is a compatibility option to act like treatment before schema version 32 (which removed infections retrospectively), 1 step or any duration which equals some whole number of steps n>0 means to clear all blood-stage infections found on the next 1 or n steps. Note on -1 compatibility option: the main difference to 1 step (clearing on the next timestep) is that parasite densities will be reduced immediately, and thus from the point of view of surveys and mass screen and treat interventions a peak in density which is immediately treated through case management will not be seen. Can be specified in steps (e.g. 1t, -1t) or days (e.g. 5d).

deploy

→ scenario → interventions → human → component → decisionTree → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

cohort

→ scenario → interventions → human → component → decisionTree → cohort

<cohort
  [ name=string ]
    component=string
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</cohort>

Documentation (type)

A switch which choses a branch deterministically, based on whether the host is part of the cohort (defined by the intervention component) or not.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Number of days to look back for fevers. This must be less than or equal to the healthsystem memory parameter. In general, this should be less than or equal to the repeatStep in MSAT with contiuous deployment

component=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

positive

→ scenario → interventions → human → component → decisionTree → multiple → cohort → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

negative

→ scenario → interventions → human → component → decisionTree → multiple → cohort → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

negative

→ scenario → interventions → human → component → decisionTree → multiple → severe → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

negative

→ scenario → interventions → human → component → decisionTree → multiple → uncomplicated → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

negative

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

uncomplicated

→ scenario → interventions → human → component → decisionTree → multiple → uncomplicated

<uncomplicated
  [ name=string ]
  [ memory=string ] DEFAULT VALUE 1
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</uncomplicated>

Documentation (type)

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Number of days to look back for fevers. This must be less than or equal to the healthsystem memory parameter. In general, this should be less than or equal to the repeatStep in MSAT with contiuous deployment

memory=string

Units: User-defined (defaults to steps)

Default value: 1

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

severe

→ scenario → interventions → human → component → decisionTree → multiple → severe

<severe
  [ name=string ]
  [ memory=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</severe>

Documentation (type)

A switch which choses a branch deterministically, based on whether the host has a severe case or not. Note that this include severe cases due to comorbidities.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Number of days to look back for fevers. This must be less than or equal to the healthsystem memory parameter. In general, this should be less than or equal to the repeatStep in MSAT with contiuous deployment

memory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

random

→ scenario → interventions → human → component → decisionTree → multiple → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

age

→ scenario → interventions → human → component → decisionTree → multiple → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → multiple → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → multiple → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → multiple → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

report

→ scenario → interventions → human → component → decisionTree → multiple → report

<report
  [ name=string ]
  [ outputNumber=int ] DEFAULT VALUE 0
  />

Documentation (type)

This increments measure 80 (nCMDTReport) by one every time this node is visited. This can be useful to report the results of mass test and treat interventions using the decision tree.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Delay (hours)

outputNumber=int

Default value: 0

cohort

→ scenario → interventions → human → component → decisionTree → multiple → cohort

<cohort
  [ name=string ]
    component=string
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</cohort>

Documentation (type)

A switch which choses a branch deterministically, based on whether the host is part of the cohort (defined by the intervention component) or not.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Number of days to look back for fevers. This must be less than or equal to the healthsystem memory parameter. In general, this should be less than or equal to the repeatStep in MSAT with contiuous deployment

component=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</complicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: Days Min: 0 Max: unbounded

Maximum number of timesteps (including first day of case) that an individual with an uncomplicated case of malaria will remember he/she was sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial or non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of a complicated or severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

It is sometimes desirable to model delays to treatment-seeking in uncomplicated cases. While treatment of drugs can be delayed within case management trees to provide a similar effect, this doesn't delay any of the decisions, including diagnostics using the current parasite density.

Instead a list of dailyPrImmUCTS elements can be used, describing successive daily probabilities of treatment (sum must be 1). For example, with a list of two elements with values 0.8 and 0.2, for 80% of UC cases the decision tree is evaluated immediately, and for 20% of cases evaluation is delayed by one day.

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

Description of non-malaria fever health-system modelling (treatment, outcomes and costing). Incidence is described by the model->clinical->NonMalariaFevers element. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

As further explanation of the parameters below, we first take: β₀ = logit(P₀) - β₃·P(need), and then calculate the probability of antibiotic administration, P(AB), dependent on treatment seeking location. No seeking: P(AB) = 0 Informal sector: logit(P(AB)) = β₀ + β₄ Health facility: logit(P(AB)) = β₀ + β₁·I(neg) + β₂·I(pos) + β₃·I(need) (where I(X) is 1 when event X is true and 0 otherwise, logit(p)=log(p/(1-p)), event "need" is the event that death may occur without treatment, events "neg" and "pos" are the events that a malaria parasite diagnositic was used and indicated no parasites and parasites respectively).

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

Interpolation algorithm. Normally it is desirable for age-based values to be continuous w.r.t. age. By default linear interpolation is used. With all algorithms except "none", the age groups are converted to a set of points centred within each age range. Extra points are added at each end (zero and infinity) to keep value constant at both ends of the function. A zero-length age group may be used as a kind of barrier to adjust the distribution; e.g. with age group boundaries at 15, 20 and 25 years, a (linear) spline would be drawn between ages 17.5 and 22.5, whereas with boundaries at 15, 20 and 20 years, a spline would be drawn between ages 17.5 and 20 years (may be desired if individuals are assumed to reach adult size at 20). Algorithms:

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

A series of values according to age groups, each specified with a lower-bound and a value. The first lower-bound specified must be zero; a final upper-bound of infinity is added to complete the last age group. At least one age group is required. Normally these are interpolated by a continuous function (see interpolation attribute).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
  [ name=string ]
  [ useDiagnosticUC=boolean ] DEFAULT VALUE false
  >
IN ANY ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <treatmentActions ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
</ImmediateOutcomes>

Documentation (type)

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Name of case management parameterisation

name=string

Name of health system

useDiagnosticUC

useDiagnosticUC=boolean

Default value: false

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Description of drug regimen.

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Artemisinine based combination therapy

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Quinine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0 Max: 1name:P(self-treat)

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Effectiveness of treatment for non-compliant patients

treatmentActions

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions

<treatmentActions>
IN ANY ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
</treatmentActions>

CQ
SP
AQ
SPAQ
ACT
QN

CQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ

<CQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</CQ>

Documentation (type)

Describes the effects of the treatment, assuming this compliance/adherence/... option is selected. Effects are described in terms of a list of options, each of which acts independently but with all effects being activated simultaneously.

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Components are referenced from one or more sub-lists. Each of these lists is deployed independently if and only if its age constraints are met by the human host and a random sample with the given probability of a positive outcome is positive.

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

deploy

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy

<deploy
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ p=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| ( <component ... /> )+
</deploy>

component

Attributes

Maximum age of eligible humans

maxAge=double

Units: Years Min: 0

Maximum age of eligible humans (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible humans

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible humans (defaults to 0). Input is rounded to the nearest time step.

Probability of delivery to eligible humans

p=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Probability of this list of components being deployed, given that other constraints are met.

component

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Prophylactic treatment

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere → clearInfections

<clearInfections
    timesteps=string
    stage=("liver" or "blood" or "both")
  />

Documentation (element)

This clears infections according to several options: it can clear all blood stage infections, all liver stage infections or both, and it can act on multiple timesteps. To have a probability of no action add another treatment option (which does nothing) and set the probabilities of selection appropriately.

This allows immediate (legacy) or delayed action, a prophylactic period, and selection of which stages are targeted. It is a simple model but appropriate enough for use with the five day timestep when assuming no resistance and that drug failure is mainly caused by bad drugs or compliance.

The old treatment action for the five-day timestep model is essentially this, with immediateAction (timesteps=-1) and stage=both, except for the IPT model's SP action, which was more like with timesteps>1 and stage=blood.

Attributes

Length of effect

timesteps=string

Units: User defined (defaults to steps)

The number of timesteps during which this action remains in effect (e.g. 2 means clear infections during the next two timestep updates). Full clearance of the targeted stages occurs during this time. A special value of -1 means act immediately (retrospectively); this the old behaviour. A value of 1 means act on the next timestep only. Both of these can be thought of as a model for short-acting effective drug treatment; the main differences are that the latter means parasite densities will remain high from the point of view of surveys and diagnostics (i.e. mass screen and treat) used before the next timestep and that the latter will also remove infections starting the next timestep. Arguably the latter is a better model, but the differences are perhaps small, excepting where immediate treatment of fevers (i.e. through the health system) can hide high parasite densities from reporting and mass-screen-and-treat diagnostics. For use by interventions, the latter model has nicer behaviour in that the order of deployment of multiple interventions deployed at the same time does not matter, and that the former model retrospectively treats infections which may already have caused fever, thus may have a lower health impact than it should. It is recommended to use the new model (value 1, or greater than 1 if prophylactic effect is desired) unless wanting to emulate the old behaviour. Values of 0 or less than -1 are not allowed. Can be specified in steps (e.g. 1t, -1t) or days (e.g. 5d).

Target stage

stage=("liver" or "blood" or "both")

Controls whether liver-stage or blood-stage infections are cleared, or both. Infections are considered liver-stage for one 5-day timestep, blood-stage but pre-patent for some number of timesteps (latentp - 1), then start the patent blood stage. If stage is set to "liver", infections are only cleared during their first timestep; if stage is set to "blood", infections are cleared during pre-patent and patent blood stages; if stage is set to "both" all infections are cleared. The old behaviour (oddly considering the drugs it is meant to emulate) is to clear both stages, except for the IPT model of SP action, which cleared only patent blood-stage infections.

SP

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SP

<SP
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SP>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

AQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → AQ

<AQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</AQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

SPAQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SPAQ

<SPAQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SPAQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

ACT

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → ACT

<ACT
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</ACT>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

QN

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → QN

<QN
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</QN>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

Probability that human is incompatible with liver-stage drug treatment

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pHumanCannotReceive

<pHumanCannotReceive
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that a human is determined to be unable to receive liver-stage drug treatment. Treatment is neither reported or given for such humans.

This is sampled once per human at birth.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Ignore liver-stage drug treatment incompatibility

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → ignoreCannotReceive

<ignoreCannotReceive
    value=boolean
  />

Documentation (element)

If true, ignore pHumanCannotReceive and consider all humans eligible for treatment; if false (or not specified), do not treat those demed incompatible with liver-stage drug treatment.

The point of this is that pHumanCannotReceive cannot be altered by changeHS interventions, but this property can be.

Attributes

Input parameter value

value=boolean

A boolean value.

Prob use in UC case

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pUseUncomplicated

<pUseUncomplicated
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

This feature is deprecated; it is suggested to use the "simple treatment" feature configured to clear liver-stage parasites, leaving this option unset or zero.

Chance of liver-stage drug treatment being used for routine treatment of an uncomplicated case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Effectiveness

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → effectivenessOnUse

<effectivenessOnUse
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that liver-stage drug treatment is effective.

On application, a random variable is sampled against this probability. If false, the treatment does nothing; if true, the treatment clears all liver stage parasites. Where effectiveness is longer than a single time step (prophylactic effect), this sample still only happens once (thus either no effect or all liver stages cleared over multiple steps).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

DecisionTree5Day

<DecisionTree5Day
  [ name=string ]
  >
IN ANY ORDER:
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
|   <treeUCOfficial ... /> 
|   <treeUCSelfTreat ... /> 
|   <cureRateSevere ... /> 
|   <treatmentSevere ... /> 
</DecisionTree5Day>

Documentation (type)

Description of the health system using the 5-day timestep with decision tree model: access is configured as in the Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103) while treatment decisions are configured via decision trees.

Besides greater flexibility, this allows treatment via PK/PD models.

Attributes

Name of case management parameterisation

name=string

Name of health system

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → DecisionTree5Day → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → DecisionTree5Day → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

treeUCOfficial

→ scenario → healthSystem → DecisionTree5Day → treeUCOfficial

<treeUCOfficial
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</treeUCOfficial>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treeUCSelfTreat

→ scenario → healthSystem → DecisionTree5Day → treeUCSelfTreat

<treeUCSelfTreat
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</treeUCSelfTreat>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Cure rate (severe cases)

→ scenario → healthSystem → DecisionTree5Day → cureRateSevere

<cureRateSevere
    value=double
  />

Documentation (element)

Min: 0 Max: 1

The probability of clearing parasites given access to appropriate (hospital) care, for a severe case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

treatmentSevere

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere

<treatmentSevere
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</treatmentSevere>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Case fatality rate for inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: Dimensionless

List of age-specific probabilities of sequelae in inpatients, during a severe bout of malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeEIR>

timedDeployment

Documentation (element)

New description of transmission level for models not supporting vector control interventions. Use of this overrides previous transmission levels such that human infectiousness no longer has any feedback effect on transmission. Supplied EIR data must last until end of simulation.

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeEIR → timedDeployment

<timedDeployment
    eipDuration=int
    time=string
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timedDeployment>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Time

time=string

Units: User defined (defauls to steps) Min: 0

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

In the non-vector model, EIR is input as a sequence of daily values. There must be at least one years' worth of entries (365), and if there are more, values are wrapped and averaged (i.e. value for first day of year is taken as the mean of values for days 0, 365+0, 2*365+0, etc.).

Attributes

Time origin of EIR sequence

origin=string

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=string ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=string

Units: User defined (default: steps) Min: 0

Default value: 0

If period is 0 (or effectively infinite), the last specified value remains indefinitely in effect. If period is less than the length of the simulation's intervention phase, then all "rate" deployments are repeated with this periodicity. In this case, the first "rate" deployment must coincide with the start of the intervention phase (monitoring/startDate). Can be specified in steps (e.g. 1t) or days (e.g. 365d).

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=string
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time of start

time=string

Units: User defined (defauls to steps) Min: 0

Time at which this importation rate becomes active. See doc on intervention period and on monitoring/startDate for details of how times work. Can be specified in steps, days, years, or as a date (examples: 15t, 75d, 0.2y, 2000-03-16).

Insert R_0 case

<insertR_0Case
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</insertR_0Case>

timedDeployment

Documentation (element)

Used to simulate R_0. First, infections should be eliminated, immunity removed, and the population given an effective transmission- blocking vaccine (not done by this intervention). Then this intervention may be used to: pick one human, infect him, administer a fully effective Preerythrocytic vaccine and remove transmission-blocking vaccine effect on this human. Thus only this one human will be a source of infections in an unprotected population, and will not reinfected himself.

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → insertR_0Case → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Time at which this intervention occurs. See doc on intervention period and on monitoring/startDate for details of how times work. Can be specified in steps, days, years, or as a date (examples: 15t, 75d, 0.2y, 2000-03-16).

Uninfect vectors

<uninfectVectors
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</uninfectVectors>

timedDeployment

Documentation (element)

Units: List of elements

Removes all infections from mosquitoes -- resulting in zero EIR to humans, until such time that mosquitoes are re-infected and become infectious. Only efficacious in dynamic EIR mode (when changeEIR was not used).

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → uninfectVectors → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Vector population intervention

→ scenario → interventions → vectorPop

<vectorPop>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorPop>

intervention

Documentation (element)

Units: List of elements

A list of parameterisations of generic vector host-inspecific interventions.

intervention

→ scenario → interventions → vectorPop → intervention

<intervention
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

Units: List of elements

An intervention which may have various effects on the vector populations as a whole. (Not host specific.)

Multiple instances of this intervention class are allowed (multiple parameterisations, not just deployments).

Each instance may have multiple deployments. In this case the effects of each instance are independent (effects are combined) but the effects of multiple deployments of a single instance are not independent (only the latest deployment has any effect).

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → vectorPop → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → vectorPop → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <seekingDeathRateIncrease ... /> ]
| [ <probDeathOvipositing ... /> ]
| [ <emergenceReduction ... /> ]
| [ <probAdditionalDeathSugarFeeding ... /> ]
</anopheles>

Documentation (type)

Units: dimensionless Min: 0 Max: 1

Descriptions of the effects of vector interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Proportional increase in deaths while host searching

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease

<seekingDeathRateIncrease
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</seekingDeathRateIncrease>

decay

Documentation (element)

Units: dimensionless

Describe an effect on the increase in the death rate while host seeking (mu_vA) due to this intervention.

Enter the rate increase (i.e. if rate increases to 120% of normal, give 0.2). New death rate while seeking is old × (1 + increase) where increase is this factor given. Must have increas ≥ -1.

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

Determines which decay function to use. Available decay functions, for age t in years: constant: 1 step: 1 for t less than L, otherwise 0 linear: 1 - t/L for t less than L, otherwise 0 exponential: exp( - t/L * log(2) ) weibull: exp( -(t/L)^k * log(2) ) hill: 1 / (1 + (t/L)^k) smooth-compact: exp( k - k / (1 - (t/L)^2) ) for t less than L, otherwise 0

L

L=string

Units: User-defined (defaults to years) Min: 0

(Time) scale parameter of distribution: this is either the age of complete decay (smooth-compact, step and linear functions) or the age at which the parameter has decayed to half its original value (exponential, weibull and hill). Not used when function="constant" (i.e. no decay). This value can be specified in years, days or steps (e.g. 2y, 180d or 100t). When the unit is not specified years are assumed. The value is used without rounding except when sampling an age of decay, when the rounding happens as late as possible.

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

If CV is non-zero, heterogeneity of decay is introduced via a random variable sampled from the log-normal distribution. This distribution is parameterised with mean=1 and CV as given. The effective age of decay is the real age multiplied by this variable (for decay functions with a half-life, this is equivalent to dividing the half-life by the variable).

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

(Boolean) If True, this tells OpenMalaria to use the complement of the DecayFunction defined as 1-f(x). This is useful to model increasing functions that will "decay" to 1. This only works if f(x) is contained between 0 and 1.

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

decay

→ scenario → interventions → nonHumanHostsModifications → intervention → decay → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Proportion ovipositing mosquitoes killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing

<probDeathOvipositing
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probDeathOvipositing>

decay

Documentation (element)

Units: dimensionless

Describe an effect of increased mortality while ovipositing due to this intervention. Enter the probability of dying due to this intervention.

Attributes

Initial probability of killing

initial=double

Units: dimensionless Min: 0 Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Proportion of emerging pupa killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction

<emergenceReduction
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</emergenceReduction>

decay

Documentation (element)

Units: dimensionless

Describe an effect on emergence of pupa into adults: this value is the proportion of emerging pupa which are killed by this intervention.

This can be used as a crude way of modelling larviciding. It ca also be used to increase emergence by giving a negative value. The emergence rate is "old rate" × (1 - factor) where factor is the value given here; thus, for example, using -1 will double emergence.

Attributes

Initial proportion reduction

initial=double

Units: dimensionless Min: -inf Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Probability of death while host searching as a result of feeding on a sugar bait (used to dynamically adjust mu_vA)

→ scenario → interventions → vectorPop → intervention → description → anopheles → probAdditionalDeathSugarFeeding

<probAdditionalDeathSugarFeeding
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probAdditionalDeathSugarFeeding>

decay

Documentation (element)

Units: dimensionless

Describe an effect on the increase in the death rate while host seeking (mu_vA) due to this intervention. This works like adding an non-human host with its own availability. The difference is that biting this sugar bait is associated with a probability of dying of 1: all mosquitoes biting the sugar bait will die. OpenMalaria will automatically compute the availability for this host so that the probability of biting this 'host' (and thus dying) is equal to the input parameter.

Enter the probability of dying while host seeking due to this intervention. If multiple interventions overlap, the cumulative probability will be used. Note that it cannot exceed 1, and OpenMalaria will return an error during the simulation if this ever happens.

OpenMalaria will dynamically compute the necessary increase in mu_vA based on the given probability. Note that this is done by solving an equation numerically every timestep, which can cause a small drop in performance.

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probAdditionalDeathSugarFeeding → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Vector population intervention deployment

→ scenario → interventions → vectorPop → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

deploy

→ scenario → interventions → vectorPop → intervention → timed → deploy

<deploy
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Time at which this deployment occurs. See doc on intervention period and on monitoring/startDate for details of how times work. Can be specified in steps, days, years, or as a date (examples: 15t, 75d, 0.2y, 2000-03-16).

Baited trap

→ scenario → interventions → vectorTrap

<vectorTrap>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorTrap>

intervention

Documentation (element)

Traps attract and kill mosquitoes. They are modelled as a non-human-host where the probability of mosquitoes surviving feeding is zero (since otherwise the simulator would assume surviving mosquitoes have had a blood meal), and where this "host" is initially not present.

Model: each type of trap has has an initial availability relative to a human and a decay in availability. Each deployment has a fixed maximum lifespan, after which the traps from that deployment are removed (it is up to the user whether this is after availability is effectively zero or sooner, either coinciding with a redeployment or causing a reduction in overall effectiveness of traps).

intervention

→ scenario → interventions → vectorTrap → intervention

<intervention
  [ name=string ]
  >
IN THIS ORDER:
| ( <description ... /> )+
| [ <timed ... /> ]
</intervention>

Documentation (type)

Parameters and deployment of one type of trap. In case multiple types of trap are needed simultaneously, multiple elements can be used. Note that different types of trap do not interact except that all will attract mosquitoes.

Attributes

Descriptive name for type of trap

name=string

Optional name for this type of trap

Description

→ scenario → interventions → vectorTrap → intervention → description

<description
    mosquito=string
  >
IN THIS ORDER:
|   <relativeAvailability ... /> 
|   <decayOfAvailability ... /> 
</description>

Documentation (element)

Parameters associated with a vector trap intervention, per mosquito species.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Initial relative availability

→ scenario → interventions → vectorTrap → intervention → description → relativeAvailability

<relativeAvailability
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: inf

Describes the availiability of a trap to a host-seeking mosquito relative to an average unprotected adult.

I.e. if this parameter is 2, then each trap will on average attract twice as many mosquitoes as unprotected adults.

This is the initial availability; it may decay towards zero depending on the configured decay function.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay of availability

→ scenario → interventions → vectorTrap → intervention → description → decayOfAvailability

<decayOfAvailability
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decayOfAvailability>

decay

Documentation (element)

Describes how availability decays to zero.

If decay heterogeneity/variance is used, there will be a sample once-per-deployment (i.e. all traps of the same deployment will be affected the same way). There is no support for variances between traps (except in this crude way, between deployments).

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Vector trap intervention deployment

→ scenario → interventions → vectorTrap → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )*
</timed>

deploy

Documentation (element)

List of timed vector trap intervention deployment

deploy

→ scenario → interventions → vectorTrap → intervention → timed → deploy

<deploy
    time=string
    ratioToHumans=double
    lifespan=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Ratio to humans

ratioToHumans=double

Min: 0 Max: inf

The number of traps deployed, by this deployment, per adult human. E.g. if there are currently 100 traps and 1000 humans, then a ratio of 0.1 will increase the number of traps to 200.

Lifespan

lifespan=string

Units: Steps or Days or Years

Life of the trap until replaced or removed, e.g. "73t" or "1y". After this time period, these traps will be removed from the simulation. New deployments do not automatically remove old traps. Existing traps cannot be refurbished in the model. It may make sense to make the end-of-life coincide with a new deployment.

nonHumanHostsModifications

→ scenario → interventions → nonHumanHostsModifications

<nonHumanHostsModifications>
IN THIS ORDER:
| ( <intervention ... /> )+
</nonHumanHostsModifications>

intervention

Documentation (element)

List of interventions that modify parameters of non-human hosts described in the .

intervention

→ scenario → interventions → nonHumanHostsModifications → intervention

<intervention
    name=string
    nonHumanHostsName=string
  >
IN THIS ORDER:
|   <decay ... /> 
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

This intervention modifies parameters of non-human hosts described in the section of the input scenario file.

The intervention is described by 5 parameters that define the change in each of non-human host parameters:

reduceAvailability: Reduction in the availability rate, αi. For example a value of 0 will result in no change; a value of 0.2 will reduce the availability to 0.8 of its initial value; and a value of 1 will set the availability to 0;

prePrandialKillingEffect: Reduction in the pre-prandial survival probability, PBi. For example a value of 0 will result in no change; a value of 0.2 will reduce PBi to 0.8 of its initial value; and a value of 1 will set PBi to 0;

postPrandialKillingEffect: Reduction in the post-prandial survival probability, PCi. For example a value of 0 will result in no change; a value of 0.2 will reduce PCi to 0.8 of its initial value; and a value of 1 will set PCi to 0;

restingKillingEffect: Reduction in the survival probability of the resting period, PDi. For example a value of 0 will result in no change; a value of 0.2 will reduce PDi to 0.8 of its initial value; and a value of 1 will set PDi to 0;

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

Name of intervention

nonHumanHostsName=string

Name of intervention (e.g. larviciding, sugar bait).

decay

→ scenario → interventions → nonHumanHostsModifications → intervention → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

description

→ scenario → interventions → nonHumanHostsModifications → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <availabilityReduction ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
| [ <restingKillingEffect ... /> ]
| [ <fecundityReduction ... /> ]
</anopheles>

Documentation (type)

Descriptions of the effects of non human hosts interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

availabilityReduction

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → availabilityReduction

<availabilityReduction
    initial=double
  />

Documentation (element)

Reduction in the availability rate, αi. For example a value of 0 will result in no change; a value of 0.2 will reduce the availability to 0.8 of its initial value; and a value of 1 will set the availability to 0;

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

preprandialKillingEffect

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
  />

Documentation (element)

Reduction in the pre-prandial survival probability, PBi. For example a value of 0 will result in no change; a value of 0.2 will reduce PBi to 0.8 of its initial value; and a value of 1 will set PBi to 0;

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

postprandialKillingEffect

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
  />

Documentation (element)

Reduction in the post-prandial survival probability, PCi. For example a value of 0 will result in no change; a value of 0.2 will reduce PCi to 0.8 of its initial value; and a value of 1 will set PCi to 0;

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

restingKillingEffect

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → restingKillingEffect

<restingKillingEffect
    initial=double
  />

Documentation (element)

Reduction in the survival probability of the resting period, PDi. For example a value of 0 will result in no change; a value of 0.2 will reduce PDi to 0.8 of its initial value; and a value of 1 will set PDi to 0;

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

fecundityReduction

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → fecundityReduction

<fecundityReduction
    initial=double
  />

Documentation (element)

Reduction in the number of fertile eggs laid by a mosquito after biting this type of host, relative to an unprotected human. For example a value of 0 will result in no change; a value of 0.2 will reduce the fecundity factor to 0.8 of its initial value; and a value of 1 will set the fecundity factor to 0;

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

Vector population intervention deployment

→ scenario → interventions → nonHumanHostsModifications → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

addNonHumanHosts

<addNonHumanHosts>
IN THIS ORDER:
| ( <nonHumanHosts ... /> )+
</addNonHumanHosts>

nonHumanHosts

Documentation (element)

List of intervention that add new non-human hosts that have not been described in the .

nonHumanHosts

→ scenario → interventions → addNonHumanHosts → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</nonHumanHosts>

Documentation (type)

Describes a new non-human hosts that have not been described in the .

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
|   <mosqRelativeAvailabilityHuman ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <hostFecundityFactor ... /> 
</anopheles>

Documentation (type)

Descriptions of the effects of new non human hosts with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Relative availability of non-human host (ξ_i)

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqRelativeAvailabilityHuman

<mosqRelativeAvailabilityHuman
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of the population of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → hostFecundityFactor

<hostFecundityFactor
    value=double
  />

Documentation (element)

Units: Proportion

Multiplicative factor for the number of fertile eggs laid by a mosquito after biting this type of host, relative to an unprotected human.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vector trap intervention deployment

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )*
</timed>

deploy

Documentation (element)

List of timed vector trap intervention deployment

deploy

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → timed → deploy

<deploy
    time=string
    lifespan=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Lifespan

lifespan=string

Units: Steps or Days or Years

Human-specific interventions

→ scenario → interventions → human

<human>
IN THIS ORDER:
| ( <component ... /> )+
| ( <deployment ... /> )*
</human>

Documentation (element)

Encapsulates all interventions whose effects are specific to the human host: any interventions where target humans may be selected via population-coverage, age limits and sub-population membership.

Component

→ scenario → interventions → human → component

<component
    id=string
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <screen ... /> 
| |   <treatSimple ... /> 
| |   <treatPKPD ... /> 
| |   <decisionTree ... /> 
| |   <PEV ... /> 
| |   <BSV ... /> 
| |   <TBV ... /> 
| |   <ITN ... /> 
| |   <IRS ... /> 
| |   <GVI ... /> 
| | [ <recruitmentOnly ... /> ]
| |   <clearImmunity ... /> 
| [ <subPopRemoval ... /> ]
</component>

Documentation (element)

A parameterisation of an effect achieved by one component of an intervention. (An intervention is described as the effects of a set of components plus deployments of those components. This describes the components individually, not deployments or which components comprise an intervention.)

Each element describes one component: its effects, decay of the(se) effect(s), and related stuff (e.g. description of indirect decay and of usage levels).

Different interventions can deploy the same component to the same perso. In most cases this will just deploy a fresh instance (e.g. a new bed net will replace the old (nobody uses multiple bed nets), or a new drug dose will act on top of previous doses, or in the case of a vaccine, effect depends on the total number of previous inoculations (including from other interventions).

Where multiple components of the same type (but with different ids) are deployed (whether within a single intervention or by multiple interventions), they act independently (e.g. two bed nets deployed to a single host would act to reduce attractiveness or survival of mosquitoes biting that host twice — this may be useful to simulate some novel vector intervention since the two nets may have separate parameters).

Attributes

Component identifier

id=string

A short name or code identifying the intervention component (used to refer to this component when describing an intervention). Also the id of the sub-population defined as those hosts who have received this intervention and who haven't subsequently been removed from the sub-population.

Name of component

name=string

An informal name/description for the component

screen

→ scenario → interventions → human → component → screen

<screen
    diagnostic=string
  >
IN THIS ORDER:
| ( <positive ... /> )*
| ( <negative ... /> )*
</screen>

Documentation (type)

This can be combined with MDA to achieve mass screen and treat (MSAT) or other types of mass screening intervention.

When deployed to a host, this simulates a test of patent malaria (microscopy, RDT or some such), then triggers deployment of whichever intervention components are configured (deployments for both positive and negative test outcomes can be configured).

The use of the screening itself is reported (if enabled), but not the outcome. Deployment of interventions triggered by the screening may be reported, however.

Attributes

Name of diagnostic

diagnostic=string

Name of a parameterised diagnostic (see scenario/diagnostics).

positive

→ scenario → interventions → human → component → screen → positive

<positive
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → screen → negative

<negative
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

treatSimple

→ scenario → interventions → human → component → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

treatPKPD

→ scenario → interventions → human → component → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

decisionTree

→ scenario → interventions → human → component → decisionTree

<decisionTree
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</decisionTree>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Vaccines

→ scenario → interventions → human → component → PEV

<PEV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )*
| ( <phenotype ... /> )*
</PEV>

Documentation (element)

Pre-erythrocytic vaccine (PEV): prevents a proportion of infections from commencing.

Documentation (type)

Description of a vaccine's effect

Decay of effect

→ scenario → interventions → human → component → PEV → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (element)

Specification of decay of efficacy. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Variance parameter for vaccine efficacy

→ scenario → interventions → human → component → PEV → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy: efficacy is sampled from a beta distribution with efficacyB its beta parameter and its alpha parameter fixed such that the mean is that given by initialEfficacy.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Mean efficacy values before decay (see efficacyB and decay parameter descriptions for sampling and decay). The i-th value in this list is used for the efficacy of the vaccine after the i-th dose. Where more doses are given than there are values in this list, the last value is repeated.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

PD parameters for some allele / resistance phenotype

→ scenario → interventions → human → component → PEV → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
| ( <initialEfficacy ... /> )+
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

restriction

→ scenario → interventions → human → component → PEV → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (type)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → phenotype → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vaccines

→ scenario → interventions → human → component → BSV

<BSV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )*
| ( <phenotype ... /> )*
</BSV>

Documentation (element)

Blood-stage vaccine (BSV): acts as a killing factor on blood-stage parasites. Exact action depends on the within host model.

Documentation (type)

Description of a vaccine's effect

Vaccines

→ scenario → interventions → human → component → TBV

<TBV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )*
| ( <phenotype ... /> )*
</TBV>

Documentation (element)

Transmission-blocking vaccine (TBV): one minus this scales the probability of transmission to mosquitoes

Documentation (type)

Description of a vaccine's effect

Bed nets

→ scenario → interventions → human → component → ITN

<ITN>
IN THIS ORDER:
| [ <usage ... /> ]
|   <holeRate ... /> 
|   <ripRate ... /> 
|   <ripFactor ... /> 
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
|   <attritionOfNets ... /> 
| ( <anophelesParams ... /> )+
</ITN>

Documentation (element)

Description of bed-net interventions (ITNs, LLINs).

Proportion of time nets are used by humans

→ scenario → interventions → human → component → ITN → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of nets by humans, from 0 to 1.

At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing.

See also "propActing" (proportion of bits for which net acts).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Rate at which holes are made

→ scenario → interventions → human → component → ITN → holeRate

<holeRate
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: Holes per annum Min: 0

The rate at which new holes are made in nets.

nHoles(t) = nHoles(t-1) + X where X~Pois(R/T) where T is the number of time-steps per year. R is sampled from log-normal: R ~ log N( log(mean)-sigma²/2, sigma² ) and is covariant with ripRate and insecticideDecay. (To be exact, a single Gaussian sample is taken, adjusted for each sigma then exponentiated.)

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

The (linear) coefficient of variation. This value must be specified when a (non-constant) distribution is used. Note: since version 46, variance can be used instead. Note that specifying CV="0" has the same effect as distr="const" and disables sampling of this parameter, even if distr is not "const".

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

To allow heterogeneity, a distribution must be specified. Valid options are as follows. "const": no variation or sampling. Specifying distr="const" has the same effect as not specifying distr at all. "lognormal": the parameter is sampled from a log-normal distribution. Note that the "mean" and "CV" values are linear (arithmetic) properties of the distribution and not log-space properties.

Coefficient of variation

variance=double

Units: unitless

The variance parameter of the distirbution. This value can be specified when a (non-constant) distribution is used. Note that specifying variance="0" has the same effect as distr="const" and disables sampling of this parameter, even if distr is not "const".

mean

mean=double

The (linear) mean value.

Rate at which holes are enlarged

→ scenario → interventions → human → component → ITN → ripRate

<ripRate
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: Rips per existing hole per annum Min: 0

Each existing hole has a probability of being ripped bigger according to a Poisson process with this rate as (only) parameter.

New rips occur in a net at rate X~Pois(h×R/T) where h is the number of existing holes and T the number of time-steps per year. R is sampled from log-normal: R ~ log N( log(mean)-sigma²/2, sigma² ) and is covariant with holeRate and insecticideDecay. (To be exact, a single Gaussian sample is taken, adjusted for the each and sigma then exponentiated.)

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Rip factor

→ scenario → interventions → human → component → ITN → ripFactor

<ripFactor
    value=double
  />

Documentation (element)

Units: none Min: 0

This factor expresses how important rips are in increasing the hole.

The hole index of a net is h + F×x where h and x are the total numbers of holes and rips respectively and F is the rip factor.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → ITN → initialInsecticide

<initialInsecticide
    mean=double
  [ SD=double ]
  [ distr=("const" or "normal") ] DEFAULT VALUE const
  />

Documentation (element)

Units: mg/m² Min: 0

The insecticide concentration of new nets is Gaussian distributed with mean "mu" and a standard deviation "sigma". The standard deviation should be small relative to the mean to avoid negative initial concentration. Any negative values sampled are set to 0.

Documentation (type)

A parameter with optional heterogeneity.

Optionally, a distribution ("distr") and standard of deviation ("SD") may be specified.

Attributes

mean

mean=double

The mean value.

standard deviation

SD=double

The standard deviation of variates.

Distribution

distr=("const" or "normal")

Default value: const

Decay of insecticide

→ scenario → interventions → human → component → ITN → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</insecticideDecay>

decay

Documentation (element)

Units: none

Decay curve for insecticide content of nets. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

The distribution of decay rates over nets is covariant with the distribution of ripRate and holeRate over nets. This distribution is generated by taking one sample per net from a Gaussian distribution with mean 0 and standard deviation 1. For each variable, the sample is multiplied by the respective sigma and a constant added such that, once exponentiated, the mean of the variable over nets is 1. The variable is then exponentiated and multiplied by the required mean rate for the respective variable.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Attrition of nets

→ scenario → interventions → human → component → ITN → attritionOfNets

<attritionOfNets
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</attritionOfNets>

decay

Documentation (element)

Units: dimensionless

Specifies the rate at which nets are disposed of over time. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

In the current model, nets are disposed of randomly (no correlation with state of decay) such that the chance of each net surviving until age t is the value of this decay function at time t. Equivalently (where a large number of nets are distributed at the same time), the proportion of nets remaining in use should match this decay function over time.

Humans are removed from the intervention component's sub-population on disposal (attrition) of their nets. Currently this event is not reported.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

anophelesParams

→ scenario → interventions → human → component → ITN → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <holeIndexMax ... /> ]
| EXACTLY ONE OF:
| |   <deterrency ... /> 
| |   <twoStageDeterrency ... /> 
| EXACTLY ONE OF:
| |   <preprandialKillingEffect ... /> 
| |   <preprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| |   <postprandialKillingEffect ... /> 
| |   <postprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| | [ <fecundityReduction ... /> ]
| | [ <fecundityReductionLogit ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which net acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Deprecated: propActive can still be used but its value must be set to either 0 or 1. Any other value will result in an error at initialization. The proportion of bites, when nets are in use, for which the net has any action whatsoever on the mosquito. At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing. See also "usage" (proportion of time nets are used by humans).

maximum of holed surface area that has an effect (comparable to no net)

→ scenario → interventions → human → component → ITN → anophelesParams → holeIndexMax

<holeIndexMax
    value=double
  />

Documentation (element)

Units: in same unit as holeIndex

Used by logit attacking and killing models only, holeIndexMax is a user defined maximum hole index (typically, the total surface area of a net).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied by exp(log(H)×h + log(P)×p + log(I)×h×p where H, P and I are the hole, insecticide and interaction factors respectively, h=exp(-holeIndex×holeScalingFactor) and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency

<twoStageDeterrency>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <entering ... /> 
| |   <enteringLogit ... /> 
| EXACTLY ONE OF:
| |   <attacking ... /> 
| |   <attackingLogit ... /> 
</twoStageDeterrency>

Documentation (element)

Units: dimensionless

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

This deterrency model multiplies human attractiveness by pEnt×pAtt.

Deterrency: entering

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → entering

<entering
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless

pEnt represents the relative probability of entering due to ITNs: pEnt = exp(log(P)×p) where P is the insecticide factor and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Deterrency: entering (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → enteringLogit

<enteringLogit
    baseFactor=double
    insecticideFactor=double
  />

Documentation (element)

Units: dimensionless

pEnt represents the relative probability of entering due to insecticide in the hut: pEnt = exp(logit.pEnt) / (exp(logit.pEnt) + 1) logit.pEnt = B + P * p where B is the basefactor (without net); P is insecticide factor, and p = log(insecticideContent+1). Without a net, probability of entering a house is pEnt0 = exp(logit.pEnt0) / (exp(logit.pEnt0) + 1) logit.pEnt0 = B Entering of mosquitoes is adjusted via multiplication by pEnt / pEnt0. To keep this in the range [0,1], we (normally) require that pEnt ≤ pEnt0 and thus P ≤ 0 and give a warning if this is not fulfilled.

Attributes

Base factor

baseFactor=double

Units: none

See parent element documentation

Insecticide factor

insecticideFactor=double

Units: none

See parent element documentation

Deterrency: attacking

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attacking

<attacking
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless

pAtt represents the relative probability of attacking a human after entering a house due to ITNs (i.e. of feeding/dying vs. flying off): pAtt = B + H×h + P×p + I×h×p where B is the base (without net) probability; H, P and I are the hole, insecticide and interaction factors respectively, h=exp(-holeIndex × holeScalingFactor) and p=1 - exp(-insecticideContent × insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Deterrency: attacking (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attackingLogit

<attackingLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless

pAtt represents the relative probability of attacking a human after entering a house due to ITNs (i.e. of feeding/dying vs. flying off): pAtt = exp(logit.pAtt) / (exp(logit.pAtt) + 1) logit.pAtt = B + H×min(h, hMax) + P×p + I×min(h, hMax)×p where B is the base factor (without net); H, P and I are the hole, insecticide and interaction factors respectively, and: h = log(holeIndex + 1) p = log(insecticideContent + 1) Without a net, probability of attacking a human after entering a house is pAtt0 = exp(logit.pAtt0) / (exp(logit.pAtt0) + 1) logit.pAtt0 = B + H×hMax where hMax=log(holeIndexMax + 1) and holeIndexMax is a user defined maximum hole index (typically, the total surface area of a net). Attacking of mosquitoes is adjusted via multiplication by pAtt / pAtt0. This may be larger and smaller than 1 (but will not be negative). By definition (through the logit transformation) pAtt0 > 0.

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Pre-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on survival mosquitoes as they seek to bite a human after choosing that human, relative to the same person not sleeping under a net. Parameterisations should take into account that mosquitoes do not always bite indoors.

Killing proportion is calculated as K = B + H×h + P×p + I×h×p where B is the base (without net) probability of death, H, P and I are the hole, insecticide and interaction factors respectively, h=exp(-holeIndex×holeScalingFactor) and p=1−exp(-insecticideContent×insecticideScalingFactor).

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Pre-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffectLogit

<preprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on survival mosquitoes as they seek to bite a human after choosing that human, relative to the same person not sleeping under a net.
Killing proportion is calculated as K=exp(logit.K)/(exp(logit.K)+1) logit.K = B + H×min(h,hMax) + P×p + I×min(h,hMax)×p where B is the basefactor (without net), H, P and I are the hole, insecticide and interaction factors respectively, h=log(holeIndex+1) and p=log(insecticideContent+1). Without a net, the killing proportion K0=exp(logit.K0)/(exp(logit.K0)+1) logit.K0 = B + H×hMax where hMax=log(holeIndexMax+1) and holeIndexMax is a user defined maximum hole index (typically, the total surface area of a net). Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−K0). To keep this in the range [0,1], we require that K ≥ K0. We enforce that P ≥ 0 (It would not make sense biologically if P were negative) and P+I*hMax ≥ 0 and H ≤ 0 and holeIndex ≤ holeIndexMax and give a warning if these conditions are not fulfilled.

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Post-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on survival mosquitoes as they seek to escape from a human host and rest after a blood meal, relative to the same person not sleeping under a net. Parameterisations should take into account that mosquitoes do not always bite indoors.

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffectLogit

<postprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on survival mosquitoes as they seek to escape from a human host and rest after a blood meal, relative to the same person not sleeping under a net. Killing proportion is calculated as K=exp(logit.K)/(exp(logit.K)+1) logit.K = B + H×min(h,hMax) + P×p + I×min(h,hMax)×p where B is the basefactor (without net), H, P and I are the hole, insecticide and interaction factors respectively, h=log(holeIndex+1) and p=log(insecticideContent+1). Without a net, the killing proportion K0=exp(logit.K0)/(exp(logit.K0)+1) logit.K0 = B + H×hMax where hMax=log(holeIndexMax+1) and holeIndexMax is a user defined maximum hole index (typically, the total surface area of a net). Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−K0). To keep this in the range [0,1], we require that K ≥ K0. We enforce that P ≥ 0 (It would not make sense biologically if P were negative) and P+I*hMax ≥ 0 and H ≤ 0 and holeIndex ≤ holeIndexMax and give a warning if these conditions are not fulfilled.

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Fecundity reduction

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-B), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReductionLogit

<fecundityReductionLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-K0), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Indoor residual spraying

→ scenario → interventions → human → component → IRS

<IRS>
IN THIS ORDER:
| [ <usage ... /> ]
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
| ( <anophelesParams ... /> )+
</IRS>

Documentation (element)

Description of indoor residual spraying interventions.

Documentation (type)

Description of effect for the more complex and probably more realistic Briet model: IRS has three effects, whos strength is calculated as a function of surviving insecticide content.

Proportion of Indoor residual spraying (IRS) interventions

→ scenario → interventions → human → component → IRS → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Indoor residual spraying (IRS) interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → IRS → initialInsecticide

<initialInsecticide
    mean=double
  [ SD=double ]
  [ distr=("const" or "normal") ] DEFAULT VALUE const
  />

Documentation (element)

Units: μg/cm² Min: 0

The insecticide concentration of IRS (at time of spraying) is Gaussian distributed with mean "mu" and a standard deviation "sigma". The standard deviation should be small relative to the mean to avoid negative initial concentration. Any negative values sampled are set to 0.

Documentation (type)

A parameter with optional heterogeneity.

Optionally, a distribution ("distr") and standard of deviation ("SD") may be specified.

Attributes

mean

mean=double

The mean value.

standard deviation

SD=double

The standard deviation of variates.

Distribution

distr=("const" or "normal")

Default value: const

Decay of insecticide

→ scenario → interventions → human → component → IRS → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</insecticideDecay>

decay

Documentation (element)

Units: none

Decay curve for insecticide content of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Per-mosquito species parameters

→ scenario → interventions → human → component → IRS → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

The proportion of bites for which the IRS has any action whatsoever on the mosquito. At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-propActing) + intervention_factor*propActing.

Relative attractiveness

→ scenario → interventions → human → component → IRS → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied by exp(P×log(p)) where P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on survival mosquitoes as they seek to bite a human after choosing that human, relative to the same person not protected by IRS. Parameterisations should take into account that mosquitoes do not always bite indoors. This parameter has been added since some data shows IRS to have a preprandial killing effect.

Killing proportion is calculated as K = B + P×p where B is the base (without protection) probability of death, and P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on survival mosquitoes as they seek to escape from a human host and rest after a blood meal, relative to the same person not protected by IRS. Parameterisations should take into account that mosquitoes do not always bite indoors.

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction

→ scenario → interventions → human → component → IRS → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Effect of IRS on fertility mosquitoes after successfully feeding on a human host, relative to an unproteced human. Parameterisations should take into account that mosquitoes do not always bite indoors.

First, we calculate K = B + P×p where B is the base (without protection) probability of death, and P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Fecundity is multiplied by (1−K) / (1−B). It is not allowed to be greater than 1. To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Generic vector intervention

→ scenario → interventions → human → component → GVI

<GVI>
IN THIS ORDER:
| [ <usage ... /> ]
|   <decay ... /> 
| ( <anophelesParams ... /> )+
</GVI>

Documentation (element)

Low-level description of intervention effects on vectors (i.e. mosquitoes). Can be used to describe simple ITN or IRS interventions (though more complex models are available for these interventions) or other interventions such as mosquito repellant or ivermectin.

Note that all actions of this intervention component will decay according to a single decay function. If independant decay is wanted, a separate component can be used for each action.

Proportion of generic vector interventions

→ scenario → interventions → human → component → GVI → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Generic vector interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay

→ scenario → interventions → human → component → GVI → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (element)

Description of decay of all intervention effects. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Per-mosquito species parameters

→ scenario → interventions → human → component → GVI → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <deterrency ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → GVI → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of intervention on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied this factor times survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of intervention on survival of mosquitoes as they seek to bite a human after choosing that human, relative to the same person not protected by the intervention. Parameterisations should take into account that mosquitoes do not always bite indoors. This parameter has been added since some data shows IRS to have a preprandial killing effect.

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of intervention on survival of mosquitoes as they seek to escape from a human host and rest after a blood meal, relative to the same person not protected by the intervention. Parameterisations should take into account that mosquitoes do not always bite indoors.

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Fecundity reduction effect

→ scenario → interventions → human → component → GVI → anophelesParams → fecundityReduction

<fecundityReduction
    value=double
  />

Documentation (element)

Min: 0

Effect of intervention on fertility mosquitoes after successfully feeding on a human host, relative to an unproteced human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Fertility is multiplied by 1 - (fecundityReduction * decay).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Recruitment only

→ scenario → interventions → human → component → recruitmentOnly

<recruitmentOnly/>

Documentation (element)

Recruitment of a host into a sub-population.

All human-targeting intervention deployments recruit simulated humans into a sub-population which can be used for the purposes of cumulative deployment, deployment only to a sub-population and defining a cohort. This pseudo-intervention can be used to define a sub-population without also deploying some intervention.

Clear Immunity

→ scenario → interventions → human → component → clearImmunity

<clearImmunity/>

Documentation (element)

Removes all exposure-related immunitsy gained over time by hosts without removing infections (or affecting the ability to gain immunity through exposure).

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

subPopRemoval

→ scenario → interventions → human → component → subPopRemoval

<subPopRemoval
  [ onFirstBout=boolean ] DEFAULT VALUE false
  [ onFirstTreatment=boolean ] DEFAULT VALUE false
  [ onFirstInfection=boolean ] DEFAULT VALUE false
  [ afterYears=double ]
  />

Documentation (type)

Each human intervention component corresponds to a sub-population: those who have received or are considered to be protected by the intervention component. Humans automatically become members of this sub-population when receiving an intervention component; this element controls how humans are removed from the sub-population.

ITN attrition also removes humans from sub-populations.

Note that sub-populations do not directly correspond to an intervention's effects: lack of effectiveness does not imply removal from the sub-population (except as explicitly configured here) and removal from the sub-population does not halt an intervention's effects.

Sub-populations may be used to define a cohort, to restrict deployment of other interventions and to use cumulative deployment mode. A sub- population may or may not correspond (roughly) to humans protected by some intervention.

Attributes

Time to first episode only

onFirstBout=boolean

Default value: false

If true, remove individuals from the sub-population at the start of the first episode (start of a clinical bout) since they were recruited into the sub-population. This is intended for cohort studies which measure time to the first episode, using active case detection. Reports delayed due to health-system memory are forced out when this occurs. Note that this can increase the number of uncomplicated cases reported across the entire population; for this reason reports are not forced on recruitment or most removal options. This does not prevent re-recruitment in the case that recruitment settings could conceivably recruit the same individual twice.

Time to first treatment only

onFirstTreatment=boolean

Default value: false

If true, remove individuals from the sub-population when they first seektreatment since they were recruited into the sub-population. This is intended for cohort studies which measure the time to first episode, using passive case detection. Reports delayed due to health-system memory are forced out when this occurs. Note that this can increase the number of uncomplicated cases reported across the entire population; for this reason reports are not forced on recruitment or most removal options. This does not prevent re-recruitment in the case that recruitment settings could conceivably recruit the same individual twice.

Time to first infection only

onFirstInfection=boolean

Default value: false

If true, remove individuals from the sub-population at completion of the first survey in which they present with a patent infection since they were recruited into the sub-population. This intended for cohort studies which measure time to the first infection, using active case detection. Reports delayed due to health-system memory are forced out when this occurs. Note that this can increase the number of uncomplicated cases reported across the entire population; for this reason reports are not forced on recruitment or most removal options. This does not prevent re-recruitment in the case that recruitment settings could conceivably recruit the same individual twice.

Remove from sub-population after

afterYears=double

Units: Years Min: 0

If given, membership to the sub-population of humans who have received this intervention component expires after the given number of years. Note that future deployments renew membership (e.g. if this parameter is 4 years and the intervention is redeployed 3 years from now, expiry happens after 7 years). This provides a crude way of modelling a cohort protected by some intervention. A few interventions provide more detailed ways of modelling expiry of protection. In any case, "expiry of protection" is an abstract concept and does not imply that all protection has ceased, even in the simulator. This may also be useful for cumulative deployment. Minimum duration is zero, which implies the human is effectively never a member of the sub-population; a duration of one timestep implies the human is a member of the sub-population while any futher interventions are deployed on the same time as this human becomes a member and on the next update of the human (including transmission and health system events) but not beyond that. If this attribute is not given, the simulated human is a member until death or some other option triggers removal. Input is rounded to the nearest time step.

Deployment

→ scenario → interventions → human → deployment

<deployment
  [ name=string ]
  >
IN THIS ORDER:
| ( <component ... /> )+
| ( <condition ... /> )*
| ( <continuous ... /> )*
| ( <timed ... /> )*
</deployment>

Documentation (element)

This element describes deployment of an intervention: which components are deployed, how humans are selected for deployment (via timed or age-based deployment) as well as a few additional restrictions (e.g. vaccine dosing restrictions).

All components deployed by this intervention are deployed to the same people (each timed or continuous deployment selects recipients and then gives each recipient all components of the intervention).

Attributes

Intervention name

name=string

Name of intervention

component

→ scenario → interventions → human → deployment → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Condition

→ scenario → interventions → human → deployment → condition

<condition
    measure=string
  [ minValue=double ]
  [ maxValue=double ]
    initialState=boolean
  />

Documentation (element)

If conditions are specified, deployment of this intervention will only go ahead if all specified conditions are true. Condition statements are evaluated only during surveys, so deployment is enabled or disabled depending on the results of the most recent survey. So called unreported surveys can be used to reevaluate conditions without increasing granularity of output.

Conditions are evaluated for the whole population, not for individual age-groups or cohorts.

This affects all types of deployment.

Attributes

Measure

measure=string

The monitoring measure to test. Not all measures are available for use.

Minimum value

minValue=double

Minimum value. If specified, the measured variable must be greater than or equal to this value for the condition to be satisfied.

Maximum value

maxValue=double

Maximum value. If specified, the measured variable must be less than or equal to this value for the condition to be satisfied.

Initial state

initialState=boolean

Whether this condition is considered true or false before updated by a survey.

Age-based (continuous) deployment

→ scenario → interventions → human → deployment → continuous

<continuous>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| ( <deploy ... /> )+
</continuous>

Documentation (element)

List of ages at which deployment takes place (through EPI, post-natal and school-based programmes, etc.).

A sub-population restriction may be added as a property of the list of continuous deployments.

restrictToSubPop

→ scenario → interventions → human → deployment → continuous → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

If this element is specified, deployment is restricted to some sub-population (specified via the "id" attribute); otherwise the target population is the entire simulated population. Either way, other deployment restrictions (age, time, number of vaccine doeses) still apply.

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

If this is not specified or is false, deployment is restricted to the sub-population of people protected by the intervention component who's id is given. If complement is set to true, deployment is instead restricted to the complement of that sub-population, i.e. to those

deploy

→ scenario → interventions → human → deployment → continuous → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
  [ minAvailability=int ]
  [ maxAvailability=int ]
    targetAgeYrs=double
  [ begin=string ]
  [ end=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is at least this number. For example, if this is the second deployment opportunity for this vaccine and this value is 1, then this deployment cannot deploy the vaccine to individuals who did not receive the first deployment.

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Minimum ento availability

minAvailability=int

Units: percent Min: 0

Minimum ento availability percentile. This option is meant to be used with heterogeneity of availability, which can be specified in the entomology section. Without heterogenity (default), all hosts have the same availability and this option will have no effect. The percentile must be an integer value between 0 and 100. Percentile 99th represents individuals who are more available than 99% of the population. Percentile 0 represents the least available individuals. 100 is equivalent for infinity.

Maximum ento availability

maxAvailability=int

Units: percent Min: 0

Maximum ento availability percentile. This option is meant to be used with heterogeneity of availability, which can be specified in the entomology section. Without heterogenity (default), all hosts have the same availability and this option will have no effect. The percentile must be an integer value between 0 and 100. Percentile 99th represents individuals who are more available than 99% of the population. Percentile 0 represents the least available individuals. 100 is equivalent for infinity.

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention. Input is rounded to the nearest time step.

First time active

begin=string

Units: User defined (defauls to steps)

First time at which this deployment is active. If not specified, deployment starts at the beginning of the intervention period. See doc on intervention period and on monitoring/startDate for details of how times work. Can be specified in steps, days, years, or as a date (examples: 15t, 75d, 0.2y, 2000-03-16).

End step

end=string

Units: User defined (defauls to steps)

End of the period during which the intervention is active (to be exact, the first step of the intervention period at which the item becomes inactive). If not specified, deployment never ceases after starting during the simulation. See doc on intervention period and on monitoring/startDate for details of how times work. Can be specified in steps, days, years, or as a date (examples: 15t, 75d, 0.2y, 2000-03-16).

Mass (timed) deployment

→ scenario → interventions → human → deployment → timed

<timed>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| [ <cumulativeCoverage ... /> ]
| ( <deploy ... /> )+
</timed>

Documentation (element)

List of timed deployments of the intervention (that is, of deployment campaigns).

Cumulative deployment mode can be specified for all deployments in a timed list. To allow multiple cumulative deployment descriptions, the entire timed list may be repeated.

restrictToSubPop

→ scenario → interventions → human → deployment → timed → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

Cumulative coverage

→ scenario → interventions → human → deployment → timed → cumulativeCoverage

<cumulativeCoverage
    component=string
  />

Documentation (element)

If this element is not specified, standard deployment occurs, where a portion of the population as given by the coverage property of this campaign is selected, and interventions are deployed to all of these people (regardless of previous coverage).

If this attribute is specified, instead, the population is divided into two sets: those who are a member of a certain sub-population and those who are not (see "subPopRemoval" element). If the proportion of people in the first set is less than the desired coverage, then the proportion of people from the second set needed to increase total coverage to the desired coverage is calculated. This proportion is then used as the probablity of selection from the second set into a third set of people who then receive all interventions deployed by this campaign.

Note that selection is stochastic so the final coverage level may not be exactly that desired. Note also that the component used when selecting people need not actually be one of the components deployed by this intervention, although that is the intended use case.

Attributes

Component identifier

component=string

The identifier (short name) of the component used when selecting people.

deploy

→ scenario → interventions → human → deployment → timed → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
  [ minAvailability=int ]
  [ maxAvailability=int ]
    time=string
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ repeatStep=string ]
  [ repeatEnd=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Minimum ento availability

minAvailability=int

Units: percent Min: 0

Maximum ento availability

maxAvailability=int

Units: percent Min: 0

Time

time=string

Units: User defined (defauls to steps) Min: 0

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0

Maximum age of eligible individuals (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible individuals (defaults to 0). Input is rounded to the nearest time step.

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

Either both repeatStep and repeatEnd should be present or neither. If present, the deployment is repeated every repeatStep timesteps (i.e. if t0 is the initial time and x is repeatStep, depolyments are done at times t0, t0+x, t0+2*x, ...), ending before repeatEnd (final repetition is the one before repeatEnd). Note that repeatEnd may be specified as a date but repeatStep must be a duration (days, steps or years).

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Description of health system.

Documentation (type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("forced" or "dynamic")
  [ scaledAnnualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Description of entomological data

Attributes

Entomology dataset name

name=string

Name of entomology data

Transmission model mode

mode=("forced" or "dynamic")

Transmission simulation mode: may be forced (in which case interventions and changes to human infectiousness cannot affect EIR) or dynamic (in which the above can affect EIR). The full vector model is only used in dynamic mode. This can not be changed by interventions, except for the changeEIR intervention for the non-vector model which replaces the EIR with a new description (used in forced mode).

Override annual EIR

scaledAnnualEIR=double

Units: Infectious bites per adult per year

If set, the annual EIR (for all species of vector) is scaled to this level; can be omitted if not needed.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters of the transmission model

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <seasonality ... /> 
|   <mosq ... /> 
| [ <lifeCycle ... /> ]
| [ <simpleMPD ... /> ]
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial estimate of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial estimate of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial estimate of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Seasonality of transmission

→ scenario → entomology → vector → anopheles → seasonality

<seasonality
    input=("EIR")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <fourierSeries ... /> 
| |   <monthlyValues ... /> 
| |   <dailyValues ... /> 
</seasonality>

Documentation (element)

Specifies the seasonality of transmission and optionally the level of annual transmission.

Attributes

Seasonality input

input=("EIR")

Specify what seasonality measure is given. At the moment, only EIR is supported, but in the future, all the below should be supported. EIR: seasonality of entomological inoculations is input. Units: entomological inoculations per adult per annum. hostSeeking: seasonality of densities of flying host-seeking mosquitoes is input (in the model this is notated N_v). Units: mosquitoes. emergence: seasonality of emergence pupa into adults. Units: mosquitoes. larvalResources: seasonality of larval resources. Units: X.

Annual EIR

annualEIR=double

Units: Inoculations per adult per annum Min: 0

If this attribute is included, EIR for this species is scaled to this level. Note that if the scaledAnnualEIR attribute of the entomology element is also used, EIR is scaled again, making this attribute the EIR relative to other species. With some seasonality inputs, this attribute is optional, in which case (if scaledAnnualEIR is also not specified) transmission depends on all parameters of the vector. With some seasonality inputs, however, this parameter must be specified.

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries

<fourierSeries
    EIRRotateAngle=double
  >
IN THIS ORDER:
| ( <coeffic ... /> )*
</fourierSeries>

coeffic

Documentation (element)

Units: Infectious bites per adult per day

Seasonality is reproduced from the exponential of a fourier series specified by the following coefficients. Note that the a0 term is not needed; the annualEIR attribute of the seasonality element should be used to scale EIR instead.

Attributes

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: Radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Pair of Fourier coefficients

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries → coeffic

<coeffic
    a=double
    b=double
  />

Documentation (element)

A pair of Fourier series coefficients. The first element specifies a1 and b1, the second a2 and b2, etc. Any number (from 0 up) of pairs may be given.

Attributes

a_n parameter of Fourier approximation to ln(EIR)

a=double

a_n parameter of Fourier approximation to ln(EIR) for some natural number n.

b_n parameter of Fourier approximation to ln(EIR)

b=double

b_n parameter of Fourier approximation to ln(EIR) for some natural number n.

List of monthly values

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues

<monthlyValues
    smoothing=("none" or "fourier")
  >
IN THIS ORDER:
| ( <value ... /> ){12,12}
</monthlyValues>

value

Documentation (element)

Description of seasonality from monthly values. Multiple smoothing methods are possible (see smoothing attribute).

List should contain twelve entries: January to December.

Attributes

Smoothing function

smoothing=("none" or "fourier")

How the monthly values are converted into a daily sequence of values:

none: no smoothing (step function)
Fourier: a Fourier series (with terms up to a2/b2) is fit to the sequence of monthly values and used to generate a smoothed list of daily values.

Monthly value

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Monthly value

List of daily values

→ scenario → entomology → vector → anopheles → seasonality → dailyValues

<dailyValues>
IN THIS ORDER:
| ( <value ... /> )+
</dailyValues>

value

Documentation (element)

Description of seasonality from daily values.

List should contain 365 entries: 1st January to 31st December.

Daily value

→ scenario → entomology → vector → anopheles → seasonality → dailyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Daily value

Mosquito feeding cycle parameters

→ scenario → entomology → vector → anopheles → mosq

<mosq
    minInfectedThreshold=double
  >
IN ANY ORDER:
|   <mosqRestDuration ... /> 
|   <extrinsicIncubationPeriod ... /> 
|   <mosqLaidEggsSameDayProportion ... /> 
|   <mosqSeekingDuration ... /> 
|   <mosqSurvivalFeedingCycleProbability ... /> 
|   <availability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <mosqProbOvipositing ... /> 
|   <mosqHumanBloodIndex ... /> 
</mosq>

Documentation (element)

Parameters describing the feeding cycle and human mosquito interaction of a single species of anopheles mosquito.

Attributes

Mininum infected threshold for mosquitos

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

Duration of the resting period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqRestDuration

<mosqRestDuration
    value=int
  />

Documentation (element)

Units: Days

name:Duration of the resting period of the vector (days);

Attributes

Input parameter value

value=int

An integer value.

Extrinsic incubation period

→ scenario → entomology → vector → anopheles → mosq → extrinsicIncubationPeriod

<extrinsicIncubationPeriod
    value=int
  />

Documentation (element)

Units: Days

name:Extrinsic incubation period (days)

Attributes

Input parameter value

value=int

An integer value.

Proportion of mosquitoes host seeking on same day as ovipositing

→ scenario → entomology → vector → anopheles → mosq → mosqLaidEggsSameDayProportion

<mosqLaidEggsSameDayProportion
    value=double
  />

Documentation (element)

Units: Proportion

Proportion of mosquitoes host seeking on same day as ovipositing

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Duration of the host-seeking period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqSeekingDuration

<mosqSeekingDuration
    value=double
  />

Documentation (element)

Units: Days

Duration of the host-seeking period of the vector (days)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito survives the feeding cycle

→ scenario → entomology → vector → anopheles → mosq → mosqSurvivalFeedingCycleProbability

<mosqSurvivalFeedingCycleProbability
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito survives the feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human availability rate heterogeneity

→ scenario → entomology → vector → anopheles → mosq → availability

<availability
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
  />

Documentation (element)

Optionally, entomological availability rate may be sampled per-human from a distribution. The distribution and coefficient of variability may be set here. The mean rate is calculated based on other parameters and not set directly.

If no attributes are specified or distr="const" or CV="0" then there will be no heterogeneity.

Documentation (type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

Probability that the mosquito succesfully bites chosen host

→ scenario → entomology → vector → anopheles → mosq → mosqProbBiting

<mosqProbBiting
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito succesfully bites chosen host

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Variates are sampled from Be(α,β) where α and β are determined from the mean and variance as follows: let v be the variance and c=mean/(1-mean). Then we set α=cβ and β=((c+1)²v - c)/((c+1)³v).

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → mosq → mosqProbFindRestSite

<mosqProbFindRestSite
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito escapes host and finds a resting place after biting

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → mosq → mosqProbResting

<mosqProbResting
    mean=double
    variance=double
  />

Documentation (element)

Probability of mosquito successfully resting after finding a resting site

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of a mosquito successfully laying eggs given that it has rested

→ scenario → entomology → vector → anopheles → mosq → mosqProbOvipositing

<mosqProbOvipositing
    value=double
  />

Documentation (element)

Probability of a mosquito successfully laying eggs given that it has rested

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human blood index

→ scenario → entomology → vector → anopheles → mosq → mosqHumanBloodIndex

<mosqHumanBloodIndex
    value=double
  />

Documentation (element)

Units: Proportion

The proportion of resting mosquitoes which fed on human blood during the last feed.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mosquito life cycle parameters

→ scenario → entomology → vector → anopheles → lifeCycle

<lifeCycle
  [ estimatedLarvalResources=double ] DEFAULT VALUE 1e8
  >
IN ANY ORDER:
|   <eggStage ... /> 
|   <larvalStage ... /> 
|   <pupalStage ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</lifeCycle>

Documentation (element)

Parameters describing the life-cycle of this species of mosquito

Attributes

Estimate of larval resources

estimatedLarvalResources=double

Units: X

Default value: 1e8

An estimate of mean annual availability of resources to larvae. Used to get the resource usage fitting algorithm going; if the algorithm fails to fit the resource availability then tweaking this parameter may help. In other cases tweaking this parameter shouldn't be necessary. Default value is 10⁸ (1e8). Units are arbitrary but must be the same as those used by the resourceUsage parameter.

Egg stage

→ scenario → entomology → vector → anopheles → lifeCycle → eggStage

<eggStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the egg stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

larvalStage

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage

<larvalStage>
</larvalStage>

daily

Documentation (type)

Parameters for the larval stage of development

Documentation (base type)

Parameters associated with a mosquito development stage.

Daily development

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage → daily

<daily
    resourceUsage=double
    effectCompetition=double
  />

Documentation (element)

List of parameters which apply during the larval stage of development. List length must equal stage duration, with first item corresponding to first 24 hours after hatching, second item to hours 24-48, and so on.

Attributes

Resource usage

resourceUsage=double

Units: X

Resource usage during larval stage of development. Units are arbitrary.

Effect of competition

effectCompetition=double

Units: none

Effect of competition over resources on development.

Pupal stage

→ scenario → entomology → vector → anopheles → lifeCycle → pupalStage

<pupalStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the pupal stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → lifeCycle → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle, after feeding on an unprotected human (non-human hosts and protected humans use a multiplication factor to adjust this number for mosquitoes feeding on them).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Simple Mosq-Pop-Dynamics parameters

→ scenario → entomology → vector → anopheles → simpleMPD

<simpleMPD>
IN ANY ORDER:
|   <developmentDuration ... /> 
|   <developmentSurvival ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</simpleMPD>

Documentation (element)

Parameters describing the simple mosquito population dynamics model.

This is a simpler version of the life-cycle model, requiring less parameters and with much simpler initialisation.

Duration

→ scenario → entomology → vector → anopheles → simpleMPD → developmentDuration

<developmentDuration
    value=int
  />

Documentation (element)

Units: Days Min: 1

Duration from egg laying to emergence in days.

Attributes

Input parameter value

value=int

An integer value.

Probability of survival

→ scenario → entomology → vector → anopheles → simpleMPD → developmentSurvival

<developmentSurvival
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that mosquito survives from the egg being laid to emergence, given no resouce limitations (no density constraints).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → simpleMPD → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Alternative (non-human) host paramters

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN ANY ORDER:
|   <mosqRelativeEntoAvailability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
| [ <hostFecundityFactor ... /> ]
</nonHumanHosts>

Documentation (element)

Min: 0

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of non-human host (ξ_i)

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqRelativeEntoAvailability

<mosqRelativeEntoAvailability
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of the population of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative fecundity of biting mosquitoes

→ scenario → entomology → vector → anopheles → nonHumanHosts → hostFecundityFactor

<hostFecundityFactor
    value=double
  />

Documentation (element)

Units: Proportion

Multiplicative factor for the number of fertile eggs laid by a mosquito after biting this type of host, relative to an unprotected human.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Name of this species of non human hosts (must match up with those described per anopheles section).

Population size of non-human host species

number=double

Units: Animals

Population size of this non-human host. Note: the availability of the population of this type of non-human host is determined by mosqRelativeEntoAvailability and mosqHumanBloodIndex. NHHs are not modelled individually, thus this parameter is not used. It might be useful in the future if there is ever an intervention to change the number of non-human hosts.

Parasite genetics

<parasiteGenetics
    samplingMode=("initial" or "tracking")
  >
IN THIS ORDER:
| ( <locus ... /> )+
</parasiteGenetics>

locus

Documentation (element)

A specification of genotypes of infection parasites.

May be omitted; in this case there is no modelling of genetic differences of infections (resistance, fitness).

Attributes

samplingMode

samplingMode=("initial" or "tracking")

This controls how genotypes are determined for new infections during the intervention period. Prior to this (in initialisation phases), genotypes are always sampled using the specified initial frequencies. Mode "initial" continues to sample genotypes using initial frequencies (i.e. independent of the success of parent generations of parasites). Mode "tracking" samples genotypes based on the success parent generations of parasites have in infecting mosquitoes, tracked per genotype. It is possible that in the future a recombination option will be added to this list, however designing a suitable model is not trivial.

Locus

→ scenario → parasiteGenetics → locus

<locus
    name=string
  >
IN THIS ORDER:
| ( <allele ... /> )+
</locus>

allele

Documentation (element)

Describes a locus, or a point at which an infection may vary. The genotype of an infection is determined by choosing one allele at each locus. Initial frequencies of alleles are specified independently for each locus, but subsequent infections are selected according to success of genotypes.

Alleles at loci can affect fitness and resistance to any number of drugs.

Attributes

Name of locus

name=string

Name of the Locus

Allele

→ scenario → parasiteGenetics → locus → allele

<allele
    name=string
    initialFrequency=double
    fitness=double
  [ hrp2_deletion=boolean ] DEFAULT VALUE false
  />

Documentation (element)

Describes an allele, or one possible genetic option of multiple at one point of variance.

Attributes

Name

name=string

Name of the allele; used to refer to it elsewhere.

Initial frequency

initialFrequency=double

Specification of how commonly this allele occurs during warmup relative to other alleles of the same locus. During the simulation's initialisation phases, the frequency at which each allele of each locus occurs is fixed. After the initialisation phase, frequency of alleles is modelled as an emergent property of the success of genotypes.

Fitness factor

fitness=double

Fitness factor of the allele. This is multiplication factor used to speed up or slow down replication of parasites. For example, if a genotype has an allele with a fitness factor of 1 at one locus and another allele with a fitness factor of 0.8 at a second locus, then the parasites with the genotype will replicate 20% slower than the baseline.

HRP2 deletion

hrp2_deletion=boolean

Default value: false

If true, marks this allele as having deleted HRP2. The effect on the simulation is that any diagnostic dependent on HRP2 behaves as if infections with deleted HRP2 have density 0. A diagnostic MUST explicitly set mechanism="HRP2" for this to have any effect.

Drug parameters (PK, PD and usage)

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
|   <treatments ... /> 
|   <drugs ... /> 
</pharmacology>

Documentation (element)

Drug model parameters and drug usage parameters

Documentation (type)

A library of drug related data for the PK/PD model.

Treatments library

→ scenario → pharmacology → treatments

<treatments>
IN THIS ORDER:
| ( <schedule ... /> )+
| ( <dosages ... /> )+
</treatments>

Documentation (element)

A library of drug deployment schedules and dosages.

schedule

→ scenario → pharmacology → treatments → schedule

<schedule
    name=string
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

A schedule for the administration of drugs in a course of treatment.

Note that dose sizes are multiplied by some multiplier (see dosages) and the times of all doses may be delayed.

Attributes

Name

name=string

Name for referring to this deployment schedule

medicate

→ scenario → pharmacology → treatments → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  />

Attributes

drug

drug=string

Abbreviated name of drug compound

Drug dose (mg with multiplier)

mg=double

Units: mg per something

Quantity of drug compound in mg per something. A separate dosage table must be used when medicating, which may specify multipliers of this number based on patient age or weight.

Time of administration

hour=double

Units: Hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

dosages

→ scenario → pharmacology → treatments → dosages

<dosages
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | ( <age ... /> )+
| | ( <bodymass ... /> )+
| |   <multiply ... /> 
</dosages>

Documentation (type)

A table for selecting a dose size. There are several ways this can work: using the patient's age or body mass in a look-up table to get a multplier, or directly using body mass as the multiplier.

The doses specified in "mg" in the treatment schedule are then multiplied by this multiplier.

Attributes

Name

name=string

Name for referring to this dosage table

Look-up table (age)

→ scenario → pharmacology → treatments → dosages → age

<age
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's age.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Look-up table (weight)

→ scenario → pharmacology → treatments → dosages → bodymass

<bodymass
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's body mass.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Multiply dose

→ scenario → pharmacology → treatments → dosages → multiply

<multiply
    by=("kg")
  />

Documentation (element)

Multiply the dose by some quantity, such as patient weight.

Attributes

By what?

by=("kg")

Quantity to multiply the dose by. Only option is "kg" (patient weight in kg).

Drug library

→ scenario → pharmacology → drugs

<drugs>
IN THIS ORDER:
| ( <drug ... /> )+
</drugs>

drug

Documentation (element)

A library of drug PK/PD data.

drug

→ scenario → pharmacology → drugs → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (type)

A drug description with PK/PD parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drugs → drug → PD

<PD
  [ locus=string ]
  >
IN THIS ORDER:
| ( <phenotype ... /> )+
</PD>

phenotype

Attributes

Locus

locus=string

Optional; if present specifies the locus corresponding to this drug's PD phenotypes: each phenotype must then match one of that locus's alleles. Otherwise the drug should specify only one phenotype. There is currently a one-to-many correspondance between loci and drugs.

PD parameters for some allele / resistance phenotype

→ scenario → pharmacology → drugs → drug → PD → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

Restrict phenotype applicability to certain alleles

→ scenario → pharmacology → drugs → drug → PD → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (element)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Maximal parasite killing rate

→ scenario → pharmacology → drugs → drug → PD → phenotype → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drugs → drug → PD → phenotype → IC50

<IC50
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

If CV > 0, the IC50 is sampled from a log-normal distribution.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Slope of effect curve

→ scenario → pharmacology → drugs → drug → PD → phenotype → slope

<slope>
    double
</slope>

Documentation (element)

Units: dimensionless

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drugs → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
| EXACTLY ONE OF:
| |   <half_life ... /> 
| | IN THIS ORDER:
| | |   <k ... /> 
| | |   <m_exponent ... /> 
| [ <k_a ... /> ]
| [ <conversion ... /> ]
|   <vol_dist ... /> 
| [ <compartment2 ... /> ]
| [ <compartment3 ... /> ]
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drugs → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drugs → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate λ, calculated as λ = ln(2) / half_life. The basic form of decay is C(t) = C0 * exp(-λ*t).

Alternatively, elimination rate can be specified via k and m_exponent.

Constant associated with elimination rate (k)

→ scenario → pharmacology → drugs → drug → PK → k

<k
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Constant used to calculate the elimination rate λ, which is calculated as λ = k / (body_mass ^ m_exponent), where body_mass is the patient's weight in kg and m_exponent is the next parameter. The basic form of decay is C(t) = C0 * exp(-λ*t).

If CV > 0, k is sampled per-human from the log-normal distribution: ln N( ln(mean) - σ^2 / 2, σ^2).

Alternatively, elimination rate can be specified via half_life.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Constant associated with elimination rate (m_exponent)

→ scenario → pharmacology → drugs → drug → PK → m_exponent

<m_exponent>
    double
</m_exponent>

Documentation (element)

Units: day^-1 Min: 0

Constant used to calculate the elimination rate λ, which is calculated as λ = k / (body_mass ^ m_exponent), where body_mass is the patient's weight in kg and k is the previous parameter. The basic form of decay is C(t) = C0 * exp(-λ*t).

Alternatively, elimination rate can be specified via half_life.

Note that in the case of a conversion model, this applies to both the elimination and the conversion rates.

Absorption rate constant (k_a)

→ scenario → pharmacology → drugs → drug → PK → k_a

<k_a
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Min: 0

Absorption rate parameter. Not allowed for one compartment models, but required for two and three compartment models and one compartment with conversion model (for the parent drug only).

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Conversion parameters (parent drug)

→ scenario → pharmacology → drugs → drug → PK → conversion

<conversion>
IN ANY ORDER:
|   <metabolite ... /> 
|   <rate ... /> 
|   <molRatio ... /> 
|   <IC50_log_correlation ... /> 
</conversion>

Documentation (element)

Configures the parent drug in a conversion model.

To use a conversion model, the parent drug should have this section defined as well as half-life or k (direct elimination; this may be zero) and k_a (absorption rate; this may be large).

The metabolite drug should define half-life or k (elimination of metabolite), but not k_a (absorption rate) or this section (conversion). It is not possible for the metabolite to itself undergo conversion with the current models.

Metabolite drug (abbreviation)

→ scenario → pharmacology → drugs → drug → PK → conversion → metabolite

<metabolite>
    string
</metabolite>

Documentation (element)

The abbreviation of the metabolite drug (e.g. "DHA" or "DHA_AR").

Rate of conversion

→ scenario → pharmacology → drugs → drug → PK → conversion → rate

<rate
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Rate of conversion of parent drug to metabolite.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Molecular weight ratio

→ scenario → pharmacology → drugs → drug → PK → conversion → molRatio

<molRatio>
    double
</molRatio>

Documentation (element)

Ratio of molecular weights: molecular weight of the metabolite divided by molecular weight of the parent.

IC50 log correlation

→ scenario → pharmacology → drugs → drug → PK → conversion → IC50_log_correlation

<IC50_log_correlation>
    double
</IC50_log_correlation>

Documentation (element)

Min: 0 Max: 1

The IC50 values of parent and metabolite drugs may be sampled from the log-normal distribution (if CV is greater than 0). This parameter controls correlation between these samples, measured in log-space.

If this value is 1, samples are fully correlated: a single z-score is used to calculate both samples. If this is 0, two independent samples are used.

Values between 0 and 1 (partial correlation) are supported; in this case IC50 values are sampled such that cor(log(x), log(y)) matches this value (where x, y are parent and metabolite IC50 values).

Volume of Distribution (Vd)

→ scenario → pharmacology → drugs → drug → PK → vol_dist

<vol_dist
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution.

If CV > 0 this is sampled from a log-normal distribution.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Second compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment2

<compartment2>
IN ANY ORDER:
|   <k12 ... /> 
|   <k21 ... /> 
</compartment2>

Documentation (element)

Optional element specifying conversion parameters to- and from- a second compartment.

Absorption rate to compartment 2 (k12)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → k12

<k12
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the first periphery compartment (2).

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Absorption rate from compartment 2 (k21)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → k21

<k21
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the first periphery compartment (2) to the central compartment.

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Third compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment3

<compartment3>
IN ANY ORDER:
|   <k13 ... /> 
|   <k31 ... /> 
</compartment3>

Documentation (element)

Optional element specifying conversion parameters to- and from- a third compartment.

Absorption rate to compartment 3 (k13)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → k13

<k13
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the second periphery compartment (3).

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Absorption rate from compartment 3 (k31)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → k31

<k31
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the second periphery compartment (3) to the central compartment.

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Diagnostic parameters

→ scenario → diagnostics

<diagnostics>
IN THIS ORDER:
| ( <diagnostic ... /> )*
</diagnostics>

diagnostic

Documentation (element)

Diagnostic model parameters

diagnostic

→ scenario → diagnostics → diagnostic

<diagnostic
    name=string
  [ units=("Other" or "Garki" or "Malariatherapy") ]
  [ mechanism=("Other" or "HRP2") ] DEFAULT VALUE Other
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterministic ... /> 
| |   <stochastic ... /> 
</diagnostic>

Attributes

Name of diagnostic

name=string

Name of this diagnostic (parameterisation). May be used elsewhere in the XML document to refer to this set of diagnostic parameters.

Parasite density units / methodology

units=("Other" or "Garki" or "Malariatherapy")

Parasite densities, as estimated according to standard microscopy methods, the Garki method, and as derived from Malariatherapy data are not equivalent. Internally, a "bias" factor is used to convert values estimated by one methods to values comparable with another (see AJTMHv75 supplement 2 pp20-21). This option allows specification of which methodology the density given in the diagnostic specification is measured with. Values allowed are: Malariatherapy, Garki and Other. If not specified, Other is assumed, unless the GARKI_DENSITY_BIAS model option is used, in which case this option must be specified.

Mechanism

mechanism=("Other" or "HRP2")

Default value: Other

Mechanism by which this diagnostic functions. Possible values are: HRP2, Other. In the case of HRP2, infections with an hrp2_deletion will be invisible to this diagnostic. In the case of Other, the diagnostic is unaffected by infection genome. The diagnostic used for monitoring cannot use HRP2. (This is a restriction made to simplify implementation.)

Deterministic detection

→ scenario → diagnostics → diagnostic → deterministic

<deterministic
    minDensity=double
  />

Documentation (element)

Specify that an artificial deterministic test is used: outcome is positive if parasite density is at least the minimum given.

Attributes

Minimum detectible density

minDensity=double

Units: parasites/microlitre Min: 0

The minimum density at which parasites can be detected. If 0, the test outcome is always positive.

Non-deterministic detection

→ scenario → diagnostics → diagnostic → stochastic

<stochastic
    dens_50=double
    specificity=double
  />

Documentation (element)

An improved model of detection which is non-deterministic, including false positive results as well as false negatives.

The probability of a positive outcome is modelled as 1 + s×(x/(x+d) - 1) where x is the parasite density, d is the density at which the test outcome has a 50% chance of being positive, and s is the probability of a positive outcome given no parasites (the specificity).

Some parameterisations:

Microscopy sensitivity/specificity data in Africa; Source: expert opinion — Allan Schapira dens_50 = 20.0 specificity = .75

RDT sensitivity/specificity for Plasmodium falciparum in Africa Source: Murray et al (Clinical Microbiological Reviews, Jan. 2008) dens_50 = 50.0; specificity = .942;

Attributes

Density 50

dens_50=double

Units: parasites/microlitre Min: 0

The density at which the test outcome has a 50% chance of being positive.

Specificity

specificity=double

Units: Dimensionless Min: 0 Max: 1

The probability of a positive test outcome in the absense of parasites.

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
| [ <vivax ... /> ]
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: model/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=string
  >
IN ANY ORDER:
| [ <NeonatalMortality ... /> ]
| [ <NonMalariaFevers ... /> ]
</clinical>

Documentation (type)

Description of clinical parameters that are related to the health-system description, but which contain data that cannot be changed as part of an intervention and that are not restricted to treatment.

Attributes

Follow-up period during which recurrence is considered a treatment failure

healthSystemMemory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

Neonatal mortality parameters

→ scenario → model → clinical → NeonatalMortality

<NeonatalMortality
    diagnostic=string
  />

Attributes

Diagnostic used to parameterise model

diagnostic=string

The name of a diagnostic used to parameterise the model. Neonatal mortality is derived from malaria patency of a certain sub-population of humans. This is the diagnostic used to asses patency for this purpose. If this is not specified, the monitoring diagnostic is used.

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
| [ <prNeedTreatmentNMF ... /> ]
| [ <prNeedTreatmentMF ... /> ]
</NonMalariaFevers>

Documentation (type)

Description of the incidence of non-malaria fever. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a non-malarial fever requires treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

Availability of humans to mosquitoes relative to an adult, categorized by age group

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ]
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

Each human is assigned a weight multiplier from a normal distribution with mean 1 and this standard deviation at birth. His/her weight is this multiplier times the mean from age distribution. A standard deviation of zero for no heterogeneity is valid; a rough value from Tanzanian data is 0.14.

Vivax model parameters

→ scenario → model → vivax

<vivax>
IN ANY ORDER:
|   <probBloodStageInfectiousToMosq ... /> 
|   <hypnozoiteRelease ... /> 
|   <bloodStageProtectionLatency ... /> 
|   <bloodStageLengthDays ... /> 
|   <clinicalEvents ... /> 
</vivax>

Documentation (element)

This describes Vivax model parameters, and is required when using the VIVAX_SIMPLE_MODEL model option.

Probability of mosquito infection

→ scenario → model → vivax → probBloodStageInfectiousToMosq

<probBloodStageInfectiousToMosq
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

The chance of a feeding mosquito becoming infected, given that the host is patent. (This may be adjusted by transmission-blocking vaccines.)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Hypnozoite releases

→ scenario → model → vivax → hypnozoiteRelease

<hypnozoiteRelease
  [ pSecondRelease=double ] DEFAULT VALUE 0
  >
IN ANY ORDER:
|   <numberHypnozoites ... /> 
|   <firstReleaseDays ... /> 
| [ <secondReleaseDays ... /> ]
</hypnozoiteRelease>

Documentation (element)

Describes the number and times of hypnozoite releases.

Documentation (type)

This element defines probabilites when and how many hypnozoites are released from the liverstage into the blood.

The gap between the start of a new brood of hypnozoites and its release are defined as follows:

latentP + latentRelapse + randomReleaseDelay

randomReleaseDelay is based on one or two lognormal distributions, which are defined in firstRelease and optionally secondRelease.

You can define 2 release distributions, which get added together and represent the probability of hypnozoites which get released before winter (first release) or after (second release).

You can omit the secondRelease element if no release to the blood happens after winter.

Attributes

latent relapse days

pSecondRelease=double

Default value: 0

Probability of a second release. If undefined it is zero.

Number of Hypnozoites

→ scenario → model → vivax → hypnozoiteRelease → numberHypnozoites

<numberHypnozoites
    max=int
    base=double
  />

Documentation (element)

numberHypnozoites calculates the number of hypnozoites in the liver stage based on a base which is between 0 and 1.

This number is random based on the following distribution and normalized:

max ∑ (base ^ n) n = 0

Attributes

max

max=int

base

base=double

firstReleaseDays

→ scenario → model → vivax → hypnozoiteRelease → firstReleaseDays

<firstReleaseDays
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
    latentRelapse=double
  />

Documentation (type)

Hypnozoites are released after a delay, calculated as: roundToTSFromDays(delay + latentRelapse)

Here, roundToTSFromDays rounds the input (in days) to the nearest timestep, delay is sampled from a log-normal, and latentRelapse is the parameter specified here.

The delay is sampled from a log-normal distribution, parameterised via the (linear) mean and CV (coefficient of variation) given here.

Documentation (base type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

latent relapse days

latentRelapse=double

Usually between 10 and 15 days.

secondReleaseDays

→ scenario → model → vivax → hypnozoiteRelease → secondReleaseDays

<secondReleaseDays
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
    latentRelapse=double
  />

Documentation (type)

Hypnozoites are released after a delay, calculated as: roundToTSFromDays(delay + latentRelapse)

Here, roundToTSFromDays rounds the input (in days) to the nearest timestep, delay is sampled from a log-normal, and latentRelapse is the parameter specified here.

The delay is sampled from a log-normal distribution, parameterised via the (linear) mean and CV (coefficient of variation) given here.

Documentation (base type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

latent relapse days

latentRelapse=double

Usually between 10 and 15 days.

Blood stage protection latency

→ scenario → model → vivax → bloodStageProtectionLatency

<bloodStageProtectionLatency
    value=double
  />

Documentation (element)

Min: 0

The length of time after expiry of a blood-stage infection during which relapses from the same brood are supressed by the immune system.

This is rounded to the nearest time-step.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Blood stage length

→ scenario → model → vivax → bloodStageLengthDays

<bloodStageLengthDays
    scale=double
    shape=double
    distr=("weibull")
  />

Documentation (element)

Units: Days

Parameters used to sample the length of blood-stage infections from a Weibull distribution (scale parameter lambda, shape parameter k).

Documentation (type)

Parameters of a Weibull distribution.

Attributes

Scale

scale=double

The Weibull scale parameter (λ).

shape

shape=double

The Weibull shape parameter (k).

Distribution

distr=("weibull")

To allow heterogeneity, a distribution must be specified. In this case, only "weibull" is allowed.

clinicalEvents

→ scenario → model → vivax → clinicalEvents

<clinicalEvents>
IN THIS ORDER:
|   <pPrimaryInfection ... /> 
|   <pRelapseOne ... /> 
|   <pRelapseTwoPlus ... /> 
|   <pEventIsSevere ... /> 
|   <vivaxClinOption ... /> 
</clinicalEvents>

Documentation (type)

This elements holds all information about probabilites for clinical events from infections and relapses.

pPrimaryInfection

→ scenario → model → vivax → clinicalEvents → pPrimaryInfection

<pPrimaryInfection
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseOne

→ scenario → model → vivax → clinicalEvents → pRelapseOne

<pRelapseOne
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseTwoPlus

→ scenario → model → vivax → clinicalEvents → pRelapseTwoPlus

<pRelapseTwoPlus
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pEventIsSevere

→ scenario → model → vivax → clinicalEvents → pEventIsSevere

<pEventIsSevere
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

vivaxClinOption

→ scenario → model → vivax → clinicalEvents → vivaxClinOption

<vivaxClinOption>
    string
</vivaxClinOption>

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=string
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=string

Units: User defined (default: steps) Min: 0 Max: 20

Pre-erythrocytic latent period Can be specified in steps (e.g. 3t) or days (e.g. 15d).

parameter

→ scenario → model → parameters → parameter

<parameter
  [ name=string ]
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema current documentation

Generated from: scenario_current.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
  [ analysisNo=int ]
    name=string
  [ wuID=int ]
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:om="http://openmalaria.org/schema/scenario_current"
    xsi:schemaLocation="http://openmalaria.org/schema/scenario_current scenario_current.xsd"
  >
IN ANY ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entomology ... /> 
| [ <parasiteGenetics ... /> ]
| [ <pharmacology ... /> ]
| [ <diagnostics ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Name of intervention

Work unit identifier

wuID=int

Units: Number

Work unit ID. Obselete and no longer required.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Description of demography

Attributes

Name of demography data

name=string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Years Min: 0 Max: 100

Maximum age of simulated humans in years

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

list of age groups included in demography

Documentation (type)

list of age groups included in demography or surveys

Attributes

Lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Units: Percentage Min: 0 Max: 100

Percentage of human population in age group

Upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ startDate=string ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
| [ <cohorts ... /> ]
</monitoring>

Documentation (element)

Description of surveys

Attributes

Name of monitoring settings

name=string

Name of monitoring settings

Start of monitoring

startDate=string

continuous

→ scenario → monitoring → continuous

<continuous
    period=string
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Delay between reports

period=string

Units: User defined (default: steps)

Delay between reports; typically one time step but can be greater. Can be specified in steps (e.g. 1t) or days (e.g. 5d).

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions
  [ onlyNewEpisode=boolean ] DEFAULT VALUE false
  >
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See model/mon/OutputMeasures.h for a list of supported outputs. Should also be on the wiki.

Attributes

Report only for new cases

onlyNewEpisode=boolean

Default value: false

option

→ scenario → monitoring → SurveyOptions → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  [ outputNumber=int ]
  [ byAge=boolean ]
  [ byCohort=boolean ]
  [ bySpecies=boolean ]
  [ byGenotype=boolean ]
  [ byDrugType=boolean ]
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Number identifying measure in output

outputNumber=int

Report by age category

byAge=boolean

Report by cohort

byCohort=boolean

Report by mosquito species

bySpecies=boolean

Report by parasite genotype

byGenotype=boolean

Report by drug type

byDrugType=boolean

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
  [ detectionLimit=double ]
  [ diagnostic=string ]
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/microlitre Min: 0

Deprecated: limit above which a human's infection is reported as patent. Alternative: do not specify this; instead specify "diagnostic".

Name of monitoring diagnostic

diagnostic=string

Name of a parameterised diagnostic to use in surveys (see scenario/diagnostics).

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime
  [ repeatStep=string ]
  [ repeatEnd=string ]
  [ reported=boolean ] DEFAULT VALUE true
  >
    string
</surveyTime>

Documentation (element)

Units: User defined (defaults to steps) Min: 0

The simulation ends immediately after the last survey is taken.

Attributes

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

reported

reported=boolean

Default value: true

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Cohorts

→ scenario → monitoring → cohorts

<cohorts>
IN THIS ORDER:
| ( <subPop ... /> )+
</cohorts>

subPop

Documentation (element)

Allows the configuration of multiple cohorts (output segregated according to membership within specific sub-populations).

If this element is omitted, monitoring surveys cover the entire simulated human population.

It does not affect the "continuous" outputs (these never take cohorts into account).

Sub-population

→ scenario → monitoring → cohorts → subPop

<subPop
    id=string
    number=integer
  />

Documentation (element)

In the output file, the output set is identified by multiplying this number by 1000 then adding it to the age group column.

Attributes

Sub-population identifier

id=string

Textual identifier for the sub-population (i.e. for an intervention component, since sub-populations are defined as the hosts an intervention component is deployed to).

Sub-population number

number=integer

Units: dimensionless Min: 1 Max: 2097152

Number identifying a sub-population; used to define identifiers of output sets. This number must be a power of 2 (i.e. 1, 2, 4, 8, ...). See documentation of subPop element.

Preventative interventions

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfections ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <vectorPop ... /> ]
| [ <vectorTrap ... /> ]
| [ <nonHumanHostsModifications ... /> ]
| [ <addNonHumanHosts ... /> ]
| [ <human ... /> ]
</interventions>

Documentation (element)

Attributes

Name of intervention set

name=string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeHS>

timedDeployment

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeHS → timedDeployment

<timedDeployment
    time=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timedDeployment>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <infectionOrigin ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</uncomplicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

multiple

→ scenario → interventions → human → component → decisionTree → multiple

<multiple
  [ name=string ]
  >
EXACTLY ONE OF:
| ( <caseType ... /> )*
| ( <infectionOrigin ... /> )*
| ( <diagnostic ... /> )*
| ( <uncomplicated ... /> )*
| ( <severe ... /> )*
| ( <random ... /> )*
| ( <age ... /> )*
| ( <treatPKPD ... /> )*
| [ <treatSimple ... /> ]
| ( <deploy ... /> )*
| ( <report ... /> )*
| ( <cohort ... /> )*
</multiple>

Documentation (type)

A special node allowing multiple sub-trees to be evaluated.

This is different from an ordinary decision tree node in that:

a) multiple types of child can occur simultaneously (e.g. multiple types of treatment or treatment plus a 'random' sub-tree)

b) the 'noTreatment' and 'treatFailure' nodes are not allowed

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → multiple → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

firstLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → firstLine

<firstLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <infectionOrigin ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</firstLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

secondLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → secondLine

<secondLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <infectionOrigin ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</secondLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

infectionOrigin

→ scenario → interventions → human → component → decisionTree → infectionOrigin

<infectionOrigin
  [ name=string ]
  >
IN ANY ORDER:
|   <imported ... /> 
|   <introduced ... /> 
|   <indigenous ... /> 
</infectionOrigin>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient has an imported, introduced or indigenous infection.

If the patient is not infected, this will execute the indigenous branch by default. You must use a diagnostic test first to find out if the patient is infected.

If there are no imported cases, all infections will appear indigenous.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

imported

→ scenario → interventions → human → component → decisionTree → multiple → infectionOrigin → imported

<imported
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <infectionOrigin ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</imported>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

positive

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <infectionOrigin ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

uncomplicated

→ scenario → interventions → human → component → decisionTree → uncomplicated

<uncomplicated
  [ name=string ]
  [ memory=string ] DEFAULT VALUE 1
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</uncomplicated>

Documentation (type)

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Number of days to look back for fevers. This must be less than or equal to the healthsystem memory parameter. In general, this should be less than or equal to the repeatStep in MSAT with contiuous deployment

memory=string

Units: User-defined (defaults to steps)

Default value: 1

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

positive

→ scenario → interventions → human → component → decisionTree → multiple → uncomplicated → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <infectionOrigin ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

severe

→ scenario → interventions → human → component → decisionTree → severe

<severe
  [ name=string ]
  [ memory=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</severe>

Documentation (type)

A switch which choses a branch deterministically, based on whether the host has a severe case or not. Note that this include severe cases due to comorbidities.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Number of days to look back for fevers. This must be less than or equal to the healthsystem memory parameter. In general, this should be less than or equal to the repeatStep in MSAT with contiuous deployment

memory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

positive

→ scenario → interventions → human → component → decisionTree → multiple → severe → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <infectionOrigin ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

outcome

→ scenario → interventions → human → component → decisionTree → multiple → random → outcome

<outcome
  [ name=string ]
    p=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <infectionOrigin ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</outcome>

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Probability

p=double

Units: None Min: 0 Max: 1

Probability of selecting this outcome. The sum of probabilities across all outcomes must be 1.

age

→ scenario → interventions → human → component → decisionTree → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Age range

→ scenario → interventions → human → component → decisionTree → multiple → age → age

<age
  [ name=string ]
    lb=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <infectionOrigin ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</age>

Documentation (element)

Describes a branch, selected for patients of a certain age.

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Lower bound (inclusive)

lb=double

Min: 0

noTreatment

→ scenario → interventions → human → component → decisionTree → noTreatment

<noTreatment
  [ name=string ]
  />

Documentation (type)

An end node doing nothing. This exists to explicitly state that no treatment happens and to prevent trees from accidentally being left incomplete.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

report

→ scenario → interventions → human → component → decisionTree → report

<report
  [ name=string ]
  [ outputNumber=int ] DEFAULT VALUE 0
  />

Documentation (type)

This increments measure 80 (nCMDTReport) by one every time this node is visited. This can be useful to report the results of mass test and treat interventions using the decision tree.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Delay (hours)

outputNumber=int

Default value: 0

treatFailure

→ scenario → interventions → human → component → decisionTree → treatFailure

<treatFailure
  [ name=string ]
  />

Documentation (type)

An end node which reports treatment but does not change parasitalogical status. This allows correct labelling of second-line cases.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

cohort

→ scenario → interventions → human → component → decisionTree → cohort

<cohort
  [ name=string ]
    component=string
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</cohort>

Documentation (type)

A switch which choses a branch deterministically, based on whether the host is part of the cohort (defined by the intervention component) or not.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Number of days to look back for fevers. This must be less than or equal to the healthsystem memory parameter. In general, this should be less than or equal to the repeatStep in MSAT with contiuous deployment

component=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

positive

→ scenario → interventions → human → component → decisionTree → multiple → cohort → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <infectionOrigin ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

negative

→ scenario → interventions → human → component → decisionTree → multiple → cohort → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <infectionOrigin ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

negative

→ scenario → interventions → human → component → decisionTree → multiple → severe → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <infectionOrigin ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

negative

→ scenario → interventions → human → component → decisionTree → multiple → uncomplicated → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <infectionOrigin ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

negative

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <infectionOrigin ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

introduced

→ scenario → interventions → human → component → decisionTree → multiple → infectionOrigin → introduced

<introduced
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <infectionOrigin ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</introduced>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

indigenous

→ scenario → interventions → human → component → decisionTree → multiple → infectionOrigin → indigenous

<indigenous
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <infectionOrigin ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</indigenous>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

infectionOrigin

→ scenario → interventions → human → component → decisionTree → multiple → infectionOrigin

<infectionOrigin
  [ name=string ]
  >
IN ANY ORDER:
|   <imported ... /> 
|   <introduced ... /> 
|   <indigenous ... /> 
</infectionOrigin>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient has an imported, introduced or indigenous infection.

If the patient is not infected, this will execute the indigenous branch by default. You must use a diagnostic test first to find out if the patient is infected.

If there are no imported cases, all infections will appear indigenous.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

uncomplicated

→ scenario → interventions → human → component → decisionTree → multiple → uncomplicated

<uncomplicated
  [ name=string ]
  [ memory=string ] DEFAULT VALUE 1
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</uncomplicated>

Documentation (type)

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Number of days to look back for fevers. This must be less than or equal to the healthsystem memory parameter. In general, this should be less than or equal to the repeatStep in MSAT with contiuous deployment

memory=string

Units: User-defined (defaults to steps)

Default value: 1

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

severe

→ scenario → interventions → human → component → decisionTree → multiple → severe

<severe
  [ name=string ]
  [ memory=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</severe>

Documentation (type)

A switch which choses a branch deterministically, based on whether the host has a severe case or not. Note that this include severe cases due to comorbidities.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Number of days to look back for fevers. This must be less than or equal to the healthsystem memory parameter. In general, this should be less than or equal to the repeatStep in MSAT with contiuous deployment

memory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

random

→ scenario → interventions → human → component → decisionTree → multiple → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

age

→ scenario → interventions → human → component → decisionTree → multiple → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → multiple → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → multiple → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → multiple → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

report

→ scenario → interventions → human → component → decisionTree → multiple → report

<report
  [ name=string ]
  [ outputNumber=int ] DEFAULT VALUE 0
  />

Documentation (type)

This increments measure 80 (nCMDTReport) by one every time this node is visited. This can be useful to report the results of mass test and treat interventions using the decision tree.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Delay (hours)

outputNumber=int

Default value: 0

cohort

→ scenario → interventions → human → component → decisionTree → multiple → cohort

<cohort
  [ name=string ]
    component=string
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</cohort>

Documentation (type)

A switch which choses a branch deterministically, based on whether the host is part of the cohort (defined by the intervention component) or not.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Number of days to look back for fevers. This must be less than or equal to the healthsystem memory parameter. In general, this should be less than or equal to the repeatStep in MSAT with contiuous deployment

component=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <infectionOrigin ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</complicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: Days Min: 0 Max: unbounded

Maximum number of timesteps (including first day of case) that an individual with an uncomplicated case of malaria will remember he/she was sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial or non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of a complicated or severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
  [ name=string ]
  [ useDiagnosticUC=boolean ] DEFAULT VALUE false
  >
IN ANY ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <treatmentActions ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
</ImmediateOutcomes>

Documentation (type)

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Name of case management parameterisation

name=string

Name of health system

useDiagnosticUC

useDiagnosticUC=boolean

Default value: false

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Description of drug regimen.

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Artemisinine based combination therapy

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Quinine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0 Max: 1name:P(self-treat)

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Effectiveness of treatment for non-compliant patients

treatmentActions

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions

<treatmentActions>
IN ANY ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
</treatmentActions>

CQ
SP
AQ
SPAQ
ACT
QN

CQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ

<CQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</CQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

deploy

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy

<deploy
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ p=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| ( <component ... /> )+
</deploy>

component

Attributes

Maximum age of eligible humans

maxAge=double

Units: Years Min: 0

Maximum age of eligible humans (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible humans

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible humans (defaults to 0). Input is rounded to the nearest time step.

Probability of delivery to eligible humans

p=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Probability of this list of components being deployed, given that other constraints are met.

component

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Prophylactic treatment

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere → clearInfections

<clearInfections
    timesteps=string
    stage=("liver" or "blood" or "both")
  />

Documentation (element)

Attributes

Length of effect

timesteps=string

Units: User defined (defaults to steps)

Target stage

stage=("liver" or "blood" or "both")

SP

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SP

<SP
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SP>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

AQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → AQ

<AQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</AQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

SPAQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SPAQ

<SPAQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SPAQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

ACT

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → ACT

<ACT
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</ACT>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

QN

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → QN

<QN
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</QN>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

Probability that human is incompatible with liver-stage drug treatment

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pHumanCannotReceive

<pHumanCannotReceive
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that a human is determined to be unable to receive liver-stage drug treatment. Treatment is neither reported or given for such humans.

This is sampled once per human at birth.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Ignore liver-stage drug treatment incompatibility

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → ignoreCannotReceive

<ignoreCannotReceive
    value=boolean
  />

Documentation (element)

If true, ignore pHumanCannotReceive and consider all humans eligible for treatment; if false (or not specified), do not treat those demed incompatible with liver-stage drug treatment.

The point of this is that pHumanCannotReceive cannot be altered by changeHS interventions, but this property can be.

Attributes

Input parameter value

value=boolean

A boolean value.

Prob use in UC case

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pUseUncomplicated

<pUseUncomplicated
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

This feature is deprecated; it is suggested to use the "simple treatment" feature configured to clear liver-stage parasites, leaving this option unset or zero.

Chance of liver-stage drug treatment being used for routine treatment of an uncomplicated case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Effectiveness

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → effectivenessOnUse

<effectivenessOnUse
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that liver-stage drug treatment is effective.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

DecisionTree5Day

<DecisionTree5Day
  [ name=string ]
  >
IN ANY ORDER:
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
|   <treeUCOfficial ... /> 
|   <treeUCSelfTreat ... /> 
|   <cureRateSevere ... /> 
|   <treatmentSevere ... /> 
</DecisionTree5Day>

Documentation (type)

Besides greater flexibility, this allows treatment via PK/PD models.

Attributes

Name of case management parameterisation

name=string

Name of health system

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → DecisionTree5Day → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → DecisionTree5Day → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

treeUCOfficial

→ scenario → healthSystem → DecisionTree5Day → treeUCOfficial

<treeUCOfficial
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <infectionOrigin ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</treeUCOfficial>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treeUCSelfTreat

→ scenario → healthSystem → DecisionTree5Day → treeUCSelfTreat

<treeUCSelfTreat
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <infectionOrigin ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</treeUCSelfTreat>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Cure rate (severe cases)

→ scenario → healthSystem → DecisionTree5Day → cureRateSevere

<cureRateSevere
    value=double
  />

Documentation (element)

Min: 0 Max: 1

The probability of clearing parasites given access to appropriate (hospital) care, for a severe case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

treatmentSevere

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere

<treatmentSevere
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</treatmentSevere>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Case fatality rate for inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: Dimensionless

List of age-specific probabilities of sequelae in inpatients, during a severe bout of malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeEIR>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeEIR → timedDeployment

<timedDeployment
    eipDuration=int
    time=string
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timedDeployment>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Time

time=string

Units: User defined (defauls to steps) Min: 0

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=string ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=string

Units: User defined (default: steps) Min: 0

Default value: 0

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=string
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time of start

time=string

Units: User defined (defauls to steps) Min: 0

Insert R_0 case

<insertR_0Case
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</insertR_0Case>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → insertR_0Case → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Uninfect vectors

<uninfectVectors
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</uninfectVectors>

timedDeployment

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → uninfectVectors → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Vector population intervention

→ scenario → interventions → vectorPop

<vectorPop>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorPop>

intervention

Documentation (element)

Units: List of elements

A list of parameterisations of generic vector host-inspecific interventions.

intervention

→ scenario → interventions → vectorPop → intervention

<intervention
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

Units: List of elements

An intervention which may have various effects on the vector populations as a whole. (Not host specific.)

Multiple instances of this intervention class are allowed (multiple parameterisations, not just deployments).

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → vectorPop → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → vectorPop → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <seekingDeathRateIncrease ... /> ]
| [ <probDeathOvipositing ... /> ]
| [ <emergenceReduction ... /> ]
| [ <probAdditionalDeathSugarFeeding ... /> ]
</anopheles>

Documentation (type)

Units: dimensionless Min: 0 Max: 1

Descriptions of the effects of vector interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Proportional increase in deaths while host searching

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease

<seekingDeathRateIncrease
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</seekingDeathRateIncrease>

decay

Documentation (element)

Units: dimensionless

Describe an effect on the increase in the death rate while host seeking (mu_vA) due to this intervention.

Enter the rate increase (i.e. if rate increases to 120% of normal, give 0.2). New death rate while seeking is old × (1 + increase) where increase is this factor given. Must have increas ≥ -1.

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

decay

→ scenario → interventions → nonHumanHostsModifications → intervention → decay → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Proportion ovipositing mosquitoes killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing

<probDeathOvipositing
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probDeathOvipositing>

decay

Documentation (element)

Units: dimensionless

Describe an effect of increased mortality while ovipositing due to this intervention. Enter the probability of dying due to this intervention.

Attributes

Initial probability of killing

initial=double

Units: dimensionless Min: 0 Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Proportion of emerging pupa killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction

<emergenceReduction
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</emergenceReduction>

decay

Documentation (element)

Units: dimensionless

Describe an effect on emergence of pupa into adults: this value is the proportion of emerging pupa which are killed by this intervention.

Attributes

Initial proportion reduction

initial=double

Units: dimensionless Min: -inf Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Probability of death while host searching as a result of feeding on a sugar bait (used to dynamically adjust mu_vA)

→ scenario → interventions → vectorPop → intervention → description → anopheles → probAdditionalDeathSugarFeeding

<probAdditionalDeathSugarFeeding
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probAdditionalDeathSugarFeeding>

decay

Documentation (element)

Units: dimensionless

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probAdditionalDeathSugarFeeding → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Vector population intervention deployment

→ scenario → interventions → vectorPop → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

deploy

→ scenario → interventions → vectorPop → intervention → timed → deploy

<deploy
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Baited trap

→ scenario → interventions → vectorTrap

<vectorTrap>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorTrap>

intervention

Documentation (element)

intervention

→ scenario → interventions → vectorTrap → intervention

<intervention
  [ name=string ]
  >
IN THIS ORDER:
| ( <description ... /> )+
| [ <timed ... /> ]
</intervention>

Documentation (type)

Attributes

Descriptive name for type of trap

name=string

Optional name for this type of trap

Description

→ scenario → interventions → vectorTrap → intervention → description

<description
    mosquito=string
  >
IN THIS ORDER:
|   <relativeAvailability ... /> 
|   <decayOfAvailability ... /> 
</description>

Documentation (element)

Parameters associated with a vector trap intervention, per mosquito species.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Initial relative availability

→ scenario → interventions → vectorTrap → intervention → description → relativeAvailability

<relativeAvailability
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: inf

Describes the availiability of a trap to a host-seeking mosquito relative to an average unprotected adult.

I.e. if this parameter is 2, then each trap will on average attract twice as many mosquitoes as unprotected adults.

This is the initial availability; it may decay towards zero depending on the configured decay function.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay of availability

→ scenario → interventions → vectorTrap → intervention → description → decayOfAvailability

<decayOfAvailability
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decayOfAvailability>

decay

Documentation (element)

Describes how availability decays to zero.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Vector trap intervention deployment

→ scenario → interventions → vectorTrap → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )*
</timed>

deploy

Documentation (element)

List of timed vector trap intervention deployment

deploy

→ scenario → interventions → vectorTrap → intervention → timed → deploy

<deploy
    time=string
    ratioToHumans=double
    lifespan=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Ratio to humans

ratioToHumans=double

Min: 0 Max: inf

The number of traps deployed, by this deployment, per adult human. E.g. if there are currently 100 traps and 1000 humans, then a ratio of 0.1 will increase the number of traps to 200.

Lifespan

lifespan=string

Units: Steps or Days or Years

nonHumanHostsModifications

→ scenario → interventions → nonHumanHostsModifications

<nonHumanHostsModifications>
IN THIS ORDER:
| ( <intervention ... /> )+
</nonHumanHostsModifications>

intervention

Documentation (element)

List of interventions that modify parameters of non-human hosts described in the .

intervention

→ scenario → interventions → nonHumanHostsModifications → intervention

<intervention
    name=string
    nonHumanHostsName=string
  >
IN THIS ORDER:
|   <decay ... /> 
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

This intervention modifies parameters of non-human hosts described in the section of the input scenario file.

The intervention is described by 5 parameters that define the change in each of non-human host parameters:

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

Name of intervention

nonHumanHostsName=string

Name of intervention (e.g. larviciding, sugar bait).

decay

→ scenario → interventions → nonHumanHostsModifications → intervention → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

description

→ scenario → interventions → nonHumanHostsModifications → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <availabilityReduction ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
| [ <restingKillingEffect ... /> ]
| [ <fecundityReduction ... /> ]
</anopheles>

Documentation (type)

Descriptions of the effects of non human hosts interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

availabilityReduction

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → availabilityReduction

<availabilityReduction
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

preprandialKillingEffect

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

postprandialKillingEffect

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

restingKillingEffect

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → restingKillingEffect

<restingKillingEffect
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

fecundityReduction

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → fecundityReduction

<fecundityReduction
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

Vector population intervention deployment

→ scenario → interventions → nonHumanHostsModifications → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

addNonHumanHosts

<addNonHumanHosts>
IN THIS ORDER:
| ( <nonHumanHosts ... /> )+
</addNonHumanHosts>

nonHumanHosts

Documentation (element)

List of intervention that add new non-human hosts that have not been described in the .

nonHumanHosts

→ scenario → interventions → addNonHumanHosts → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</nonHumanHosts>

Documentation (type)

Describes a new non-human hosts that have not been described in the .

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
|   <mosqRelativeAvailabilityHuman ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <hostFecundityFactor ... /> 
</anopheles>

Documentation (type)

Descriptions of the effects of new non human hosts with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Relative availability of non-human host (ξ_i)

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqRelativeAvailabilityHuman

<mosqRelativeAvailabilityHuman
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of the population of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → hostFecundityFactor

<hostFecundityFactor
    value=double
  />

Documentation (element)

Units: Proportion

Multiplicative factor for the number of fertile eggs laid by a mosquito after biting this type of host, relative to an unprotected human.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vector trap intervention deployment

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )*
</timed>

deploy

Documentation (element)

List of timed vector trap intervention deployment

deploy

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → timed → deploy

<deploy
    time=string
    lifespan=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Lifespan

lifespan=string

Units: Steps or Days or Years

Human-specific interventions

→ scenario → interventions → human

<human>
IN THIS ORDER:
| ( <component ... /> )+
| ( <deployment ... /> )*
</human>

Documentation (element)

Encapsulates all interventions whose effects are specific to the human host: any interventions where target humans may be selected via population-coverage, age limits and sub-population membership.

Component

→ scenario → interventions → human → component

<component
    id=string
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <screen ... /> 
| |   <treatSimple ... /> 
| |   <treatPKPD ... /> 
| |   <decisionTree ... /> 
| |   <PEV ... /> 
| |   <BSV ... /> 
| |   <TBV ... /> 
| |   <ITN ... /> 
| |   <IRS ... /> 
| |   <GVI ... /> 
| | [ <recruitmentOnly ... /> ]
| |   <clearImmunity ... /> 
| [ <subPopRemoval ... /> ]
</component>

Documentation (element)

Each element describes one component: its effects, decay of the(se) effect(s), and related stuff (e.g. description of indirect decay and of usage levels).

Attributes

Component identifier

id=string

Name of component

name=string

An informal name/description for the component

screen

→ scenario → interventions → human → component → screen

<screen
    diagnostic=string
  >
IN THIS ORDER:
| ( <positive ... /> )*
| ( <negative ... /> )*
</screen>

Documentation (type)

This can be combined with MDA to achieve mass screen and treat (MSAT) or other types of mass screening intervention.

The use of the screening itself is reported (if enabled), but not the outcome. Deployment of interventions triggered by the screening may be reported, however.

Attributes

Name of diagnostic

diagnostic=string

Name of a parameterised diagnostic (see scenario/diagnostics).

positive

→ scenario → interventions → human → component → screen → positive

<positive
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → screen → negative

<negative
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

treatSimple

→ scenario → interventions → human → component → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

treatPKPD

→ scenario → interventions → human → component → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

decisionTree

→ scenario → interventions → human → component → decisionTree

<decisionTree
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <infectionOrigin ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</decisionTree>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Vaccines

→ scenario → interventions → human → component → PEV

<PEV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )*
| ( <phenotype ... /> )*
</PEV>

Documentation (element)

Pre-erythrocytic vaccine (PEV): prevents a proportion of infections from commencing.

Documentation (type)

Description of a vaccine's effect

Decay of effect

→ scenario → interventions → human → component → PEV → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (element)

Specification of decay of efficacy. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Variance parameter for vaccine efficacy

→ scenario → interventions → human → component → PEV → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

PD parameters for some allele / resistance phenotype

→ scenario → interventions → human → component → PEV → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
| ( <initialEfficacy ... /> )+
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

restriction

→ scenario → interventions → human → component → PEV → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (type)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → phenotype → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vaccines

→ scenario → interventions → human → component → BSV

<BSV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )*
| ( <phenotype ... /> )*
</BSV>

Documentation (element)

Blood-stage vaccine (BSV): acts as a killing factor on blood-stage parasites. Exact action depends on the within host model.

Documentation (type)

Description of a vaccine's effect

Vaccines

→ scenario → interventions → human → component → TBV

<TBV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )*
| ( <phenotype ... /> )*
</TBV>

Documentation (element)

Transmission-blocking vaccine (TBV): one minus this scales the probability of transmission to mosquitoes

Documentation (type)

Description of a vaccine's effect

Bed nets

→ scenario → interventions → human → component → ITN

<ITN>
IN THIS ORDER:
| [ <usage ... /> ]
|   <holeRate ... /> 
|   <ripRate ... /> 
|   <ripFactor ... /> 
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
|   <attritionOfNets ... /> 
| ( <anophelesParams ... /> )+
</ITN>

Documentation (element)

Description of bed-net interventions (ITNs, LLINs).

Proportion of time nets are used by humans

→ scenario → interventions → human → component → ITN → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of nets by humans, from 0 to 1.

At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing.

See also "propActing" (proportion of bits for which net acts).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Rate at which holes are made

→ scenario → interventions → human → component → ITN → holeRate

<holeRate
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: Holes per annum Min: 0

The rate at which new holes are made in nets.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Rate at which holes are enlarged

→ scenario → interventions → human → component → ITN → ripRate

<ripRate
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: Rips per existing hole per annum Min: 0

Each existing hole has a probability of being ripped bigger according to a Poisson process with this rate as (only) parameter.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Rip factor

→ scenario → interventions → human → component → ITN → ripFactor

<ripFactor
    value=double
  />

Documentation (element)

Units: none Min: 0

This factor expresses how important rips are in increasing the hole.

The hole index of a net is h + F×x where h and x are the total numbers of holes and rips respectively and F is the rip factor.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → ITN → initialInsecticide

<initialInsecticide
    mean=double
  [ SD=double ]
  [ distr=("const" or "normal") ] DEFAULT VALUE const
  />

Documentation (element)

Units: mg/m² Min: 0

Documentation (type)

A parameter with optional heterogeneity.

Optionally, a distribution ("distr") and standard of deviation ("SD") may be specified.

Attributes

mean

mean=double

The mean value.

standard deviation

SD=double

The standard deviation of variates.

Distribution

distr=("const" or "normal")

Default value: const

Decay of insecticide

→ scenario → interventions → human → component → ITN → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</insecticideDecay>

decay

Documentation (element)

Units: none

Decay curve for insecticide content of nets. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Attrition of nets

→ scenario → interventions → human → component → ITN → attritionOfNets

<attritionOfNets
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</attritionOfNets>

decay

Documentation (element)

Units: dimensionless

Specifies the rate at which nets are disposed of over time. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Humans are removed from the intervention component's sub-population on disposal (attrition) of their nets. Currently this event is not reported.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

anophelesParams

→ scenario → interventions → human → component → ITN → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <holeIndexMax ... /> ]
| EXACTLY ONE OF:
| |   <deterrency ... /> 
| |   <twoStageDeterrency ... /> 
| EXACTLY ONE OF:
| |   <preprandialKillingEffect ... /> 
| |   <preprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| |   <postprandialKillingEffect ... /> 
| |   <postprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| | [ <fecundityReduction ... /> ]
| | [ <fecundityReductionLogit ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which net acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

maximum of holed surface area that has an effect (comparable to no net)

→ scenario → interventions → human → component → ITN → anophelesParams → holeIndexMax

<holeIndexMax
    value=double
  />

Documentation (element)

Units: in same unit as holeIndex

Used by logit attacking and killing models only, holeIndexMax is a user defined maximum hole index (typically, the total surface area of a net).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency

<twoStageDeterrency>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <entering ... /> 
| |   <enteringLogit ... /> 
| EXACTLY ONE OF:
| |   <attacking ... /> 
| |   <attackingLogit ... /> 
</twoStageDeterrency>

Documentation (element)

Units: dimensionless

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

This deterrency model multiplies human attractiveness by pEnt×pAtt.

Deterrency: entering

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → entering

<entering
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless

pEnt represents the relative probability of entering due to ITNs: pEnt = exp(log(P)×p) where P is the insecticide factor and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Deterrency: entering (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → enteringLogit

<enteringLogit
    baseFactor=double
    insecticideFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: none

See parent element documentation

Insecticide factor

insecticideFactor=double

Units: none

See parent element documentation

Deterrency: attacking

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attacking

<attacking
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Deterrency: attacking (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attackingLogit

<attackingLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Pre-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Pre-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffectLogit

<preprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Post-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffectLogit

<postprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Fecundity reduction

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-B), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReductionLogit

<fecundityReductionLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-K0), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Indoor residual spraying

→ scenario → interventions → human → component → IRS

<IRS>
IN THIS ORDER:
| [ <usage ... /> ]
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
| ( <anophelesParams ... /> )+
</IRS>

Documentation (element)

Description of indoor residual spraying interventions.

Documentation (type)

Description of effect for the more complex and probably more realistic Briet model: IRS has three effects, whos strength is calculated as a function of surviving insecticide content.

Proportion of Indoor residual spraying (IRS) interventions

→ scenario → interventions → human → component → IRS → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Indoor residual spraying (IRS) interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → IRS → initialInsecticide

<initialInsecticide
    mean=double
  [ SD=double ]
  [ distr=("const" or "normal") ] DEFAULT VALUE const
  />

Documentation (element)

Units: μg/cm² Min: 0

Documentation (type)

A parameter with optional heterogeneity.

Optionally, a distribution ("distr") and standard of deviation ("SD") may be specified.

Attributes

mean

mean=double

The mean value.

standard deviation

SD=double

The standard deviation of variates.

Distribution

distr=("const" or "normal")

Default value: const

Decay of insecticide

→ scenario → interventions → human → component → IRS → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</insecticideDecay>

decay

Documentation (element)

Units: none

Decay curve for insecticide content of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Per-mosquito species parameters

→ scenario → interventions → human → component → IRS → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → IRS → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied by exp(P×log(p)) where P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction

→ scenario → interventions → human → component → IRS → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

First, we calculate K = B + P×p where B is the base (without protection) probability of death, and P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Fecundity is multiplied by (1−K) / (1−B). It is not allowed to be greater than 1. To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Generic vector intervention

→ scenario → interventions → human → component → GVI

<GVI>
IN THIS ORDER:
| [ <usage ... /> ]
|   <decay ... /> 
| ( <anophelesParams ... /> )+
</GVI>

Documentation (element)

Note that all actions of this intervention component will decay according to a single decay function. If independant decay is wanted, a separate component can be used for each action.

Proportion of generic vector interventions

→ scenario → interventions → human → component → GVI → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Generic vector interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay

→ scenario → interventions → human → component → GVI → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (element)

Description of decay of all intervention effects. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Per-mosquito species parameters

→ scenario → interventions → human → component → GVI → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <deterrency ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → GVI → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of intervention on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied this factor times survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Fecundity reduction effect

→ scenario → interventions → human → component → GVI → anophelesParams → fecundityReduction

<fecundityReduction
    value=double
  />

Documentation (element)

Min: 0

Fertility is multiplied by 1 - (fecundityReduction * decay).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Recruitment only

→ scenario → interventions → human → component → recruitmentOnly

<recruitmentOnly/>

Documentation (element)

Recruitment of a host into a sub-population.

Clear Immunity

→ scenario → interventions → human → component → clearImmunity

<clearImmunity/>

Documentation (element)

Removes all exposure-related immunitsy gained over time by hosts without removing infections (or affecting the ability to gain immunity through exposure).

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

subPopRemoval

→ scenario → interventions → human → component → subPopRemoval

<subPopRemoval
  [ onFirstBout=boolean ] DEFAULT VALUE false
  [ onFirstTreatment=boolean ] DEFAULT VALUE false
  [ onFirstInfection=boolean ] DEFAULT VALUE false
  [ afterYears=double ]
  />

Documentation (type)

ITN attrition also removes humans from sub-populations.

Attributes

Time to first episode only

onFirstBout=boolean

Default value: false

Time to first treatment only

onFirstTreatment=boolean

Default value: false

Time to first infection only

onFirstInfection=boolean

Default value: false

Remove from sub-population after

afterYears=double

Units: Years Min: 0

Deployment

→ scenario → interventions → human → deployment

<deployment
  [ name=string ]
  >
IN THIS ORDER:
| ( <component ... /> )+
| ( <condition ... /> )*
| ( <continuous ... /> )*
| ( <timed ... /> )*
</deployment>

Documentation (element)

All components deployed by this intervention are deployed to the same people (each timed or continuous deployment selects recipients and then gives each recipient all components of the intervention).

Attributes

Intervention name

name=string

Name of intervention

component

→ scenario → interventions → human → deployment → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Condition

→ scenario → interventions → human → deployment → condition

<condition
    measure=string
  [ minValue=double ]
  [ maxValue=double ]
    initialState=boolean
  />

Documentation (element)

Conditions are evaluated for the whole population, not for individual age-groups or cohorts.

This affects all types of deployment.

Attributes

Measure

measure=string

The monitoring measure to test. Not all measures are available for use.

Minimum value

minValue=double

Minimum value. If specified, the measured variable must be greater than or equal to this value for the condition to be satisfied.

Maximum value

maxValue=double

Maximum value. If specified, the measured variable must be less than or equal to this value for the condition to be satisfied.

Initial state

initialState=boolean

Whether this condition is considered true or false before updated by a survey.

Age-based (continuous) deployment

→ scenario → interventions → human → deployment → continuous

<continuous>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| ( <deploy ... /> )+
</continuous>

Documentation (element)

List of ages at which deployment takes place (through EPI, post-natal and school-based programmes, etc.).

A sub-population restriction may be added as a property of the list of continuous deployments.

restrictToSubPop

→ scenario → interventions → human → deployment → continuous → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

deploy

→ scenario → interventions → human → deployment → continuous → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
  [ minAvailability=int ]
  [ maxAvailability=int ]
    targetAgeYrs=double
  [ begin=string ]
  [ end=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Minimum ento availability

minAvailability=int

Units: percent Min: 0

Maximum ento availability

maxAvailability=int

Units: percent Min: 0

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention. Input is rounded to the nearest time step.

First time active

begin=string

Units: User defined (defauls to steps)

End step

end=string

Units: User defined (defauls to steps)

Mass (timed) deployment

→ scenario → interventions → human → deployment → timed

<timed>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| [ <cumulativeCoverage ... /> ]
| ( <deploy ... /> )+
</timed>

Documentation (element)

List of timed deployments of the intervention (that is, of deployment campaigns).

Cumulative deployment mode can be specified for all deployments in a timed list. To allow multiple cumulative deployment descriptions, the entire timed list may be repeated.

restrictToSubPop

→ scenario → interventions → human → deployment → timed → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

Cumulative coverage

→ scenario → interventions → human → deployment → timed → cumulativeCoverage

<cumulativeCoverage
    component=string
  />

Documentation (element)

Attributes

Component identifier

component=string

The identifier (short name) of the component used when selecting people.

deploy

→ scenario → interventions → human → deployment → timed → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
  [ minAvailability=int ]
  [ maxAvailability=int ]
    time=string
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ repeatStep=string ]
  [ repeatEnd=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Minimum ento availability

minAvailability=int

Units: percent Min: 0

Maximum ento availability

maxAvailability=int

Units: percent Min: 0

Time

time=string

Units: User defined (defauls to steps) Min: 0

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0

Maximum age of eligible individuals (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible individuals (defaults to 0). Input is rounded to the nearest time step.

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Description of health system.

Documentation (type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("forced" or "dynamic")
  [ scaledAnnualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Description of entomological data

Attributes

Entomology dataset name

name=string

Name of entomology data

Transmission model mode

mode=("forced" or "dynamic")

Override annual EIR

scaledAnnualEIR=double

Units: Infectious bites per adult per year

If set, the annual EIR (for all species of vector) is scaled to this level; can be omitted if not needed.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters of the transmission model

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <seasonality ... /> 
|   <mosq ... /> 
| [ <lifeCycle ... /> ]
| [ <simpleMPD ... /> ]
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial estimate of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial estimate of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial estimate of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Seasonality of transmission

→ scenario → entomology → vector → anopheles → seasonality

<seasonality
    input=("EIR")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <fourierSeries ... /> 
| |   <monthlyValues ... /> 
| |   <dailyValues ... /> 
</seasonality>

Documentation (element)

Specifies the seasonality of transmission and optionally the level of annual transmission.

Attributes

Seasonality input

input=("EIR")

Annual EIR

annualEIR=double

Units: Inoculations per adult per annum Min: 0

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries

<fourierSeries
    EIRRotateAngle=double
  >
IN THIS ORDER:
| ( <coeffic ... /> )*
</fourierSeries>

coeffic

Documentation (element)

Units: Infectious bites per adult per day

Attributes

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: Radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Pair of Fourier coefficients

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries → coeffic

<coeffic
    a=double
    b=double
  />

Documentation (element)

A pair of Fourier series coefficients. The first element specifies a1 and b1, the second a2 and b2, etc. Any number (from 0 up) of pairs may be given.

Attributes

a_n parameter of Fourier approximation to ln(EIR)

a=double

a_n parameter of Fourier approximation to ln(EIR) for some natural number n.

b_n parameter of Fourier approximation to ln(EIR)

b=double

b_n parameter of Fourier approximation to ln(EIR) for some natural number n.

List of monthly values

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues

<monthlyValues
    smoothing=("none" or "fourier")
  >
IN THIS ORDER:
| ( <value ... /> ){12,12}
</monthlyValues>

value

Documentation (element)

Description of seasonality from monthly values. Multiple smoothing methods are possible (see smoothing attribute).

List should contain twelve entries: January to December.

Attributes

Smoothing function

smoothing=("none" or "fourier")

How the monthly values are converted into a daily sequence of values:

none: no smoothing (step function)
Fourier: a Fourier series (with terms up to a2/b2) is fit to the sequence of monthly values and used to generate a smoothed list of daily values.

Monthly value

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Monthly value

List of daily values

→ scenario → entomology → vector → anopheles → seasonality → dailyValues

<dailyValues>
IN THIS ORDER:
| ( <value ... /> )+
</dailyValues>

value

Documentation (element)

Description of seasonality from daily values.

List should contain 365 entries: 1st January to 31st December.

Daily value

→ scenario → entomology → vector → anopheles → seasonality → dailyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Daily value

Mosquito feeding cycle parameters

→ scenario → entomology → vector → anopheles → mosq

<mosq
    minInfectedThreshold=double
  >
IN ANY ORDER:
|   <mosqRestDuration ... /> 
|   <extrinsicIncubationPeriod ... /> 
|   <mosqLaidEggsSameDayProportion ... /> 
|   <mosqSeekingDuration ... /> 
|   <mosqSurvivalFeedingCycleProbability ... /> 
|   <availability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <mosqProbOvipositing ... /> 
|   <mosqHumanBloodIndex ... /> 
</mosq>

Documentation (element)

Parameters describing the feeding cycle and human mosquito interaction of a single species of anopheles mosquito.

Attributes

Mininum infected threshold for mosquitos

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

Duration of the resting period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqRestDuration

<mosqRestDuration
    value=int
  />

Documentation (element)

Units: Days

name:Duration of the resting period of the vector (days);

Attributes

Input parameter value

value=int

An integer value.

Extrinsic incubation period

→ scenario → entomology → vector → anopheles → mosq → extrinsicIncubationPeriod

<extrinsicIncubationPeriod
    value=int
  />

Documentation (element)

Units: Days

name:Extrinsic incubation period (days)

Attributes

Input parameter value

value=int

An integer value.

Proportion of mosquitoes host seeking on same day as ovipositing

→ scenario → entomology → vector → anopheles → mosq → mosqLaidEggsSameDayProportion

<mosqLaidEggsSameDayProportion
    value=double
  />

Documentation (element)

Units: Proportion

Proportion of mosquitoes host seeking on same day as ovipositing

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Duration of the host-seeking period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqSeekingDuration

<mosqSeekingDuration
    value=double
  />

Documentation (element)

Units: Days

Duration of the host-seeking period of the vector (days)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito survives the feeding cycle

→ scenario → entomology → vector → anopheles → mosq → mosqSurvivalFeedingCycleProbability

<mosqSurvivalFeedingCycleProbability
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito survives the feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human availability rate heterogeneity

→ scenario → entomology → vector → anopheles → mosq → availability

<availability
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
  />

Documentation (element)

If no attributes are specified or distr="const" or CV="0" then there will be no heterogeneity.

Documentation (type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

Probability that the mosquito succesfully bites chosen host

→ scenario → entomology → vector → anopheles → mosq → mosqProbBiting

<mosqProbBiting
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito succesfully bites chosen host

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → mosq → mosqProbFindRestSite

<mosqProbFindRestSite
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito escapes host and finds a resting place after biting

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → mosq → mosqProbResting

<mosqProbResting
    mean=double
    variance=double
  />

Documentation (element)

Probability of mosquito successfully resting after finding a resting site

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of a mosquito successfully laying eggs given that it has rested

→ scenario → entomology → vector → anopheles → mosq → mosqProbOvipositing

<mosqProbOvipositing
    value=double
  />

Documentation (element)

Probability of a mosquito successfully laying eggs given that it has rested

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human blood index

→ scenario → entomology → vector → anopheles → mosq → mosqHumanBloodIndex

<mosqHumanBloodIndex
    value=double
  />

Documentation (element)

Units: Proportion

The proportion of resting mosquitoes which fed on human blood during the last feed.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mosquito life cycle parameters

→ scenario → entomology → vector → anopheles → lifeCycle

<lifeCycle
  [ estimatedLarvalResources=double ] DEFAULT VALUE 1e8
  >
IN ANY ORDER:
|   <eggStage ... /> 
|   <larvalStage ... /> 
|   <pupalStage ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</lifeCycle>

Documentation (element)

Parameters describing the life-cycle of this species of mosquito

Attributes

Estimate of larval resources

estimatedLarvalResources=double

Units: X

Default value: 1e8

Egg stage

→ scenario → entomology → vector → anopheles → lifeCycle → eggStage

<eggStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the egg stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

larvalStage

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage

<larvalStage>
</larvalStage>

daily

Documentation (type)

Parameters for the larval stage of development

Documentation (base type)

Parameters associated with a mosquito development stage.

Daily development

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage → daily

<daily
    resourceUsage=double
    effectCompetition=double
  />

Documentation (element)

Attributes

Resource usage

resourceUsage=double

Units: X

Resource usage during larval stage of development. Units are arbitrary.

Effect of competition

effectCompetition=double

Units: none

Effect of competition over resources on development.

Pupal stage

→ scenario → entomology → vector → anopheles → lifeCycle → pupalStage

<pupalStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the pupal stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → lifeCycle → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Simple Mosq-Pop-Dynamics parameters

→ scenario → entomology → vector → anopheles → simpleMPD

<simpleMPD>
IN ANY ORDER:
|   <developmentDuration ... /> 
|   <developmentSurvival ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</simpleMPD>

Documentation (element)

Parameters describing the simple mosquito population dynamics model.

This is a simpler version of the life-cycle model, requiring less parameters and with much simpler initialisation.

Duration

→ scenario → entomology → vector → anopheles → simpleMPD → developmentDuration

<developmentDuration
    value=int
  />

Documentation (element)

Units: Days Min: 1

Duration from egg laying to emergence in days.

Attributes

Input parameter value

value=int

An integer value.

Probability of survival

→ scenario → entomology → vector → anopheles → simpleMPD → developmentSurvival

<developmentSurvival
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that mosquito survives from the egg being laid to emergence, given no resouce limitations (no density constraints).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → simpleMPD → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Alternative (non-human) host paramters

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN ANY ORDER:
|   <mosqRelativeEntoAvailability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
| [ <hostFecundityFactor ... /> ]
</nonHumanHosts>

Documentation (element)

Min: 0

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of non-human host (ξ_i)

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqRelativeEntoAvailability

<mosqRelativeEntoAvailability
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of the population of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative fecundity of biting mosquitoes

→ scenario → entomology → vector → anopheles → nonHumanHosts → hostFecundityFactor

<hostFecundityFactor
    value=double
  />

Documentation (element)

Units: Proportion

Multiplicative factor for the number of fertile eggs laid by a mosquito after biting this type of host, relative to an unprotected human.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Name of this species of non human hosts (must match up with those described per anopheles section).

Population size of non-human host species

number=double

Units: Animals

Parasite genetics

<parasiteGenetics
    samplingMode=("initial" or "tracking")
  >
IN THIS ORDER:
| ( <locus ... /> )+
</parasiteGenetics>

locus

Documentation (element)

A specification of genotypes of infection parasites.

May be omitted; in this case there is no modelling of genetic differences of infections (resistance, fitness).

Attributes

samplingMode

samplingMode=("initial" or "tracking")

Locus

→ scenario → parasiteGenetics → locus

<locus
    name=string
  >
IN THIS ORDER:
| ( <allele ... /> )+
</locus>

allele

Documentation (element)

Alleles at loci can affect fitness and resistance to any number of drugs.

Attributes

Name of locus

name=string

Name of the Locus

Allele

→ scenario → parasiteGenetics → locus → allele

<allele
    name=string
    initialFrequency=double
    fitness=double
  [ hrp2_deletion=boolean ] DEFAULT VALUE false
  />

Documentation (element)

Describes an allele, or one possible genetic option of multiple at one point of variance.

Attributes

Name

name=string

Name of the allele; used to refer to it elsewhere.

Initial frequency

initialFrequency=double

Fitness factor

fitness=double

HRP2 deletion

hrp2_deletion=boolean

Default value: false

Drug parameters (PK, PD and usage)

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
|   <treatments ... /> 
|   <drugs ... /> 
</pharmacology>

Documentation (element)

Drug model parameters and drug usage parameters

Documentation (type)

A library of drug related data for the PK/PD model.

Treatments library

→ scenario → pharmacology → treatments

<treatments>
IN THIS ORDER:
| ( <schedule ... /> )+
| ( <dosages ... /> )+
</treatments>

Documentation (element)

A library of drug deployment schedules and dosages.

schedule

→ scenario → pharmacology → treatments → schedule

<schedule
    name=string
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

A schedule for the administration of drugs in a course of treatment.

Note that dose sizes are multiplied by some multiplier (see dosages) and the times of all doses may be delayed.

Attributes

Name

name=string

Name for referring to this deployment schedule

medicate

→ scenario → pharmacology → treatments → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  />

Attributes

drug

drug=string

Abbreviated name of drug compound

Drug dose (mg with multiplier)

mg=double

Units: mg per something

Quantity of drug compound in mg per something. A separate dosage table must be used when medicating, which may specify multipliers of this number based on patient age or weight.

Time of administration

hour=double

Units: Hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

dosages

→ scenario → pharmacology → treatments → dosages

<dosages
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | ( <age ... /> )+
| | ( <bodymass ... /> )+
| |   <multiply ... /> 
</dosages>

Documentation (type)

A table for selecting a dose size. There are several ways this can work: using the patient's age or body mass in a look-up table to get a multplier, or directly using body mass as the multiplier.

The doses specified in "mg" in the treatment schedule are then multiplied by this multiplier.

Attributes

Name

name=string

Name for referring to this dosage table

Look-up table (age)

→ scenario → pharmacology → treatments → dosages → age

<age
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's age.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Look-up table (weight)

→ scenario → pharmacology → treatments → dosages → bodymass

<bodymass
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's body mass.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Multiply dose

→ scenario → pharmacology → treatments → dosages → multiply

<multiply
    by=("kg")
  />

Documentation (element)

Multiply the dose by some quantity, such as patient weight.

Attributes

By what?

by=("kg")

Quantity to multiply the dose by. Only option is "kg" (patient weight in kg).

Drug library

→ scenario → pharmacology → drugs

<drugs>
IN THIS ORDER:
| ( <drug ... /> )+
</drugs>

drug

Documentation (element)

A library of drug PK/PD data.

drug

→ scenario → pharmacology → drugs → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (type)

A drug description with PK/PD parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drugs → drug → PD

<PD
  [ locus=string ]
  >
IN THIS ORDER:
| ( <phenotype ... /> )+
</PD>

phenotype

Attributes

Locus

locus=string

PD parameters for some allele / resistance phenotype

→ scenario → pharmacology → drugs → drug → PD → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

Restrict phenotype applicability to certain alleles

→ scenario → pharmacology → drugs → drug → PD → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (element)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Maximal parasite killing rate

→ scenario → pharmacology → drugs → drug → PD → phenotype → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drugs → drug → PD → phenotype → IC50

<IC50
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

If CV > 0, the IC50 is sampled from a log-normal distribution.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Slope of effect curve

→ scenario → pharmacology → drugs → drug → PD → phenotype → slope

<slope>
    double
</slope>

Documentation (element)

Units: dimensionless

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drugs → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
| EXACTLY ONE OF:
| |   <half_life ... /> 
| | IN THIS ORDER:
| | |   <k ... /> 
| | |   <m_exponent ... /> 
| [ <k_a ... /> ]
| [ <conversion ... /> ]
|   <vol_dist ... /> 
| [ <compartment2 ... /> ]
| [ <compartment3 ... /> ]
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drugs → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drugs → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate λ, calculated as λ = ln(2) / half_life. The basic form of decay is C(t) = C0 * exp(-λ*t).

Alternatively, elimination rate can be specified via k and m_exponent.

Constant associated with elimination rate (k)

→ scenario → pharmacology → drugs → drug → PK → k

<k
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

If CV > 0, k is sampled per-human from the log-normal distribution: ln N( ln(mean) - σ^2 / 2, σ^2).

Alternatively, elimination rate can be specified via half_life.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Constant associated with elimination rate (m_exponent)

→ scenario → pharmacology → drugs → drug → PK → m_exponent

<m_exponent>
    double
</m_exponent>

Documentation (element)

Units: day^-1 Min: 0

Alternatively, elimination rate can be specified via half_life.

Note that in the case of a conversion model, this applies to both the elimination and the conversion rates.

Absorption rate constant (k_a)

→ scenario → pharmacology → drugs → drug → PK → k_a

<k_a
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Min: 0

Absorption rate parameter. Not allowed for one compartment models, but required for two and three compartment models and one compartment with conversion model (for the parent drug only).

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Conversion parameters (parent drug)

→ scenario → pharmacology → drugs → drug → PK → conversion

<conversion>
IN ANY ORDER:
|   <metabolite ... /> 
|   <rate ... /> 
|   <molRatio ... /> 
|   <IC50_log_correlation ... /> 
</conversion>

Documentation (element)

Configures the parent drug in a conversion model.

To use a conversion model, the parent drug should have this section defined as well as half-life or k (direct elimination; this may be zero) and k_a (absorption rate; this may be large).

Metabolite drug (abbreviation)

→ scenario → pharmacology → drugs → drug → PK → conversion → metabolite

<metabolite>
    string
</metabolite>

Documentation (element)

The abbreviation of the metabolite drug (e.g. "DHA" or "DHA_AR").

Rate of conversion

→ scenario → pharmacology → drugs → drug → PK → conversion → rate

<rate
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Rate of conversion of parent drug to metabolite.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Molecular weight ratio

→ scenario → pharmacology → drugs → drug → PK → conversion → molRatio

<molRatio>
    double
</molRatio>

Documentation (element)

Ratio of molecular weights: molecular weight of the metabolite divided by molecular weight of the parent.

IC50 log correlation

→ scenario → pharmacology → drugs → drug → PK → conversion → IC50_log_correlation

<IC50_log_correlation>
    double
</IC50_log_correlation>

Documentation (element)

Min: 0 Max: 1

If this value is 1, samples are fully correlated: a single z-score is used to calculate both samples. If this is 0, two independent samples are used.

Values between 0 and 1 (partial correlation) are supported; in this case IC50 values are sampled such that cor(log(x), log(y)) matches this value (where x, y are parent and metabolite IC50 values).

Volume of Distribution (Vd)

→ scenario → pharmacology → drugs → drug → PK → vol_dist

<vol_dist
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution.

If CV > 0 this is sampled from a log-normal distribution.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Second compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment2

<compartment2>
IN ANY ORDER:
|   <k12 ... /> 
|   <k21 ... /> 
</compartment2>

Documentation (element)

Optional element specifying conversion parameters to- and from- a second compartment.

Absorption rate to compartment 2 (k12)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → k12

<k12
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the first periphery compartment (2).

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Absorption rate from compartment 2 (k21)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → k21

<k21
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the first periphery compartment (2) to the central compartment.

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Third compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment3

<compartment3>
IN ANY ORDER:
|   <k13 ... /> 
|   <k31 ... /> 
</compartment3>

Documentation (element)

Optional element specifying conversion parameters to- and from- a third compartment.

Absorption rate to compartment 3 (k13)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → k13

<k13
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the second periphery compartment (3).

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Absorption rate from compartment 3 (k31)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → k31

<k31
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the second periphery compartment (3) to the central compartment.

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Diagnostic parameters

→ scenario → diagnostics

<diagnostics>
IN THIS ORDER:
| ( <diagnostic ... /> )*
</diagnostics>

diagnostic

Documentation (element)

Diagnostic model parameters

diagnostic

→ scenario → diagnostics → diagnostic

<diagnostic
    name=string
  [ units=("Other" or "Garki" or "Malariatherapy") ]
  [ mechanism=("Other" or "HRP2") ] DEFAULT VALUE Other
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterministic ... /> 
| |   <stochastic ... /> 
</diagnostic>

Attributes

Name of diagnostic

name=string

Name of this diagnostic (parameterisation). May be used elsewhere in the XML document to refer to this set of diagnostic parameters.

Parasite density units / methodology

units=("Other" or "Garki" or "Malariatherapy")

Mechanism

mechanism=("Other" or "HRP2")

Default value: Other

Deterministic detection

→ scenario → diagnostics → diagnostic → deterministic

<deterministic
    minDensity=double
  />

Documentation (element)

Specify that an artificial deterministic test is used: outcome is positive if parasite density is at least the minimum given.

Attributes

Minimum detectible density

minDensity=double

Units: parasites/microlitre Min: 0

The minimum density at which parasites can be detected. If 0, the test outcome is always positive.

Non-deterministic detection

→ scenario → diagnostics → diagnostic → stochastic

<stochastic
    dens_50=double
    specificity=double
  />

Documentation (element)

An improved model of detection which is non-deterministic, including false positive results as well as false negatives.

Some parameterisations:

Microscopy sensitivity/specificity data in Africa; Source: expert opinion — Allan Schapira dens_50 = 20.0 specificity = .75

RDT sensitivity/specificity for Plasmodium falciparum in Africa Source: Murray et al (Clinical Microbiological Reviews, Jan. 2008) dens_50 = 50.0; specificity = .942;

Attributes

Density 50

dens_50=double

Units: parasites/microlitre Min: 0

The density at which the test outcome has a 50% chance of being positive.

Specificity

specificity=double

Units: Dimensionless Min: 0 Max: 1

The probability of a positive test outcome in the absense of parasites.

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
| [ <vivax ... /> ]
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: model/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=string
  >
IN ANY ORDER:
| [ <NeonatalMortality ... /> ]
| [ <NonMalariaFevers ... /> ]
</clinical>

Documentation (type)

Attributes

Follow-up period during which recurrence is considered a treatment failure

healthSystemMemory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

Neonatal mortality parameters

→ scenario → model → clinical → NeonatalMortality

<NeonatalMortality
    diagnostic=string
  />

Attributes

Diagnostic used to parameterise model

diagnostic=string

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
| [ <prNeedTreatmentNMF ... /> ]
| [ <prNeedTreatmentMF ... /> ]
</NonMalariaFevers>

Documentation (type)

Description of the incidence of non-malaria fever. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a non-malarial fever requires treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

Availability of humans to mosquitoes relative to an adult, categorized by age group

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ]
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

Vivax model parameters

→ scenario → model → vivax

<vivax>
IN ANY ORDER:
|   <probBloodStageInfectiousToMosq ... /> 
|   <hypnozoiteRelease ... /> 
|   <bloodStageProtectionLatency ... /> 
|   <bloodStageLengthDays ... /> 
|   <clinicalEvents ... /> 
</vivax>

Documentation (element)

This describes Vivax model parameters, and is required when using the VIVAX_SIMPLE_MODEL model option.

Probability of mosquito infection

→ scenario → model → vivax → probBloodStageInfectiousToMosq

<probBloodStageInfectiousToMosq
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

The chance of a feeding mosquito becoming infected, given that the host is patent. (This may be adjusted by transmission-blocking vaccines.)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Hypnozoite releases

→ scenario → model → vivax → hypnozoiteRelease

<hypnozoiteRelease
  [ pSecondRelease=double ] DEFAULT VALUE 0
  >
IN ANY ORDER:
|   <numberHypnozoites ... /> 
|   <firstReleaseDays ... /> 
| [ <secondReleaseDays ... /> ]
</hypnozoiteRelease>

Documentation (element)

Describes the number and times of hypnozoite releases.

Documentation (type)

This element defines probabilites when and how many hypnozoites are released from the liverstage into the blood.

The gap between the start of a new brood of hypnozoites and its release are defined as follows:

latentP + latentRelapse + randomReleaseDelay

randomReleaseDelay is based on one or two lognormal distributions, which are defined in firstRelease and optionally secondRelease.

You can define 2 release distributions, which get added together and represent the probability of hypnozoites which get released before winter (first release) or after (second release).

You can omit the secondRelease element if no release to the blood happens after winter.

Attributes

latent relapse days

pSecondRelease=double

Default value: 0

Probability of a second release. If undefined it is zero.

Number of Hypnozoites

→ scenario → model → vivax → hypnozoiteRelease → numberHypnozoites

<numberHypnozoites
    max=int
    base=double
  />

Documentation (element)

numberHypnozoites calculates the number of hypnozoites in the liver stage based on a base which is between 0 and 1.

This number is random based on the following distribution and normalized:

max ∑ (base ^ n) n = 0

Attributes

max

max=int

base

base=double

firstReleaseDays

→ scenario → model → vivax → hypnozoiteRelease → firstReleaseDays

<firstReleaseDays
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
    latentRelapse=double
  />

Documentation (type)

Hypnozoites are released after a delay, calculated as: roundToTSFromDays(delay + latentRelapse)

Here, roundToTSFromDays rounds the input (in days) to the nearest timestep, delay is sampled from a log-normal, and latentRelapse is the parameter specified here.

The delay is sampled from a log-normal distribution, parameterised via the (linear) mean and CV (coefficient of variation) given here.

Documentation (base type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

latent relapse days

latentRelapse=double

Usually between 10 and 15 days.

secondReleaseDays

→ scenario → model → vivax → hypnozoiteRelease → secondReleaseDays

<secondReleaseDays
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
    latentRelapse=double
  />

Documentation (type)

Hypnozoites are released after a delay, calculated as: roundToTSFromDays(delay + latentRelapse)

Here, roundToTSFromDays rounds the input (in days) to the nearest timestep, delay is sampled from a log-normal, and latentRelapse is the parameter specified here.

The delay is sampled from a log-normal distribution, parameterised via the (linear) mean and CV (coefficient of variation) given here.

Documentation (base type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

latent relapse days

latentRelapse=double

Usually between 10 and 15 days.

Blood stage protection latency

→ scenario → model → vivax → bloodStageProtectionLatency

<bloodStageProtectionLatency
    value=double
  />

Documentation (element)

Min: 0

The length of time after expiry of a blood-stage infection during which relapses from the same brood are supressed by the immune system.

This is rounded to the nearest time-step.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Blood stage length

→ scenario → model → vivax → bloodStageLengthDays

<bloodStageLengthDays
    scale=double
    shape=double
    distr=("weibull")
  />

Documentation (element)

Units: Days

Parameters used to sample the length of blood-stage infections from a Weibull distribution (scale parameter lambda, shape parameter k).

Documentation (type)

Parameters of a Weibull distribution.

Attributes

Scale

scale=double

The Weibull scale parameter (λ).

shape

shape=double

The Weibull shape parameter (k).

Distribution

distr=("weibull")

To allow heterogeneity, a distribution must be specified. In this case, only "weibull" is allowed.

clinicalEvents

→ scenario → model → vivax → clinicalEvents

<clinicalEvents>
IN THIS ORDER:
|   <pPrimaryInfection ... /> 
|   <pRelapseOne ... /> 
|   <pRelapseTwoPlus ... /> 
|   <pEventIsSevere ... /> 
|   <vivaxClinOption ... /> 
</clinicalEvents>

Documentation (type)

This elements holds all information about probabilites for clinical events from infections and relapses.

pPrimaryInfection

→ scenario → model → vivax → clinicalEvents → pPrimaryInfection

<pPrimaryInfection
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseOne

→ scenario → model → vivax → clinicalEvents → pRelapseOne

<pRelapseOne
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseTwoPlus

→ scenario → model → vivax → clinicalEvents → pRelapseTwoPlus

<pRelapseTwoPlus
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pEventIsSevere

→ scenario → model → vivax → clinicalEvents → pEventIsSevere

<pEventIsSevere
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

vivaxClinOption

→ scenario → model → vivax → clinicalEvents → vivaxClinOption

<vivaxClinOption>
    string
</vivaxClinOption>

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=string
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=string

Units: User defined (default: steps) Min: 0 Max: 20

Pre-erythrocytic latent period Can be specified in steps (e.g. 3t) or days (e.g. 15d).

parameter

→ scenario → model → parameters → parameter

<parameter
  [ name=string ]
    number=int
    value=double
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Schema 47 documentation

Generated from: scenario_47.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
  [ analysisNo=int ]
    name=string
  [ wuID=int ]
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:om="http://openmalaria.org/schema/scenario_47"
    xsi:schemaLocation="http://openmalaria.org/schema/scenario_47 scenario_47.xsd"
  >
IN ANY ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entomology ... /> 
| [ <parasiteGenetics ... /> ]
| [ <pharmacology ... /> ]
| [ <diagnostics ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Name of intervention

Work unit identifier

wuID=int

Units: Number

Work unit ID. Obselete and no longer required.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Description of demography

Attributes

Name of demography data

name=string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Years Min: 0 Max: 100

Maximum age of simulated humans in years

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

list of age groups included in demography

Documentation (type)

list of age groups included in demography or surveys

Attributes

Lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Units: Percentage Min: 0 Max: 100

Percentage of human population in age group

Upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ startDate=string ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
| [ <cohorts ... /> ]
</monitoring>

Documentation (element)

Description of surveys

Attributes

Name of monitoring settings

name=string

Name of monitoring settings

Start of monitoring

startDate=string

continuous

→ scenario → monitoring → continuous

<continuous
    period=string
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Delay between reports

period=string

Units: User defined (default: steps)

Delay between reports; typically one time step but can be greater. Can be specified in steps (e.g. 1t) or days (e.g. 5d).

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions
  [ onlyNewEpisode=boolean ] DEFAULT VALUE false
  >
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See model/mon/OutputMeasures.h for a list of supported outputs. Should also be on the wiki.

Attributes

Report only for new cases

onlyNewEpisode=boolean

Default value: false

option

→ scenario → monitoring → SurveyOptions → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  [ outputNumber=int ]
  [ byAge=boolean ]
  [ byCohort=boolean ]
  [ bySpecies=boolean ]
  [ byGenotype=boolean ]
  [ byDrugType=boolean ]
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Number identifying measure in output

outputNumber=int

Report by age category

byAge=boolean

Report by cohort

byCohort=boolean

Report by mosquito species

bySpecies=boolean

Report by parasite genotype

byGenotype=boolean

Report by drug type

byDrugType=boolean

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
  [ detectionLimit=double ]
  [ diagnostic=string ]
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/microlitre Min: 0

Deprecated: limit above which a human's infection is reported as patent. Alternative: do not specify this; instead specify "diagnostic".

Name of monitoring diagnostic

diagnostic=string

Name of a parameterised diagnostic to use in surveys (see scenario/diagnostics).

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime
  [ repeatStep=string ]
  [ repeatEnd=string ]
  [ reported=boolean ] DEFAULT VALUE true
  >
    string
</surveyTime>

Documentation (element)

Units: User defined (defaults to steps) Min: 0

The simulation ends immediately after the last survey is taken.

Attributes

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

reported

reported=boolean

Default value: true

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Cohorts

→ scenario → monitoring → cohorts

<cohorts>
IN THIS ORDER:
| ( <subPop ... /> )+
</cohorts>

subPop

Documentation (element)

Allows the configuration of multiple cohorts (output segregated according to membership within specific sub-populations).

If this element is omitted, monitoring surveys cover the entire simulated human population.

It does not affect the "continuous" outputs (these never take cohorts into account).

Sub-population

→ scenario → monitoring → cohorts → subPop

<subPop
    id=string
    number=integer
  />

Documentation (element)

In the output file, the output set is identified by multiplying this number by 1000 then adding it to the age group column.

Attributes

Sub-population identifier

id=string

Textual identifier for the sub-population (i.e. for an intervention component, since sub-populations are defined as the hosts an intervention component is deployed to).

Sub-population number

number=integer

Units: dimensionless Min: 1 Max: 2097152

Number identifying a sub-population; used to define identifiers of output sets. This number must be a power of 2 (i.e. 1, 2, 4, 8, ...). See documentation of subPop element.

Preventative interventions

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfections ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <vectorPop ... /> ]
| [ <vectorTrap ... /> ]
| [ <nonHumanHostsModifications ... /> ]
| [ <addNonHumanHosts ... /> ]
| [ <human ... /> ]
</interventions>

Documentation (element)

Attributes

Name of intervention set

name=string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeHS>

timedDeployment

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeHS → timedDeployment

<timedDeployment
    time=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timedDeployment>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</uncomplicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

multiple

→ scenario → interventions → human → component → decisionTree → multiple

<multiple
  [ name=string ]
  >
EXACTLY ONE OF:
| ( <caseType ... /> )*
| ( <diagnostic ... /> )*
| ( <uncomplicated ... /> )*
| ( <severe ... /> )*
| ( <random ... /> )*
| ( <age ... /> )*
| ( <treatPKPD ... /> )*
| [ <treatSimple ... /> ]
| ( <deploy ... /> )*
| ( <report ... /> )*
| ( <cohort ... /> )*
</multiple>

Documentation (type)

A special node allowing multiple sub-trees to be evaluated.

This is different from an ordinary decision tree node in that:

a) multiple types of child can occur simultaneously (e.g. multiple types of treatment or treatment plus a 'random' sub-tree)

b) the 'noTreatment' and 'treatFailure' nodes are not allowed

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → multiple → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

firstLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → firstLine

<firstLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</firstLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

secondLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → secondLine

<secondLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</secondLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

positive

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

uncomplicated

→ scenario → interventions → human → component → decisionTree → uncomplicated

<uncomplicated
  [ name=string ]
  [ memory=string ] DEFAULT VALUE 1
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</uncomplicated>

Documentation (type)

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Number of days to look back for fevers. This must be less than or equal to the healthsystem memory parameter. In general, this should be less than or equal to the repeatStep in MSAT with contiuous deployment

memory=string

Units: User-defined (defaults to steps)

Default value: 1

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

positive

→ scenario → interventions → human → component → decisionTree → multiple → uncomplicated → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

severe

→ scenario → interventions → human → component → decisionTree → severe

<severe
  [ name=string ]
  [ memory=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</severe>

Documentation (type)

A switch which choses a branch deterministically, based on whether the host has a severe case or not. Note that this include severe cases due to comorbidities.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Number of days to look back for fevers. This must be less than or equal to the healthsystem memory parameter. In general, this should be less than or equal to the repeatStep in MSAT with contiuous deployment

memory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

positive

→ scenario → interventions → human → component → decisionTree → multiple → severe → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

outcome

→ scenario → interventions → human → component → decisionTree → multiple → random → outcome

<outcome
  [ name=string ]
    p=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</outcome>

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Probability

p=double

Units: None Min: 0 Max: 1

Probability of selecting this outcome. The sum of probabilities across all outcomes must be 1.

age

→ scenario → interventions → human → component → decisionTree → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Age range

→ scenario → interventions → human → component → decisionTree → multiple → age → age

<age
  [ name=string ]
    lb=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</age>

Documentation (element)

Describes a branch, selected for patients of a certain age.

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Lower bound (inclusive)

lb=double

Min: 0

noTreatment

→ scenario → interventions → human → component → decisionTree → noTreatment

<noTreatment
  [ name=string ]
  />

Documentation (type)

An end node doing nothing. This exists to explicitly state that no treatment happens and to prevent trees from accidentally being left incomplete.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

report

→ scenario → interventions → human → component → decisionTree → report

<report
  [ name=string ]
  [ outputNumber=int ] DEFAULT VALUE 0
  />

Documentation (type)

This increments measure 80 (nCMDTReport) by one every time this node is visited. This can be useful to report the results of mass test and treat interventions using the decision tree.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Delay (hours)

outputNumber=int

Default value: 0

treatFailure

→ scenario → interventions → human → component → decisionTree → treatFailure

<treatFailure
  [ name=string ]
  />

Documentation (type)

An end node which reports treatment but does not change parasitalogical status. This allows correct labelling of second-line cases.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

cohort

→ scenario → interventions → human → component → decisionTree → cohort

<cohort
  [ name=string ]
    component=string
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</cohort>

Documentation (type)

A switch which choses a branch deterministically, based on whether the host is part of the cohort (defined by the intervention component) or not.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Number of days to look back for fevers. This must be less than or equal to the healthsystem memory parameter. In general, this should be less than or equal to the repeatStep in MSAT with contiuous deployment

component=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

positive

→ scenario → interventions → human → component → decisionTree → multiple → cohort → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

negative

→ scenario → interventions → human → component → decisionTree → multiple → cohort → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

negative

→ scenario → interventions → human → component → decisionTree → multiple → severe → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

negative

→ scenario → interventions → human → component → decisionTree → multiple → uncomplicated → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

negative

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

uncomplicated

→ scenario → interventions → human → component → decisionTree → multiple → uncomplicated

<uncomplicated
  [ name=string ]
  [ memory=string ] DEFAULT VALUE 1
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</uncomplicated>

Documentation (type)

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Number of days to look back for fevers. This must be less than or equal to the healthsystem memory parameter. In general, this should be less than or equal to the repeatStep in MSAT with contiuous deployment

memory=string

Units: User-defined (defaults to steps)

Default value: 1

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

severe

→ scenario → interventions → human → component → decisionTree → multiple → severe

<severe
  [ name=string ]
  [ memory=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</severe>

Documentation (type)

A switch which choses a branch deterministically, based on whether the host has a severe case or not. Note that this include severe cases due to comorbidities.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Number of days to look back for fevers. This must be less than or equal to the healthsystem memory parameter. In general, this should be less than or equal to the repeatStep in MSAT with contiuous deployment

memory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

random

→ scenario → interventions → human → component → decisionTree → multiple → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

age

→ scenario → interventions → human → component → decisionTree → multiple → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → multiple → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → multiple → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → multiple → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

report

→ scenario → interventions → human → component → decisionTree → multiple → report

<report
  [ name=string ]
  [ outputNumber=int ] DEFAULT VALUE 0
  />

Documentation (type)

This increments measure 80 (nCMDTReport) by one every time this node is visited. This can be useful to report the results of mass test and treat interventions using the decision tree.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Delay (hours)

outputNumber=int

Default value: 0

cohort

→ scenario → interventions → human → component → decisionTree → multiple → cohort

<cohort
  [ name=string ]
    component=string
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</cohort>

Documentation (type)

A switch which choses a branch deterministically, based on whether the host is part of the cohort (defined by the intervention component) or not.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Number of days to look back for fevers. This must be less than or equal to the healthsystem memory parameter. In general, this should be less than or equal to the repeatStep in MSAT with contiuous deployment

component=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</complicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: Days Min: 0 Max: unbounded

Maximum number of timesteps (including first day of case) that an individual with an uncomplicated case of malaria will remember he/she was sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial or non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of a complicated or severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
  [ name=string ]
  [ useDiagnosticUC=boolean ] DEFAULT VALUE false
  >
IN ANY ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <treatmentActions ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
</ImmediateOutcomes>

Documentation (type)

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Name of case management parameterisation

name=string

Name of health system

useDiagnosticUC

useDiagnosticUC=boolean

Default value: false

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Description of drug regimen.

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Artemisinine based combination therapy

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Quinine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0 Max: 1name:P(self-treat)

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Effectiveness of treatment for non-compliant patients

treatmentActions

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions

<treatmentActions>
IN ANY ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
</treatmentActions>

CQ
SP
AQ
SPAQ
ACT
QN

CQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ

<CQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</CQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

deploy

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy

<deploy
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ p=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| ( <component ... /> )+
</deploy>

component

Attributes

Maximum age of eligible humans

maxAge=double

Units: Years Min: 0

Maximum age of eligible humans (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible humans

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible humans (defaults to 0). Input is rounded to the nearest time step.

Probability of delivery to eligible humans

p=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Probability of this list of components being deployed, given that other constraints are met.

component

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Prophylactic treatment

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere → clearInfections

<clearInfections
    timesteps=string
    stage=("liver" or "blood" or "both")
  />

Documentation (element)

Attributes

Length of effect

timesteps=string

Units: User defined (defaults to steps)

Target stage

stage=("liver" or "blood" or "both")

SP

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SP

<SP
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SP>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

AQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → AQ

<AQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</AQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

SPAQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SPAQ

<SPAQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SPAQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

ACT

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → ACT

<ACT
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</ACT>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

QN

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → QN

<QN
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</QN>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

Probability that human is incompatible with liver-stage drug treatment

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pHumanCannotReceive

<pHumanCannotReceive
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that a human is determined to be unable to receive liver-stage drug treatment. Treatment is neither reported or given for such humans.

This is sampled once per human at birth.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Ignore liver-stage drug treatment incompatibility

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → ignoreCannotReceive

<ignoreCannotReceive
    value=boolean
  />

Documentation (element)

If true, ignore pHumanCannotReceive and consider all humans eligible for treatment; if false (or not specified), do not treat those demed incompatible with liver-stage drug treatment.

The point of this is that pHumanCannotReceive cannot be altered by changeHS interventions, but this property can be.

Attributes

Input parameter value

value=boolean

A boolean value.

Prob use in UC case

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pUseUncomplicated

<pUseUncomplicated
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

This feature is deprecated; it is suggested to use the "simple treatment" feature configured to clear liver-stage parasites, leaving this option unset or zero.

Chance of liver-stage drug treatment being used for routine treatment of an uncomplicated case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Effectiveness

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → effectivenessOnUse

<effectivenessOnUse
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that liver-stage drug treatment is effective.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

DecisionTree5Day

<DecisionTree5Day
  [ name=string ]
  >
IN ANY ORDER:
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
|   <treeUCOfficial ... /> 
|   <treeUCSelfTreat ... /> 
|   <cureRateSevere ... /> 
|   <treatmentSevere ... /> 
</DecisionTree5Day>

Documentation (type)

Besides greater flexibility, this allows treatment via PK/PD models.

Attributes

Name of case management parameterisation

name=string

Name of health system

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → DecisionTree5Day → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → DecisionTree5Day → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

treeUCOfficial

→ scenario → healthSystem → DecisionTree5Day → treeUCOfficial

<treeUCOfficial
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</treeUCOfficial>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treeUCSelfTreat

→ scenario → healthSystem → DecisionTree5Day → treeUCSelfTreat

<treeUCSelfTreat
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</treeUCSelfTreat>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Cure rate (severe cases)

→ scenario → healthSystem → DecisionTree5Day → cureRateSevere

<cureRateSevere
    value=double
  />

Documentation (element)

Min: 0 Max: 1

The probability of clearing parasites given access to appropriate (hospital) care, for a severe case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

treatmentSevere

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere

<treatmentSevere
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</treatmentSevere>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Case fatality rate for inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: Dimensionless

List of age-specific probabilities of sequelae in inpatients, during a severe bout of malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeEIR>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeEIR → timedDeployment

<timedDeployment
    eipDuration=int
    time=string
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timedDeployment>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Time

time=string

Units: User defined (defauls to steps) Min: 0

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=string ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=string

Units: User defined (default: steps) Min: 0

Default value: 0

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=string
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time of start

time=string

Units: User defined (defauls to steps) Min: 0

Insert R_0 case

<insertR_0Case
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</insertR_0Case>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → insertR_0Case → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Uninfect vectors

<uninfectVectors
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</uninfectVectors>

timedDeployment

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → uninfectVectors → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Vector population intervention

→ scenario → interventions → vectorPop

<vectorPop>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorPop>

intervention

Documentation (element)

Units: List of elements

A list of parameterisations of generic vector host-inspecific interventions.

intervention

→ scenario → interventions → vectorPop → intervention

<intervention
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

Units: List of elements

An intervention which may have various effects on the vector populations as a whole. (Not host specific.)

Multiple instances of this intervention class are allowed (multiple parameterisations, not just deployments).

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → vectorPop → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → vectorPop → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <seekingDeathRateIncrease ... /> ]
| [ <probDeathOvipositing ... /> ]
| [ <emergenceReduction ... /> ]
| [ <probAdditionalDeathSugarFeeding ... /> ]
</anopheles>

Documentation (type)

Units: dimensionless Min: 0 Max: 1

Descriptions of the effects of vector interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Proportional increase in deaths while host searching

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease

<seekingDeathRateIncrease
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</seekingDeathRateIncrease>

decay

Documentation (element)

Units: dimensionless

Describe an effect on the increase in the death rate while host seeking (mu_vA) due to this intervention.

Enter the rate increase (i.e. if rate increases to 120% of normal, give 0.2). New death rate while seeking is old × (1 + increase) where increase is this factor given. Must have increas ≥ -1.

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

decay

→ scenario → interventions → nonHumanHostsModifications → intervention → decay → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Proportion ovipositing mosquitoes killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing

<probDeathOvipositing
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probDeathOvipositing>

decay

Documentation (element)

Units: dimensionless

Describe an effect of increased mortality while ovipositing due to this intervention. Enter the probability of dying due to this intervention.

Attributes

Initial probability of killing

initial=double

Units: dimensionless Min: 0 Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Proportion of emerging pupa killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction

<emergenceReduction
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</emergenceReduction>

decay

Documentation (element)

Units: dimensionless

Describe an effect on emergence of pupa into adults: this value is the proportion of emerging pupa which are killed by this intervention.

Attributes

Initial proportion reduction

initial=double

Units: dimensionless Min: -inf Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Probability of death while host searching as a result of feeding on a sugar bait (used to dynamically adjust mu_vA)

→ scenario → interventions → vectorPop → intervention → description → anopheles → probAdditionalDeathSugarFeeding

<probAdditionalDeathSugarFeeding
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probAdditionalDeathSugarFeeding>

decay

Documentation (element)

Units: dimensionless

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probAdditionalDeathSugarFeeding → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Vector population intervention deployment

→ scenario → interventions → vectorPop → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

deploy

→ scenario → interventions → vectorPop → intervention → timed → deploy

<deploy
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Baited trap

→ scenario → interventions → vectorTrap

<vectorTrap>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorTrap>

intervention

Documentation (element)

intervention

→ scenario → interventions → vectorTrap → intervention

<intervention
  [ name=string ]
  >
IN THIS ORDER:
| ( <description ... /> )+
| [ <timed ... /> ]
</intervention>

Documentation (type)

Attributes

Descriptive name for type of trap

name=string

Optional name for this type of trap

Description

→ scenario → interventions → vectorTrap → intervention → description

<description
    mosquito=string
  >
IN THIS ORDER:
|   <relativeAvailability ... /> 
|   <decayOfAvailability ... /> 
</description>

Documentation (element)

Parameters associated with a vector trap intervention, per mosquito species.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Initial relative availability

→ scenario → interventions → vectorTrap → intervention → description → relativeAvailability

<relativeAvailability
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: inf

Describes the availiability of a trap to a host-seeking mosquito relative to an average unprotected adult.

I.e. if this parameter is 2, then each trap will on average attract twice as many mosquitoes as unprotected adults.

This is the initial availability; it may decay towards zero depending on the configured decay function.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay of availability

→ scenario → interventions → vectorTrap → intervention → description → decayOfAvailability

<decayOfAvailability
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decayOfAvailability>

decay

Documentation (element)

Describes how availability decays to zero.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Vector trap intervention deployment

→ scenario → interventions → vectorTrap → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )*
</timed>

deploy

Documentation (element)

List of timed vector trap intervention deployment

deploy

→ scenario → interventions → vectorTrap → intervention → timed → deploy

<deploy
    time=string
    ratioToHumans=double
    lifespan=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Ratio to humans

ratioToHumans=double

Min: 0 Max: inf

The number of traps deployed, by this deployment, per adult human. E.g. if there are currently 100 traps and 1000 humans, then a ratio of 0.1 will increase the number of traps to 200.

Lifespan

lifespan=string

Units: Steps or Days or Years

nonHumanHostsModifications

→ scenario → interventions → nonHumanHostsModifications

<nonHumanHostsModifications>
IN THIS ORDER:
| ( <intervention ... /> )+
</nonHumanHostsModifications>

intervention

Documentation (element)

List of interventions that modify parameters of non-human hosts described in the .

intervention

→ scenario → interventions → nonHumanHostsModifications → intervention

<intervention
    name=string
    nonHumanHostsName=string
  >
IN THIS ORDER:
|   <decay ... /> 
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

This intervention modifies parameters of non-human hosts described in the section of the input scenario file.

The intervention is described by 5 parameters that define the change in each of non-human host parameters:

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

Name of intervention

nonHumanHostsName=string

Name of intervention (e.g. larviciding, sugar bait).

decay

→ scenario → interventions → nonHumanHostsModifications → intervention → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

description

→ scenario → interventions → nonHumanHostsModifications → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <availabilityReduction ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
| [ <restingKillingEffect ... /> ]
| [ <fecundityReduction ... /> ]
</anopheles>

Documentation (type)

Descriptions of the effects of non human hosts interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

availabilityReduction

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → availabilityReduction

<availabilityReduction
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

preprandialKillingEffect

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

postprandialKillingEffect

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

restingKillingEffect

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → restingKillingEffect

<restingKillingEffect
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

fecundityReduction

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → fecundityReduction

<fecundityReduction
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

Vector population intervention deployment

→ scenario → interventions → nonHumanHostsModifications → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

addNonHumanHosts

<addNonHumanHosts>
IN THIS ORDER:
| ( <nonHumanHosts ... /> )+
</addNonHumanHosts>

nonHumanHosts

Documentation (element)

List of intervention that add new non-human hosts that have not been described in the .

nonHumanHosts

→ scenario → interventions → addNonHumanHosts → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</nonHumanHosts>

Documentation (type)

Describes a new non-human hosts that have not been described in the .

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
|   <mosqRelativeAvailabilityHuman ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <hostFecundityFactor ... /> 
</anopheles>

Documentation (type)

Descriptions of the effects of new non human hosts with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Relative availability of non-human host (ξ_i)

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqRelativeAvailabilityHuman

<mosqRelativeAvailabilityHuman
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of the population of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → hostFecundityFactor

<hostFecundityFactor
    value=double
  />

Documentation (element)

Units: Proportion

Multiplicative factor for the number of fertile eggs laid by a mosquito after biting this type of host, relative to an unprotected human.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vector trap intervention deployment

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )*
</timed>

deploy

Documentation (element)

List of timed vector trap intervention deployment

deploy

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → timed → deploy

<deploy
    time=string
    lifespan=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Lifespan

lifespan=string

Units: Steps or Days or Years

Human-specific interventions

→ scenario → interventions → human

<human>
IN THIS ORDER:
| ( <component ... /> )+
| ( <deployment ... /> )*
</human>

Documentation (element)

Encapsulates all interventions whose effects are specific to the human host: any interventions where target humans may be selected via population-coverage, age limits and sub-population membership.

Component

→ scenario → interventions → human → component

<component
    id=string
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <screen ... /> 
| |   <treatSimple ... /> 
| |   <treatPKPD ... /> 
| |   <decisionTree ... /> 
| |   <PEV ... /> 
| |   <BSV ... /> 
| |   <TBV ... /> 
| |   <ITN ... /> 
| |   <IRS ... /> 
| |   <GVI ... /> 
| | [ <recruitmentOnly ... /> ]
| |   <clearImmunity ... /> 
| [ <subPopRemoval ... /> ]
</component>

Documentation (element)

Each element describes one component: its effects, decay of the(se) effect(s), and related stuff (e.g. description of indirect decay and of usage levels).

Attributes

Component identifier

id=string

Name of component

name=string

An informal name/description for the component

screen

→ scenario → interventions → human → component → screen

<screen
    diagnostic=string
  >
IN THIS ORDER:
| ( <positive ... /> )*
| ( <negative ... /> )*
</screen>

Documentation (type)

This can be combined with MDA to achieve mass screen and treat (MSAT) or other types of mass screening intervention.

The use of the screening itself is reported (if enabled), but not the outcome. Deployment of interventions triggered by the screening may be reported, however.

Attributes

Name of diagnostic

diagnostic=string

Name of a parameterised diagnostic (see scenario/diagnostics).

positive

→ scenario → interventions → human → component → screen → positive

<positive
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → screen → negative

<negative
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

treatSimple

→ scenario → interventions → human → component → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

treatPKPD

→ scenario → interventions → human → component → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

decisionTree

→ scenario → interventions → human → component → decisionTree

<decisionTree
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <uncomplicated ... /> 
|   <severe ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )*
|   <cohort ... /> 
</decisionTree>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Vaccines

→ scenario → interventions → human → component → PEV

<PEV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )*
| ( <phenotype ... /> )*
</PEV>

Documentation (element)

Pre-erythrocytic vaccine (PEV): prevents a proportion of infections from commencing.

Documentation (type)

Description of a vaccine's effect

Decay of effect

→ scenario → interventions → human → component → PEV → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (element)

Specification of decay of efficacy. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Variance parameter for vaccine efficacy

→ scenario → interventions → human → component → PEV → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

PD parameters for some allele / resistance phenotype

→ scenario → interventions → human → component → PEV → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
| ( <initialEfficacy ... /> )+
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

restriction

→ scenario → interventions → human → component → PEV → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (type)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → phenotype → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vaccines

→ scenario → interventions → human → component → BSV

<BSV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )*
| ( <phenotype ... /> )*
</BSV>

Documentation (element)

Blood-stage vaccine (BSV): acts as a killing factor on blood-stage parasites. Exact action depends on the within host model.

Documentation (type)

Description of a vaccine's effect

Vaccines

→ scenario → interventions → human → component → TBV

<TBV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )*
| ( <phenotype ... /> )*
</TBV>

Documentation (element)

Transmission-blocking vaccine (TBV): one minus this scales the probability of transmission to mosquitoes

Documentation (type)

Description of a vaccine's effect

Bed nets

→ scenario → interventions → human → component → ITN

<ITN>
IN THIS ORDER:
| [ <usage ... /> ]
|   <holeRate ... /> 
|   <ripRate ... /> 
|   <ripFactor ... /> 
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
|   <attritionOfNets ... /> 
| ( <anophelesParams ... /> )+
</ITN>

Documentation (element)

Description of bed-net interventions (ITNs, LLINs).

Proportion of time nets are used by humans

→ scenario → interventions → human → component → ITN → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of nets by humans, from 0 to 1.

At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing.

See also "propActing" (proportion of bits for which net acts).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Rate at which holes are made

→ scenario → interventions → human → component → ITN → holeRate

<holeRate
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: Holes per annum Min: 0

The rate at which new holes are made in nets.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Rate at which holes are enlarged

→ scenario → interventions → human → component → ITN → ripRate

<ripRate
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: Rips per existing hole per annum Min: 0

Each existing hole has a probability of being ripped bigger according to a Poisson process with this rate as (only) parameter.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Rip factor

→ scenario → interventions → human → component → ITN → ripFactor

<ripFactor
    value=double
  />

Documentation (element)

Units: none Min: 0

This factor expresses how important rips are in increasing the hole.

The hole index of a net is h + F×x where h and x are the total numbers of holes and rips respectively and F is the rip factor.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → ITN → initialInsecticide

<initialInsecticide
    mean=double
  [ SD=double ]
  [ distr=("const" or "normal") ] DEFAULT VALUE const
  />

Documentation (element)

Units: mg/m² Min: 0

Documentation (type)

A parameter with optional heterogeneity.

Optionally, a distribution ("distr") and standard of deviation ("SD") may be specified.

Attributes

mean

mean=double

The mean value.

standard deviation

SD=double

The standard deviation of variates.

Distribution

distr=("const" or "normal")

Default value: const

Decay of insecticide

→ scenario → interventions → human → component → ITN → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</insecticideDecay>

decay

Documentation (element)

Units: none

Decay curve for insecticide content of nets. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Attrition of nets

→ scenario → interventions → human → component → ITN → attritionOfNets

<attritionOfNets
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</attritionOfNets>

decay

Documentation (element)

Units: dimensionless

Specifies the rate at which nets are disposed of over time. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Humans are removed from the intervention component's sub-population on disposal (attrition) of their nets. Currently this event is not reported.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

anophelesParams

→ scenario → interventions → human → component → ITN → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <holeIndexMax ... /> ]
| EXACTLY ONE OF:
| |   <deterrency ... /> 
| |   <twoStageDeterrency ... /> 
| EXACTLY ONE OF:
| |   <preprandialKillingEffect ... /> 
| |   <preprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| |   <postprandialKillingEffect ... /> 
| |   <postprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| | [ <fecundityReduction ... /> ]
| | [ <fecundityReductionLogit ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which net acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

maximum of holed surface area that has an effect (comparable to no net)

→ scenario → interventions → human → component → ITN → anophelesParams → holeIndexMax

<holeIndexMax
    value=double
  />

Documentation (element)

Units: in same unit as holeIndex

Used by logit attacking and killing models only, holeIndexMax is a user defined maximum hole index (typically, the total surface area of a net).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency

<twoStageDeterrency>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <entering ... /> 
| |   <enteringLogit ... /> 
| EXACTLY ONE OF:
| |   <attacking ... /> 
| |   <attackingLogit ... /> 
</twoStageDeterrency>

Documentation (element)

Units: dimensionless

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

This deterrency model multiplies human attractiveness by pEnt×pAtt.

Deterrency: entering

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → entering

<entering
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless

pEnt represents the relative probability of entering due to ITNs: pEnt = exp(log(P)×p) where P is the insecticide factor and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Deterrency: entering (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → enteringLogit

<enteringLogit
    baseFactor=double
    insecticideFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: none

See parent element documentation

Insecticide factor

insecticideFactor=double

Units: none

See parent element documentation

Deterrency: attacking

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attacking

<attacking
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Deterrency: attacking (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attackingLogit

<attackingLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Pre-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Pre-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffectLogit

<preprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Post-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffectLogit

<postprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Fecundity reduction

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-B), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReductionLogit

<fecundityReductionLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-K0), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Indoor residual spraying

→ scenario → interventions → human → component → IRS

<IRS>
IN THIS ORDER:
| [ <usage ... /> ]
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
| ( <anophelesParams ... /> )+
</IRS>

Documentation (element)

Description of indoor residual spraying interventions.

Documentation (type)

Description of effect for the more complex and probably more realistic Briet model: IRS has three effects, whos strength is calculated as a function of surviving insecticide content.

Proportion of Indoor residual spraying (IRS) interventions

→ scenario → interventions → human → component → IRS → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Indoor residual spraying (IRS) interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → IRS → initialInsecticide

<initialInsecticide
    mean=double
  [ SD=double ]
  [ distr=("const" or "normal") ] DEFAULT VALUE const
  />

Documentation (element)

Units: μg/cm² Min: 0

Documentation (type)

A parameter with optional heterogeneity.

Optionally, a distribution ("distr") and standard of deviation ("SD") may be specified.

Attributes

mean

mean=double

The mean value.

standard deviation

SD=double

The standard deviation of variates.

Distribution

distr=("const" or "normal")

Default value: const

Decay of insecticide

→ scenario → interventions → human → component → IRS → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</insecticideDecay>

decay

Documentation (element)

Units: none

Decay curve for insecticide content of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Per-mosquito species parameters

→ scenario → interventions → human → component → IRS → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → IRS → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied by exp(P×log(p)) where P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction

→ scenario → interventions → human → component → IRS → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

First, we calculate K = B + P×p where B is the base (without protection) probability of death, and P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Fecundity is multiplied by (1−K) / (1−B). It is not allowed to be greater than 1. To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Generic vector intervention

→ scenario → interventions → human → component → GVI

<GVI>
IN THIS ORDER:
| [ <usage ... /> ]
|   <decay ... /> 
| ( <anophelesParams ... /> )+
</GVI>

Documentation (element)

Note that all actions of this intervention component will decay according to a single decay function. If independant decay is wanted, a separate component can be used for each action.

Proportion of generic vector interventions

→ scenario → interventions → human → component → GVI → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Generic vector interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay

→ scenario → interventions → human → component → GVI → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (element)

Description of decay of all intervention effects. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Per-mosquito species parameters

→ scenario → interventions → human → component → GVI → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <deterrency ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → GVI → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of intervention on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied this factor times survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Fecundity reduction effect

→ scenario → interventions → human → component → GVI → anophelesParams → fecundityReduction

<fecundityReduction
    value=double
  />

Documentation (element)

Min: 0

Fertility is multiplied by 1 - (fecundityReduction * decay).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Recruitment only

→ scenario → interventions → human → component → recruitmentOnly

<recruitmentOnly/>

Documentation (element)

Recruitment of a host into a sub-population.

Clear Immunity

→ scenario → interventions → human → component → clearImmunity

<clearImmunity/>

Documentation (element)

Removes all exposure-related immunitsy gained over time by hosts without removing infections (or affecting the ability to gain immunity through exposure).

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

subPopRemoval

→ scenario → interventions → human → component → subPopRemoval

<subPopRemoval
  [ onFirstBout=boolean ] DEFAULT VALUE false
  [ onFirstTreatment=boolean ] DEFAULT VALUE false
  [ onFirstInfection=boolean ] DEFAULT VALUE false
  [ afterYears=double ]
  />

Documentation (type)

ITN attrition also removes humans from sub-populations.

Attributes

Time to first episode only

onFirstBout=boolean

Default value: false

Time to first treatment only

onFirstTreatment=boolean

Default value: false

Time to first infection only

onFirstInfection=boolean

Default value: false

Remove from sub-population after

afterYears=double

Units: Years Min: 0

Deployment

→ scenario → interventions → human → deployment

<deployment
  [ name=string ]
  >
IN THIS ORDER:
| ( <component ... /> )+
| ( <condition ... /> )*
| ( <continuous ... /> )*
| ( <timed ... /> )*
</deployment>

Documentation (element)

All components deployed by this intervention are deployed to the same people (each timed or continuous deployment selects recipients and then gives each recipient all components of the intervention).

Attributes

Intervention name

name=string

Name of intervention

component

→ scenario → interventions → human → deployment → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Condition

→ scenario → interventions → human → deployment → condition

<condition
    measure=string
  [ minValue=double ]
  [ maxValue=double ]
    initialState=boolean
  />

Documentation (element)

Conditions are evaluated for the whole population, not for individual age-groups or cohorts.

This affects all types of deployment.

Attributes

Measure

measure=string

The monitoring measure to test. Not all measures are available for use.

Minimum value

minValue=double

Minimum value. If specified, the measured variable must be greater than or equal to this value for the condition to be satisfied.

Maximum value

maxValue=double

Maximum value. If specified, the measured variable must be less than or equal to this value for the condition to be satisfied.

Initial state

initialState=boolean

Whether this condition is considered true or false before updated by a survey.

Age-based (continuous) deployment

→ scenario → interventions → human → deployment → continuous

<continuous>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| ( <deploy ... /> )+
</continuous>

Documentation (element)

List of ages at which deployment takes place (through EPI, post-natal and school-based programmes, etc.).

A sub-population restriction may be added as a property of the list of continuous deployments.

restrictToSubPop

→ scenario → interventions → human → deployment → continuous → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

deploy

→ scenario → interventions → human → deployment → continuous → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
  [ minAvailability=int ]
  [ maxAvailability=int ]
    targetAgeYrs=double
  [ begin=string ]
  [ end=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Minimum ento availability

minAvailability=int

Units: percent Min: 0

Maximum ento availability

maxAvailability=int

Units: percent Min: 0

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention. Input is rounded to the nearest time step.

First time active

begin=string

Units: User defined (defauls to steps)

End step

end=string

Units: User defined (defauls to steps)

Mass (timed) deployment

→ scenario → interventions → human → deployment → timed

<timed>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| [ <cumulativeCoverage ... /> ]
| ( <deploy ... /> )+
</timed>

Documentation (element)

List of timed deployments of the intervention (that is, of deployment campaigns).

Cumulative deployment mode can be specified for all deployments in a timed list. To allow multiple cumulative deployment descriptions, the entire timed list may be repeated.

restrictToSubPop

→ scenario → interventions → human → deployment → timed → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

Cumulative coverage

→ scenario → interventions → human → deployment → timed → cumulativeCoverage

<cumulativeCoverage
    component=string
  />

Documentation (element)

Attributes

Component identifier

component=string

The identifier (short name) of the component used when selecting people.

deploy

→ scenario → interventions → human → deployment → timed → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
  [ minAvailability=int ]
  [ maxAvailability=int ]
    time=string
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ repeatStep=string ]
  [ repeatEnd=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Minimum ento availability

minAvailability=int

Units: percent Min: 0

Maximum ento availability

maxAvailability=int

Units: percent Min: 0

Time

time=string

Units: User defined (defauls to steps) Min: 0

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0

Maximum age of eligible individuals (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible individuals (defaults to 0). Input is rounded to the nearest time step.

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Description of health system.

Documentation (type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("forced" or "dynamic")
  [ scaledAnnualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Description of entomological data

Attributes

Entomology dataset name

name=string

Name of entomology data

Transmission model mode

mode=("forced" or "dynamic")

Override annual EIR

scaledAnnualEIR=double

Units: Infectious bites per adult per year

If set, the annual EIR (for all species of vector) is scaled to this level; can be omitted if not needed.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters of the transmission model

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <seasonality ... /> 
|   <mosq ... /> 
| [ <lifeCycle ... /> ]
| [ <simpleMPD ... /> ]
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial estimate of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial estimate of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial estimate of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Seasonality of transmission

→ scenario → entomology → vector → anopheles → seasonality

<seasonality
    input=("EIR")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <fourierSeries ... /> 
| |   <monthlyValues ... /> 
| |   <dailyValues ... /> 
</seasonality>

Documentation (element)

Specifies the seasonality of transmission and optionally the level of annual transmission.

Attributes

Seasonality input

input=("EIR")

Annual EIR

annualEIR=double

Units: Inoculations per adult per annum Min: 0

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries

<fourierSeries
    EIRRotateAngle=double
  >
IN THIS ORDER:
| ( <coeffic ... /> )*
</fourierSeries>

coeffic

Documentation (element)

Units: Infectious bites per adult per day

Attributes

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: Radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Pair of Fourier coefficients

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries → coeffic

<coeffic
    a=double
    b=double
  />

Documentation (element)

A pair of Fourier series coefficients. The first element specifies a1 and b1, the second a2 and b2, etc. Any number (from 0 up) of pairs may be given.

Attributes

a_n parameter of Fourier approximation to ln(EIR)

a=double

a_n parameter of Fourier approximation to ln(EIR) for some natural number n.

b_n parameter of Fourier approximation to ln(EIR)

b=double

b_n parameter of Fourier approximation to ln(EIR) for some natural number n.

List of monthly values

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues

<monthlyValues
    smoothing=("none" or "fourier")
  >
IN THIS ORDER:
| ( <value ... /> ){12,12}
</monthlyValues>

value

Documentation (element)

Description of seasonality from monthly values. Multiple smoothing methods are possible (see smoothing attribute).

List should contain twelve entries: January to December.

Attributes

Smoothing function

smoothing=("none" or "fourier")

How the monthly values are converted into a daily sequence of values:

none: no smoothing (step function)
Fourier: a Fourier series (with terms up to a2/b2) is fit to the sequence of monthly values and used to generate a smoothed list of daily values.

Monthly value

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Monthly value

List of daily values

→ scenario → entomology → vector → anopheles → seasonality → dailyValues

<dailyValues>
IN THIS ORDER:
| ( <value ... /> )+
</dailyValues>

value

Documentation (element)

Description of seasonality from daily values.

List should contain 365 entries: 1st January to 31st December.

Daily value

→ scenario → entomology → vector → anopheles → seasonality → dailyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Daily value

Mosquito feeding cycle parameters

→ scenario → entomology → vector → anopheles → mosq

<mosq
    minInfectedThreshold=double
  >
IN ANY ORDER:
|   <mosqRestDuration ... /> 
|   <extrinsicIncubationPeriod ... /> 
|   <mosqLaidEggsSameDayProportion ... /> 
|   <mosqSeekingDuration ... /> 
|   <mosqSurvivalFeedingCycleProbability ... /> 
|   <availability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <mosqProbOvipositing ... /> 
|   <mosqHumanBloodIndex ... /> 
</mosq>

Documentation (element)

Parameters describing the feeding cycle and human mosquito interaction of a single species of anopheles mosquito.

Attributes

Mininum infected threshold for mosquitos

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

Duration of the resting period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqRestDuration

<mosqRestDuration
    value=int
  />

Documentation (element)

Units: Days

name:Duration of the resting period of the vector (days);

Attributes

Input parameter value

value=int

An integer value.

Extrinsic incubation period

→ scenario → entomology → vector → anopheles → mosq → extrinsicIncubationPeriod

<extrinsicIncubationPeriod
    value=int
  />

Documentation (element)

Units: Days

name:Extrinsic incubation period (days)

Attributes

Input parameter value

value=int

An integer value.

Proportion of mosquitoes host seeking on same day as ovipositing

→ scenario → entomology → vector → anopheles → mosq → mosqLaidEggsSameDayProportion

<mosqLaidEggsSameDayProportion
    value=double
  />

Documentation (element)

Units: Proportion

Proportion of mosquitoes host seeking on same day as ovipositing

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Duration of the host-seeking period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqSeekingDuration

<mosqSeekingDuration
    value=double
  />

Documentation (element)

Units: Days

Duration of the host-seeking period of the vector (days)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito survives the feeding cycle

→ scenario → entomology → vector → anopheles → mosq → mosqSurvivalFeedingCycleProbability

<mosqSurvivalFeedingCycleProbability
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito survives the feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human availability rate heterogeneity

→ scenario → entomology → vector → anopheles → mosq → availability

<availability
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
  />

Documentation (element)

If no attributes are specified or distr="const" or CV="0" then there will be no heterogeneity.

Documentation (type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

Probability that the mosquito succesfully bites chosen host

→ scenario → entomology → vector → anopheles → mosq → mosqProbBiting

<mosqProbBiting
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito succesfully bites chosen host

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → mosq → mosqProbFindRestSite

<mosqProbFindRestSite
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito escapes host and finds a resting place after biting

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → mosq → mosqProbResting

<mosqProbResting
    mean=double
    variance=double
  />

Documentation (element)

Probability of mosquito successfully resting after finding a resting site

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of a mosquito successfully laying eggs given that it has rested

→ scenario → entomology → vector → anopheles → mosq → mosqProbOvipositing

<mosqProbOvipositing
    value=double
  />

Documentation (element)

Probability of a mosquito successfully laying eggs given that it has rested

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human blood index

→ scenario → entomology → vector → anopheles → mosq → mosqHumanBloodIndex

<mosqHumanBloodIndex
    value=double
  />

Documentation (element)

Units: Proportion

The proportion of resting mosquitoes which fed on human blood during the last feed.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mosquito life cycle parameters

→ scenario → entomology → vector → anopheles → lifeCycle

<lifeCycle
  [ estimatedLarvalResources=double ] DEFAULT VALUE 1e8
  >
IN ANY ORDER:
|   <eggStage ... /> 
|   <larvalStage ... /> 
|   <pupalStage ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</lifeCycle>

Documentation (element)

Parameters describing the life-cycle of this species of mosquito

Attributes

Estimate of larval resources

estimatedLarvalResources=double

Units: X

Default value: 1e8

Egg stage

→ scenario → entomology → vector → anopheles → lifeCycle → eggStage

<eggStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the egg stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

larvalStage

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage

<larvalStage>
</larvalStage>

daily

Documentation (type)

Parameters for the larval stage of development

Documentation (base type)

Parameters associated with a mosquito development stage.

Daily development

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage → daily

<daily
    resourceUsage=double
    effectCompetition=double
  />

Documentation (element)

Attributes

Resource usage

resourceUsage=double

Units: X

Resource usage during larval stage of development. Units are arbitrary.

Effect of competition

effectCompetition=double

Units: none

Effect of competition over resources on development.

Pupal stage

→ scenario → entomology → vector → anopheles → lifeCycle → pupalStage

<pupalStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the pupal stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → lifeCycle → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Simple Mosq-Pop-Dynamics parameters

→ scenario → entomology → vector → anopheles → simpleMPD

<simpleMPD>
IN ANY ORDER:
|   <developmentDuration ... /> 
|   <developmentSurvival ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</simpleMPD>

Documentation (element)

Parameters describing the simple mosquito population dynamics model.

This is a simpler version of the life-cycle model, requiring less parameters and with much simpler initialisation.

Duration

→ scenario → entomology → vector → anopheles → simpleMPD → developmentDuration

<developmentDuration
    value=int
  />

Documentation (element)

Units: Days Min: 1

Duration from egg laying to emergence in days.

Attributes

Input parameter value

value=int

An integer value.

Probability of survival

→ scenario → entomology → vector → anopheles → simpleMPD → developmentSurvival

<developmentSurvival
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that mosquito survives from the egg being laid to emergence, given no resouce limitations (no density constraints).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → simpleMPD → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Alternative (non-human) host paramters

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN ANY ORDER:
|   <mosqRelativeEntoAvailability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
| [ <hostFecundityFactor ... /> ]
</nonHumanHosts>

Documentation (element)

Min: 0

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of non-human host (ξ_i)

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqRelativeEntoAvailability

<mosqRelativeEntoAvailability
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of the population of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative fecundity of biting mosquitoes

→ scenario → entomology → vector → anopheles → nonHumanHosts → hostFecundityFactor

<hostFecundityFactor
    value=double
  />

Documentation (element)

Units: Proportion

Multiplicative factor for the number of fertile eggs laid by a mosquito after biting this type of host, relative to an unprotected human.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Name of this species of non human hosts (must match up with those described per anopheles section).

Population size of non-human host species

number=double

Units: Animals

Parasite genetics

<parasiteGenetics
    samplingMode=("initial" or "tracking")
  >
IN THIS ORDER:
| ( <locus ... /> )+
</parasiteGenetics>

locus

Documentation (element)

A specification of genotypes of infection parasites.

May be omitted; in this case there is no modelling of genetic differences of infections (resistance, fitness).

Attributes

samplingMode

samplingMode=("initial" or "tracking")

Locus

→ scenario → parasiteGenetics → locus

<locus
    name=string
  >
IN THIS ORDER:
| ( <allele ... /> )+
</locus>

allele

Documentation (element)

Alleles at loci can affect fitness and resistance to any number of drugs.

Attributes

Name of locus

name=string

Name of the Locus

Allele

→ scenario → parasiteGenetics → locus → allele

<allele
    name=string
    initialFrequency=double
    fitness=double
  [ hrp2_deletion=boolean ] DEFAULT VALUE false
  />

Documentation (element)

Describes an allele, or one possible genetic option of multiple at one point of variance.

Attributes

Name

name=string

Name of the allele; used to refer to it elsewhere.

Initial frequency

initialFrequency=double

Fitness factor

fitness=double

HRP2 deletion

hrp2_deletion=boolean

Default value: false

Drug parameters (PK, PD and usage)

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
|   <treatments ... /> 
|   <drugs ... /> 
</pharmacology>

Documentation (element)

Drug model parameters and drug usage parameters

Documentation (type)

A library of drug related data for the PK/PD model.

Treatments library

→ scenario → pharmacology → treatments

<treatments>
IN THIS ORDER:
| ( <schedule ... /> )+
| ( <dosages ... /> )+
</treatments>

Documentation (element)

A library of drug deployment schedules and dosages.

schedule

→ scenario → pharmacology → treatments → schedule

<schedule
    name=string
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

A schedule for the administration of drugs in a course of treatment.

Note that dose sizes are multiplied by some multiplier (see dosages) and the times of all doses may be delayed.

Attributes

Name

name=string

Name for referring to this deployment schedule

medicate

→ scenario → pharmacology → treatments → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  />

Attributes

drug

drug=string

Abbreviated name of drug compound

Drug dose (mg with multiplier)

mg=double

Units: mg per something

Quantity of drug compound in mg per something. A separate dosage table must be used when medicating, which may specify multipliers of this number based on patient age or weight.

Time of administration

hour=double

Units: Hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

dosages

→ scenario → pharmacology → treatments → dosages

<dosages
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | ( <age ... /> )+
| | ( <bodymass ... /> )+
| |   <multiply ... /> 
</dosages>

Documentation (type)

A table for selecting a dose size. There are several ways this can work: using the patient's age or body mass in a look-up table to get a multplier, or directly using body mass as the multiplier.

The doses specified in "mg" in the treatment schedule are then multiplied by this multiplier.

Attributes

Name

name=string

Name for referring to this dosage table

Look-up table (age)

→ scenario → pharmacology → treatments → dosages → age

<age
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's age.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Look-up table (weight)

→ scenario → pharmacology → treatments → dosages → bodymass

<bodymass
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's body mass.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Multiply dose

→ scenario → pharmacology → treatments → dosages → multiply

<multiply
    by=("kg")
  />

Documentation (element)

Multiply the dose by some quantity, such as patient weight.

Attributes

By what?

by=("kg")

Quantity to multiply the dose by. Only option is "kg" (patient weight in kg).

Drug library

→ scenario → pharmacology → drugs

<drugs>
IN THIS ORDER:
| ( <drug ... /> )+
</drugs>

drug

Documentation (element)

A library of drug PK/PD data.

drug

→ scenario → pharmacology → drugs → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (type)

A drug description with PK/PD parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drugs → drug → PD

<PD
  [ locus=string ]
  >
IN THIS ORDER:
| ( <phenotype ... /> )+
</PD>

phenotype

Attributes

Locus

locus=string

PD parameters for some allele / resistance phenotype

→ scenario → pharmacology → drugs → drug → PD → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

Restrict phenotype applicability to certain alleles

→ scenario → pharmacology → drugs → drug → PD → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (element)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Maximal parasite killing rate

→ scenario → pharmacology → drugs → drug → PD → phenotype → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drugs → drug → PD → phenotype → IC50

<IC50
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

If CV > 0, the IC50 is sampled from a log-normal distribution.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Slope of effect curve

→ scenario → pharmacology → drugs → drug → PD → phenotype → slope

<slope>
    double
</slope>

Documentation (element)

Units: dimensionless

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drugs → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
| EXACTLY ONE OF:
| |   <half_life ... /> 
| | IN THIS ORDER:
| | |   <k ... /> 
| | |   <m_exponent ... /> 
| [ <k_a ... /> ]
| [ <conversion ... /> ]
|   <vol_dist ... /> 
| [ <compartment2 ... /> ]
| [ <compartment3 ... /> ]
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drugs → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drugs → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate λ, calculated as λ = ln(2) / half_life. The basic form of decay is C(t) = C0 * exp(-λ*t).

Alternatively, elimination rate can be specified via k and m_exponent.

Constant associated with elimination rate (k)

→ scenario → pharmacology → drugs → drug → PK → k

<k
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

If CV > 0, k is sampled per-human from the log-normal distribution: ln N( ln(mean) - σ^2 / 2, σ^2).

Alternatively, elimination rate can be specified via half_life.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Constant associated with elimination rate (m_exponent)

→ scenario → pharmacology → drugs → drug → PK → m_exponent

<m_exponent>
    double
</m_exponent>

Documentation (element)

Units: day^-1 Min: 0

Alternatively, elimination rate can be specified via half_life.

Note that in the case of a conversion model, this applies to both the elimination and the conversion rates.

Absorption rate constant (k_a)

→ scenario → pharmacology → drugs → drug → PK → k_a

<k_a
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Min: 0

Absorption rate parameter. Not allowed for one compartment models, but required for two and three compartment models and one compartment with conversion model (for the parent drug only).

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Conversion parameters (parent drug)

→ scenario → pharmacology → drugs → drug → PK → conversion

<conversion>
IN ANY ORDER:
|   <metabolite ... /> 
|   <rate ... /> 
|   <molRatio ... /> 
|   <IC50_log_correlation ... /> 
</conversion>

Documentation (element)

Configures the parent drug in a conversion model.

To use a conversion model, the parent drug should have this section defined as well as half-life or k (direct elimination; this may be zero) and k_a (absorption rate; this may be large).

Metabolite drug (abbreviation)

→ scenario → pharmacology → drugs → drug → PK → conversion → metabolite

<metabolite>
    string
</metabolite>

Documentation (element)

The abbreviation of the metabolite drug (e.g. "DHA" or "DHA_AR").

Rate of conversion

→ scenario → pharmacology → drugs → drug → PK → conversion → rate

<rate
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Rate of conversion of parent drug to metabolite.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Molecular weight ratio

→ scenario → pharmacology → drugs → drug → PK → conversion → molRatio

<molRatio>
    double
</molRatio>

Documentation (element)

Ratio of molecular weights: molecular weight of the metabolite divided by molecular weight of the parent.

IC50 log correlation

→ scenario → pharmacology → drugs → drug → PK → conversion → IC50_log_correlation

<IC50_log_correlation>
    double
</IC50_log_correlation>

Documentation (element)

Min: 0 Max: 1

If this value is 1, samples are fully correlated: a single z-score is used to calculate both samples. If this is 0, two independent samples are used.

Values between 0 and 1 (partial correlation) are supported; in this case IC50 values are sampled such that cor(log(x), log(y)) matches this value (where x, y are parent and metabolite IC50 values).

Volume of Distribution (Vd)

→ scenario → pharmacology → drugs → drug → PK → vol_dist

<vol_dist
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution.

If CV > 0 this is sampled from a log-normal distribution.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Second compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment2

<compartment2>
IN ANY ORDER:
|   <k12 ... /> 
|   <k21 ... /> 
</compartment2>

Documentation (element)

Optional element specifying conversion parameters to- and from- a second compartment.

Absorption rate to compartment 2 (k12)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → k12

<k12
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the first periphery compartment (2).

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Absorption rate from compartment 2 (k21)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → k21

<k21
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the first periphery compartment (2) to the central compartment.

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Third compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment3

<compartment3>
IN ANY ORDER:
|   <k13 ... /> 
|   <k31 ... /> 
</compartment3>

Documentation (element)

Optional element specifying conversion parameters to- and from- a third compartment.

Absorption rate to compartment 3 (k13)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → k13

<k13
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the second periphery compartment (3).

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Absorption rate from compartment 3 (k31)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → k31

<k31
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the second periphery compartment (3) to the central compartment.

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Diagnostic parameters

→ scenario → diagnostics

<diagnostics>
IN THIS ORDER:
| ( <diagnostic ... /> )*
</diagnostics>

diagnostic

Documentation (element)

Diagnostic model parameters

diagnostic

→ scenario → diagnostics → diagnostic

<diagnostic
    name=string
  [ units=("Other" or "Garki" or "Malariatherapy") ]
  [ mechanism=("Other" or "HRP2") ] DEFAULT VALUE Other
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterministic ... /> 
| |   <stochastic ... /> 
</diagnostic>

Attributes

Name of diagnostic

name=string

Name of this diagnostic (parameterisation). May be used elsewhere in the XML document to refer to this set of diagnostic parameters.

Parasite density units / methodology

units=("Other" or "Garki" or "Malariatherapy")

Mechanism

mechanism=("Other" or "HRP2")

Default value: Other

Deterministic detection

→ scenario → diagnostics → diagnostic → deterministic

<deterministic
    minDensity=double
  />

Documentation (element)

Specify that an artificial deterministic test is used: outcome is positive if parasite density is at least the minimum given.

Attributes

Minimum detectible density

minDensity=double

Units: parasites/microlitre Min: 0

The minimum density at which parasites can be detected. If 0, the test outcome is always positive.

Non-deterministic detection

→ scenario → diagnostics → diagnostic → stochastic

<stochastic
    dens_50=double
    specificity=double
  />

Documentation (element)

An improved model of detection which is non-deterministic, including false positive results as well as false negatives.

Some parameterisations:

Microscopy sensitivity/specificity data in Africa; Source: expert opinion — Allan Schapira dens_50 = 20.0 specificity = .75

RDT sensitivity/specificity for Plasmodium falciparum in Africa Source: Murray et al (Clinical Microbiological Reviews, Jan. 2008) dens_50 = 50.0; specificity = .942;

Attributes

Density 50

dens_50=double

Units: parasites/microlitre Min: 0

The density at which the test outcome has a 50% chance of being positive.

Specificity

specificity=double

Units: Dimensionless Min: 0 Max: 1

The probability of a positive test outcome in the absense of parasites.

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
| [ <vivax ... /> ]
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: model/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=string
  >
IN ANY ORDER:
| [ <NeonatalMortality ... /> ]
| [ <NonMalariaFevers ... /> ]
</clinical>

Documentation (type)

Attributes

Follow-up period during which recurrence is considered a treatment failure

healthSystemMemory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

Neonatal mortality parameters

→ scenario → model → clinical → NeonatalMortality

<NeonatalMortality
    diagnostic=string
  />

Attributes

Diagnostic used to parameterise model

diagnostic=string

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
| [ <prNeedTreatmentNMF ... /> ]
| [ <prNeedTreatmentMF ... /> ]
</NonMalariaFevers>

Documentation (type)

Description of the incidence of non-malaria fever. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a non-malarial fever requires treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

Availability of humans to mosquitoes relative to an adult, categorized by age group

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ]
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

Vivax model parameters

→ scenario → model → vivax

<vivax>
IN ANY ORDER:
|   <probBloodStageInfectiousToMosq ... /> 
|   <hypnozoiteRelease ... /> 
|   <bloodStageProtectionLatency ... /> 
|   <bloodStageLengthDays ... /> 
|   <clinicalEvents ... /> 
</vivax>

Documentation (element)

This describes Vivax model parameters, and is required when using the VIVAX_SIMPLE_MODEL model option.

Probability of mosquito infection

→ scenario → model → vivax → probBloodStageInfectiousToMosq

<probBloodStageInfectiousToMosq
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

The chance of a feeding mosquito becoming infected, given that the host is patent. (This may be adjusted by transmission-blocking vaccines.)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Hypnozoite releases

→ scenario → model → vivax → hypnozoiteRelease

<hypnozoiteRelease
  [ pSecondRelease=double ] DEFAULT VALUE 0
  >
IN ANY ORDER:
|   <numberHypnozoites ... /> 
|   <firstReleaseDays ... /> 
| [ <secondReleaseDays ... /> ]
</hypnozoiteRelease>

Documentation (element)

Describes the number and times of hypnozoite releases.

Documentation (type)

This element defines probabilites when and how many hypnozoites are released from the liverstage into the blood.

The gap between the start of a new brood of hypnozoites and its release are defined as follows:

latentP + latentRelapse + randomReleaseDelay

randomReleaseDelay is based on one or two lognormal distributions, which are defined in firstRelease and optionally secondRelease.

You can define 2 release distributions, which get added together and represent the probability of hypnozoites which get released before winter (first release) or after (second release).

You can omit the secondRelease element if no release to the blood happens after winter.

Attributes

latent relapse days

pSecondRelease=double

Default value: 0

Probability of a second release. If undefined it is zero.

Number of Hypnozoites

→ scenario → model → vivax → hypnozoiteRelease → numberHypnozoites

<numberHypnozoites
    max=int
    base=double
  />

Documentation (element)

numberHypnozoites calculates the number of hypnozoites in the liver stage based on a base which is between 0 and 1.

This number is random based on the following distribution and normalized:

max ∑ (base ^ n) n = 0

Attributes

max

max=int

base

base=double

firstReleaseDays

→ scenario → model → vivax → hypnozoiteRelease → firstReleaseDays

<firstReleaseDays
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
    latentRelapse=double
  />

Documentation (type)

Hypnozoites are released after a delay, calculated as: roundToTSFromDays(delay + latentRelapse)

Here, roundToTSFromDays rounds the input (in days) to the nearest timestep, delay is sampled from a log-normal, and latentRelapse is the parameter specified here.

The delay is sampled from a log-normal distribution, parameterised via the (linear) mean and CV (coefficient of variation) given here.

Documentation (base type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

latent relapse days

latentRelapse=double

Usually between 10 and 15 days.

secondReleaseDays

→ scenario → model → vivax → hypnozoiteRelease → secondReleaseDays

<secondReleaseDays
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
    latentRelapse=double
  />

Documentation (type)

Hypnozoites are released after a delay, calculated as: roundToTSFromDays(delay + latentRelapse)

Here, roundToTSFromDays rounds the input (in days) to the nearest timestep, delay is sampled from a log-normal, and latentRelapse is the parameter specified here.

The delay is sampled from a log-normal distribution, parameterised via the (linear) mean and CV (coefficient of variation) given here.

Documentation (base type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

latent relapse days

latentRelapse=double

Usually between 10 and 15 days.

Blood stage protection latency

→ scenario → model → vivax → bloodStageProtectionLatency

<bloodStageProtectionLatency
    value=double
  />

Documentation (element)

Min: 0

The length of time after expiry of a blood-stage infection during which relapses from the same brood are supressed by the immune system.

This is rounded to the nearest time-step.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Blood stage length

→ scenario → model → vivax → bloodStageLengthDays

<bloodStageLengthDays
    scale=double
    shape=double
    distr=("weibull")
  />

Documentation (element)

Units: Days

Parameters used to sample the length of blood-stage infections from a Weibull distribution (scale parameter lambda, shape parameter k).

Documentation (type)

Parameters of a Weibull distribution.

Attributes

Scale

scale=double

The Weibull scale parameter (λ).

shape

shape=double

The Weibull shape parameter (k).

Distribution

distr=("weibull")

To allow heterogeneity, a distribution must be specified. In this case, only "weibull" is allowed.

clinicalEvents

→ scenario → model → vivax → clinicalEvents

<clinicalEvents>
IN THIS ORDER:
|   <pPrimaryInfection ... /> 
|   <pRelapseOne ... /> 
|   <pRelapseTwoPlus ... /> 
|   <pEventIsSevere ... /> 
|   <vivaxClinOption ... /> 
</clinicalEvents>

Documentation (type)

This elements holds all information about probabilites for clinical events from infections and relapses.

pPrimaryInfection

→ scenario → model → vivax → clinicalEvents → pPrimaryInfection

<pPrimaryInfection
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseOne

→ scenario → model → vivax → clinicalEvents → pRelapseOne

<pRelapseOne
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseTwoPlus

→ scenario → model → vivax → clinicalEvents → pRelapseTwoPlus

<pRelapseTwoPlus
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pEventIsSevere

→ scenario → model → vivax → clinicalEvents → pEventIsSevere

<pEventIsSevere
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

vivaxClinOption

→ scenario → model → vivax → clinicalEvents → vivaxClinOption

<vivaxClinOption>
    string
</vivaxClinOption>

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=string
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=string

Units: User defined (default: steps) Min: 0 Max: 20

Pre-erythrocytic latent period Can be specified in steps (e.g. 3t) or days (e.g. 15d).

parameter

→ scenario → model → parameters → parameter

<parameter
  [ name=string ]
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 46 documentation

Generated from: scenario_46.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
  [ analysisNo=int ]
    name=string
  [ wuID=int ]
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:om="http://openmalaria.org/schema/scenario_46"
    xsi:schemaLocation="http://openmalaria.org/schema/scenario_46 scenario_46.xsd"
  >
IN ANY ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entomology ... /> 
| [ <parasiteGenetics ... /> ]
| [ <pharmacology ... /> ]
| [ <diagnostics ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Name of intervention

Work unit identifier

wuID=int

Units: Number

Work unit ID. Obselete and no longer required.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Description of demography

Attributes

Name of demography data

name=string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Years Min: 0 Max: 100

Maximum age of simulated humans in years

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

list of age groups included in demography

Documentation (type)

list of age groups included in demography or surveys

Attributes

Lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Units: Percentage Min: 0 Max: 100

Percentage of human population in age group

Upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ startDate=string ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
| [ <cohorts ... /> ]
</monitoring>

Documentation (element)

Description of surveys

Attributes

Name of monitoring settings

name=string

Name of monitoring settings

Start of monitoring

startDate=string

continuous

→ scenario → monitoring → continuous

<continuous
    period=string
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Delay between reports

period=string

Units: User defined (default: steps)

Delay between reports; typically one time step but can be greater. Can be specified in steps (e.g. 1t) or days (e.g. 5d).

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions
  [ onlyNewEpisode=boolean ] DEFAULT VALUE false
  >
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See model/mon/OutputMeasures.h for a list of supported outputs. Should also be on the wiki.

Attributes

Report only for new cases

onlyNewEpisode=boolean

Default value: false

option

→ scenario → monitoring → SurveyOptions → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  [ outputNumber=int ]
  [ byAge=boolean ]
  [ byCohort=boolean ]
  [ bySpecies=boolean ]
  [ byGenotype=boolean ]
  [ byDrugType=boolean ]
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Number identifying measure in output

outputNumber=int

Report by age category

byAge=boolean

Report by cohort

byCohort=boolean

Report by mosquito species

bySpecies=boolean

Report by parasite genotype

byGenotype=boolean

Report by drug type

byDrugType=boolean

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
  [ detectionLimit=double ]
  [ diagnostic=string ]
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/microlitre Min: 0

Deprecated: limit above which a human's infection is reported as patent. Alternative: do not specify this; instead specify "diagnostic".

Name of monitoring diagnostic

diagnostic=string

Name of a parameterised diagnostic to use in surveys (see scenario/diagnostics).

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime
  [ repeatStep=string ]
  [ repeatEnd=string ]
  [ reported=boolean ] DEFAULT VALUE true
  >
    string
</surveyTime>

Documentation (element)

Units: User defined (defaults to steps) Min: 0

The simulation ends immediately after the last survey is taken.

Attributes

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

reported

reported=boolean

Default value: true

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Cohorts

→ scenario → monitoring → cohorts

<cohorts>
IN THIS ORDER:
| ( <subPop ... /> )+
</cohorts>

subPop

Documentation (element)

Allows the configuration of multiple cohorts (output segregated according to membership within specific sub-populations).

If this element is omitted, monitoring surveys cover the entire simulated human population.

It does not affect the "continuous" outputs (these never take cohorts into account).

Sub-population

→ scenario → monitoring → cohorts → subPop

<subPop
    id=string
    number=integer
  />

Documentation (element)

In the output file, the output set is identified by multiplying this number by 1000 then adding it to the age group column.

Attributes

Sub-population identifier

id=string

Textual identifier for the sub-population (i.e. for an intervention component, since sub-populations are defined as the hosts an intervention component is deployed to).

Sub-population number

number=integer

Units: dimensionless Min: 1 Max: 2097152

Number identifying a sub-population; used to define identifiers of output sets. This number must be a power of 2 (i.e. 1, 2, 4, 8, ...). See documentation of subPop element.

Preventative interventions

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfections ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <vectorPop ... /> ]
| [ <vectorTrap ... /> ]
| [ <nonHumanHostsModifications ... /> ]
| [ <addNonHumanHosts ... /> ]
| [ <human ... /> ]
</interventions>

Documentation (element)

Attributes

Name of intervention set

name=string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeHS>

timedDeployment

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeHS → timedDeployment

<timedDeployment
    time=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timedDeployment>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</uncomplicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

multiple

→ scenario → interventions → human → component → decisionTree → multiple

<multiple
  [ name=string ]
  >
EXACTLY ONE OF:
| ( <caseType ... /> )*
| ( <diagnostic ... /> )*
| ( <fever ... /> )*
| ( <random ... /> )*
| ( <age ... /> )*
| ( <treatPKPD ... /> )*
| [ <treatSimple ... /> ]
| ( <deploy ... /> )*
| ( <report ... /> )*
</multiple>

Documentation (type)

A special node allowing multiple sub-trees to be evaluated.

This is different from an ordinary decision tree node in that:

a) multiple types of child can occur simultaneously (e.g. multiple types of treatment or treatment plus a 'random' sub-tree)

b) the 'noTreatment' and 'treatFailure' nodes are not allowed

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → multiple → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

firstLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → firstLine

<firstLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</firstLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

secondLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → secondLine

<secondLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</secondLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

positive

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

fever

→ scenario → interventions → human → component → decisionTree → fever

<fever
  [ name=string ]
    lookBack=string
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</fever>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Number of days to look back for fevers. This must be less than or equal to the healthsystem memory parameter. In general, this should be less than or equal to the repeatStep in MSAT with contiuous deployment

lookBack=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

positive

→ scenario → interventions → human → component → decisionTree → multiple → fever → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

outcome

→ scenario → interventions → human → component → decisionTree → multiple → random → outcome

<outcome
  [ name=string ]
    p=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</outcome>

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Probability

p=double

Units: None Min: 0 Max: 1

Probability of selecting this outcome. The sum of probabilities across all outcomes must be 1.

age

→ scenario → interventions → human → component → decisionTree → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Age range

→ scenario → interventions → human → component → decisionTree → multiple → age → age

<age
  [ name=string ]
    lb=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</age>

Documentation (element)

Describes a branch, selected for patients of a certain age.

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Lower bound (inclusive)

lb=double

Min: 0

noTreatment

→ scenario → interventions → human → component → decisionTree → noTreatment

<noTreatment
  [ name=string ]
  />

Documentation (type)

An end node doing nothing. This exists to explicitly state that no treatment happens and to prevent trees from accidentally being left incomplete.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

report

→ scenario → interventions → human → component → decisionTree → report

<report
  [ name=string ]
  [ outputNumber=int ] DEFAULT VALUE 0
  />

Documentation (type)

This increments measure 80 (nCMDTReport) by one every time this node is visited. This can be useful to report the results of mass test and treat interventions using the decision tree.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Delay (hours)

outputNumber=int

Default value: 0

treatFailure

→ scenario → interventions → human → component → decisionTree → treatFailure

<treatFailure
  [ name=string ]
  />

Documentation (type)

An end node which reports treatment but does not change parasitalogical status. This allows correct labelling of second-line cases.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → decisionTree → multiple → fever → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

negative

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

fever

→ scenario → interventions → human → component → decisionTree → multiple → fever

<fever
  [ name=string ]
    lookBack=string
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</fever>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Number of days to look back for fevers. This must be less than or equal to the healthsystem memory parameter. In general, this should be less than or equal to the repeatStep in MSAT with contiuous deployment

lookBack=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

random

→ scenario → interventions → human → component → decisionTree → multiple → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

age

→ scenario → interventions → human → component → decisionTree → multiple → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → multiple → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → multiple → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → multiple → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

report

→ scenario → interventions → human → component → decisionTree → multiple → report

<report
  [ name=string ]
  [ outputNumber=int ] DEFAULT VALUE 0
  />

Documentation (type)

This increments measure 80 (nCMDTReport) by one every time this node is visited. This can be useful to report the results of mass test and treat interventions using the decision tree.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Delay (hours)

outputNumber=int

Default value: 0

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</complicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: Days Min: 0 Max: unbounded

Maximum number of timesteps (including first day of case) that an individual with an uncomplicated case of malaria will remember he/she was sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial or non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of a complicated or severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
  [ name=string ]
  [ useDiagnosticUC=boolean ] DEFAULT VALUE false
  >
IN ANY ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <treatmentActions ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
</ImmediateOutcomes>

Documentation (type)

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Name of case management parameterisation

name=string

Name of health system

useDiagnosticUC

useDiagnosticUC=boolean

Default value: false

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Description of drug regimen.

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Artemisinine based combination therapy

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Quinine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0 Max: 1name:P(self-treat)

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Effectiveness of treatment for non-compliant patients

treatmentActions

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions

<treatmentActions>
IN ANY ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
</treatmentActions>

CQ
SP
AQ
SPAQ
ACT
QN

CQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ

<CQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</CQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

deploy

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy

<deploy
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ p=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| ( <component ... /> )+
</deploy>

component

Attributes

Maximum age of eligible humans

maxAge=double

Units: Years Min: 0

Maximum age of eligible humans (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible humans

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible humans (defaults to 0). Input is rounded to the nearest time step.

Probability of delivery to eligible humans

p=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Probability of this list of components being deployed, given that other constraints are met.

component

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Prophylactic treatment

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere → clearInfections

<clearInfections
    timesteps=string
    stage=("liver" or "blood" or "both")
  />

Documentation (element)

Attributes

Length of effect

timesteps=string

Units: User defined (defaults to steps)

Target stage

stage=("liver" or "blood" or "both")

SP

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SP

<SP
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SP>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

AQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → AQ

<AQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</AQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

SPAQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SPAQ

<SPAQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SPAQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

ACT

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → ACT

<ACT
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</ACT>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

QN

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → QN

<QN
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</QN>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

Probability that human is incompatible with liver-stage drug treatment

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pHumanCannotReceive

<pHumanCannotReceive
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that a human is determined to be unable to receive liver-stage drug treatment. Treatment is neither reported or given for such humans.

This is sampled once per human at birth.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Ignore liver-stage drug treatment incompatibility

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → ignoreCannotReceive

<ignoreCannotReceive
    value=boolean
  />

Documentation (element)

If true, ignore pHumanCannotReceive and consider all humans eligible for treatment; if false (or not specified), do not treat those demed incompatible with liver-stage drug treatment.

The point of this is that pHumanCannotReceive cannot be altered by changeHS interventions, but this property can be.

Attributes

Input parameter value

value=boolean

A boolean value.

Prob use in UC case

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pUseUncomplicated

<pUseUncomplicated
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

This feature is deprecated; it is suggested to use the "simple treatment" feature configured to clear liver-stage parasites, leaving this option unset or zero.

Chance of liver-stage drug treatment being used for routine treatment of an uncomplicated case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Effectiveness

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → effectivenessOnUse

<effectivenessOnUse
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that liver-stage drug treatment is effective.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

DecisionTree5Day

<DecisionTree5Day
  [ name=string ]
  >
IN ANY ORDER:
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
|   <treeUCOfficial ... /> 
|   <treeUCSelfTreat ... /> 
|   <cureRateSevere ... /> 
|   <treatmentSevere ... /> 
</DecisionTree5Day>

Documentation (type)

Besides greater flexibility, this allows treatment via PK/PD models.

Attributes

Name of case management parameterisation

name=string

Name of health system

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → DecisionTree5Day → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → DecisionTree5Day → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

treeUCOfficial

→ scenario → healthSystem → DecisionTree5Day → treeUCOfficial

<treeUCOfficial
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</treeUCOfficial>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treeUCSelfTreat

→ scenario → healthSystem → DecisionTree5Day → treeUCSelfTreat

<treeUCSelfTreat
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</treeUCSelfTreat>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Cure rate (severe cases)

→ scenario → healthSystem → DecisionTree5Day → cureRateSevere

<cureRateSevere
    value=double
  />

Documentation (element)

Min: 0 Max: 1

The probability of clearing parasites given access to appropriate (hospital) care, for a severe case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

treatmentSevere

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere

<treatmentSevere
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</treatmentSevere>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Case fatality rate for inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: Dimensionless

List of age-specific probabilities of sequelae in inpatients, during a severe bout of malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeEIR>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeEIR → timedDeployment

<timedDeployment
    eipDuration=int
    time=string
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timedDeployment>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Time

time=string

Units: User defined (defauls to steps) Min: 0

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=string ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=string

Units: User defined (default: steps) Min: 0

Default value: 0

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=string
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time of start

time=string

Units: User defined (defauls to steps) Min: 0

Insert R_0 case

<insertR_0Case
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</insertR_0Case>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → insertR_0Case → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Uninfect vectors

<uninfectVectors
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</uninfectVectors>

timedDeployment

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → uninfectVectors → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Vector population intervention

→ scenario → interventions → vectorPop

<vectorPop>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorPop>

intervention

Documentation (element)

Units: List of elements

A list of parameterisations of generic vector host-inspecific interventions.

intervention

→ scenario → interventions → vectorPop → intervention

<intervention
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

Units: List of elements

An intervention which may have various effects on the vector populations as a whole. (Not host specific.)

Multiple instances of this intervention class are allowed (multiple parameterisations, not just deployments).

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → vectorPop → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → vectorPop → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <seekingDeathRateIncrease ... /> ]
| [ <probDeathOvipositing ... /> ]
| [ <emergenceReduction ... /> ]
| [ <probAdditionalDeathSugarFeeding ... /> ]
</anopheles>

Documentation (type)

Units: dimensionless Min: 0 Max: 1

Descriptions of the effects of vector interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Proportional increase in deaths while host searching

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease

<seekingDeathRateIncrease
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</seekingDeathRateIncrease>

decay

Documentation (element)

Units: dimensionless

Describe an effect on the increase in the death rate while host seeking (mu_vA) due to this intervention.

Enter the rate increase (i.e. if rate increases to 120% of normal, give 0.2). New death rate while seeking is old × (1 + increase) where increase is this factor given. Must have increas ≥ -1.

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

decay

→ scenario → interventions → nonHumanHostsModifications → intervention → decay → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Proportion ovipositing mosquitoes killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing

<probDeathOvipositing
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probDeathOvipositing>

decay

Documentation (element)

Units: dimensionless

Describe an effect of increased mortality while ovipositing due to this intervention. Enter the probability of dying due to this intervention.

Attributes

Initial probability of killing

initial=double

Units: dimensionless Min: 0 Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Proportion of emerging pupa killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction

<emergenceReduction
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</emergenceReduction>

decay

Documentation (element)

Units: dimensionless

Describe an effect on emergence of pupa into adults: this value is the proportion of emerging pupa which are killed by this intervention.

Attributes

Initial proportion reduction

initial=double

Units: dimensionless Min: -inf Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Probability of death while host searching as a result of feeding on a sugar bait (used to dynamically adjust mu_vA)

→ scenario → interventions → vectorPop → intervention → description → anopheles → probAdditionalDeathSugarFeeding

<probAdditionalDeathSugarFeeding
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probAdditionalDeathSugarFeeding>

decay

Documentation (element)

Units: dimensionless

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probAdditionalDeathSugarFeeding → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Vector population intervention deployment

→ scenario → interventions → vectorPop → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

deploy

→ scenario → interventions → vectorPop → intervention → timed → deploy

<deploy
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Baited trap

→ scenario → interventions → vectorTrap

<vectorTrap>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorTrap>

intervention

Documentation (element)

intervention

→ scenario → interventions → vectorTrap → intervention

<intervention
  [ name=string ]
  >
IN THIS ORDER:
| ( <description ... /> )+
| [ <timed ... /> ]
</intervention>

Documentation (type)

Attributes

Descriptive name for type of trap

name=string

Optional name for this type of trap

Description

→ scenario → interventions → vectorTrap → intervention → description

<description
    mosquito=string
  >
IN THIS ORDER:
|   <relativeAvailability ... /> 
|   <decayOfAvailability ... /> 
</description>

Documentation (element)

Parameters associated with a vector trap intervention, per mosquito species.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Initial relative availability

→ scenario → interventions → vectorTrap → intervention → description → relativeAvailability

<relativeAvailability
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: inf

Describes the availiability of a trap to a host-seeking mosquito relative to an average unprotected adult.

I.e. if this parameter is 2, then each trap will on average attract twice as many mosquitoes as unprotected adults.

This is the initial availability; it may decay towards zero depending on the configured decay function.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay of availability

→ scenario → interventions → vectorTrap → intervention → description → decayOfAvailability

<decayOfAvailability
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decayOfAvailability>

decay

Documentation (element)

Describes how availability decays to zero.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Vector trap intervention deployment

→ scenario → interventions → vectorTrap → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )*
</timed>

deploy

Documentation (element)

List of timed vector trap intervention deployment

deploy

→ scenario → interventions → vectorTrap → intervention → timed → deploy

<deploy
    time=string
    ratioToHumans=double
    lifespan=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Ratio to humans

ratioToHumans=double

Min: 0 Max: inf

The number of traps deployed, by this deployment, per adult human. E.g. if there are currently 100 traps and 1000 humans, then a ratio of 0.1 will increase the number of traps to 200.

Lifespan

lifespan=string

Units: Steps or Days or Years

nonHumanHostsModifications

→ scenario → interventions → nonHumanHostsModifications

<nonHumanHostsModifications>
IN THIS ORDER:
| ( <intervention ... /> )+
</nonHumanHostsModifications>

intervention

Documentation (element)

List of interventions that modify parameters of non-human hosts described in the .

intervention

→ scenario → interventions → nonHumanHostsModifications → intervention

<intervention
    name=string
    nonHumanHostsName=string
  >
IN THIS ORDER:
|   <decay ... /> 
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

This intervention modifies parameters of non-human hosts described in the section of the input scenario file.

The intervention is described by 5 parameters that define the change in each of non-human host parameters:

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

Name of intervention

nonHumanHostsName=string

Name of intervention (e.g. larviciding, sugar bait).

decay

→ scenario → interventions → nonHumanHostsModifications → intervention → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

description

→ scenario → interventions → nonHumanHostsModifications → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <availabilityReduction ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
| [ <restingKillingEffect ... /> ]
| [ <fecundityReduction ... /> ]
</anopheles>

Documentation (type)

Descriptions of the effects of non human hosts interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

availabilityReduction

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → availabilityReduction

<availabilityReduction
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

preprandialKillingEffect

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

postprandialKillingEffect

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

restingKillingEffect

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → restingKillingEffect

<restingKillingEffect
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

fecundityReduction

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → fecundityReduction

<fecundityReduction
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

Vector population intervention deployment

→ scenario → interventions → nonHumanHostsModifications → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

addNonHumanHosts

<addNonHumanHosts>
IN THIS ORDER:
| ( <nonHumanHosts ... /> )+
</addNonHumanHosts>

nonHumanHosts

Documentation (element)

List of intervention that add new non-human hosts that have not been described in the .

nonHumanHosts

→ scenario → interventions → addNonHumanHosts → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</nonHumanHosts>

Documentation (type)

Describes a new non-human hosts that have not been described in the .

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
|   <mosqRelativeAvailabilityHuman ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <hostFecundityFactor ... /> 
</anopheles>

Documentation (type)

Descriptions of the effects of new non human hosts with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Relative availability of non-human host (ξ_i)

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqRelativeAvailabilityHuman

<mosqRelativeAvailabilityHuman
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of the population of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → hostFecundityFactor

<hostFecundityFactor
    value=double
  />

Documentation (element)

Units: Proportion

Multiplicative factor for the number of fertile eggs laid by a mosquito after biting this type of host, relative to an unprotected human.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vector trap intervention deployment

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )*
</timed>

deploy

Documentation (element)

List of timed vector trap intervention deployment

deploy

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → timed → deploy

<deploy
    time=string
    lifespan=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Lifespan

lifespan=string

Units: Steps or Days or Years

Human-specific interventions

→ scenario → interventions → human

<human>
IN THIS ORDER:
| ( <component ... /> )+
| ( <deployment ... /> )*
</human>

Documentation (element)

Encapsulates all interventions whose effects are specific to the human host: any interventions where target humans may be selected via population-coverage, age limits and sub-population membership.

Component

→ scenario → interventions → human → component

<component
    id=string
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <screen ... /> 
| |   <treatSimple ... /> 
| |   <treatPKPD ... /> 
| |   <decisionTree ... /> 
| |   <PEV ... /> 
| |   <BSV ... /> 
| |   <TBV ... /> 
| |   <ITN ... /> 
| |   <IRS ... /> 
| |   <GVI ... /> 
| | [ <recruitmentOnly ... /> ]
| |   <clearImmunity ... /> 
| [ <subPopRemoval ... /> ]
</component>

Documentation (element)

Each element describes one component: its effects, decay of the(se) effect(s), and related stuff (e.g. description of indirect decay and of usage levels).

Attributes

Component identifier

id=string

Name of component

name=string

An informal name/description for the component

screen

→ scenario → interventions → human → component → screen

<screen
    diagnostic=string
  >
IN THIS ORDER:
| ( <positive ... /> )*
| ( <negative ... /> )*
</screen>

Documentation (type)

This can be combined with MDA to achieve mass screen and treat (MSAT) or other types of mass screening intervention.

The use of the screening itself is reported (if enabled), but not the outcome. Deployment of interventions triggered by the screening may be reported, however.

Attributes

Name of diagnostic

diagnostic=string

Name of a parameterised diagnostic (see scenario/diagnostics).

positive

→ scenario → interventions → human → component → screen → positive

<positive
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → screen → negative

<negative
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

treatSimple

→ scenario → interventions → human → component → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

treatPKPD

→ scenario → interventions → human → component → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

decisionTree

→ scenario → interventions → human → component → decisionTree

<decisionTree
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</decisionTree>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Vaccines

→ scenario → interventions → human → component → PEV

<PEV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )*
| ( <phenotype ... /> )*
</PEV>

Documentation (element)

Pre-erythrocytic vaccine (PEV): prevents a proportion of infections from commencing.

Documentation (type)

Description of a vaccine's effect

Decay of effect

→ scenario → interventions → human → component → PEV → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (element)

Specification of decay of efficacy. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Variance parameter for vaccine efficacy

→ scenario → interventions → human → component → PEV → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

PD parameters for some allele / resistance phenotype

→ scenario → interventions → human → component → PEV → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
| ( <initialEfficacy ... /> )+
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

restriction

→ scenario → interventions → human → component → PEV → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (type)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → phenotype → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vaccines

→ scenario → interventions → human → component → BSV

<BSV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )*
| ( <phenotype ... /> )*
</BSV>

Documentation (element)

Blood-stage vaccine (BSV): acts as a killing factor on blood-stage parasites. Exact action depends on the within host model.

Documentation (type)

Description of a vaccine's effect

Vaccines

→ scenario → interventions → human → component → TBV

<TBV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )*
| ( <phenotype ... /> )*
</TBV>

Documentation (element)

Transmission-blocking vaccine (TBV): one minus this scales the probability of transmission to mosquitoes

Documentation (type)

Description of a vaccine's effect

Bed nets

→ scenario → interventions → human → component → ITN

<ITN>
IN THIS ORDER:
| [ <usage ... /> ]
|   <holeRate ... /> 
|   <ripRate ... /> 
|   <ripFactor ... /> 
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
|   <attritionOfNets ... /> 
| ( <anophelesParams ... /> )+
</ITN>

Documentation (element)

Description of bed-net interventions (ITNs, LLINs).

Proportion of time nets are used by humans

→ scenario → interventions → human → component → ITN → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of nets by humans, from 0 to 1.

At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing.

See also "propActing" (proportion of bits for which net acts).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Rate at which holes are made

→ scenario → interventions → human → component → ITN → holeRate

<holeRate
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: Holes per annum Min: 0

The rate at which new holes are made in nets.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Rate at which holes are enlarged

→ scenario → interventions → human → component → ITN → ripRate

<ripRate
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: Rips per existing hole per annum Min: 0

Each existing hole has a probability of being ripped bigger according to a Poisson process with this rate as (only) parameter.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Rip factor

→ scenario → interventions → human → component → ITN → ripFactor

<ripFactor
    value=double
  />

Documentation (element)

Units: none Min: 0

This factor expresses how important rips are in increasing the hole.

The hole index of a net is h + F×x where h and x are the total numbers of holes and rips respectively and F is the rip factor.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → ITN → initialInsecticide

<initialInsecticide
    mean=double
  [ SD=double ]
  [ distr=("const" or "normal") ] DEFAULT VALUE const
  />

Documentation (element)

Units: mg/m² Min: 0

Documentation (type)

A parameter with optional heterogeneity.

Optionally, a distribution ("distr") and standard of deviation ("SD") may be specified.

Attributes

mean

mean=double

The mean value.

standard deviation

SD=double

The standard deviation of variates.

Distribution

distr=("const" or "normal")

Default value: const

Decay of insecticide

→ scenario → interventions → human → component → ITN → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</insecticideDecay>

decay

Documentation (element)

Units: none

Decay curve for insecticide content of nets. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Attrition of nets

→ scenario → interventions → human → component → ITN → attritionOfNets

<attritionOfNets
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</attritionOfNets>

decay

Documentation (element)

Units: dimensionless

Specifies the rate at which nets are disposed of over time. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Humans are removed from the intervention component's sub-population on disposal (attrition) of their nets. Currently this event is not reported.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

anophelesParams

→ scenario → interventions → human → component → ITN → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <holeIndexMax ... /> ]
| EXACTLY ONE OF:
| |   <deterrency ... /> 
| |   <twoStageDeterrency ... /> 
| EXACTLY ONE OF:
| |   <preprandialKillingEffect ... /> 
| |   <preprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| |   <postprandialKillingEffect ... /> 
| |   <postprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| | [ <fecundityReduction ... /> ]
| | [ <fecundityReductionLogit ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which net acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

maximum of holed surface area that has an effect (comparable to no net)

→ scenario → interventions → human → component → ITN → anophelesParams → holeIndexMax

<holeIndexMax
    value=double
  />

Documentation (element)

Units: in same unit as holeIndex

Used by logit attacking and killing models only, holeIndexMax is a user defined maximum hole index (typically, the total surface area of a net).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency

<twoStageDeterrency>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <entering ... /> 
| |   <enteringLogit ... /> 
| EXACTLY ONE OF:
| |   <attacking ... /> 
| |   <attackingLogit ... /> 
</twoStageDeterrency>

Documentation (element)

Units: dimensionless

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

This deterrency model multiplies human attractiveness by pEnt×pAtt.

Deterrency: entering

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → entering

<entering
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless

pEnt represents the relative probability of entering due to ITNs: pEnt = exp(log(P)×p) where P is the insecticide factor and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Deterrency: entering (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → enteringLogit

<enteringLogit
    baseFactor=double
    insecticideFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: none

See parent element documentation

Insecticide factor

insecticideFactor=double

Units: none

See parent element documentation

Deterrency: attacking

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attacking

<attacking
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Deterrency: attacking (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attackingLogit

<attackingLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Pre-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Pre-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffectLogit

<preprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Post-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffectLogit

<postprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Fecundity reduction

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-B), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReductionLogit

<fecundityReductionLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-K0), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Indoor residual spraying

→ scenario → interventions → human → component → IRS

<IRS>
IN THIS ORDER:
| [ <usage ... /> ]
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
| ( <anophelesParams ... /> )+
</IRS>

Documentation (element)

Description of indoor residual spraying interventions.

Documentation (type)

Description of effect for the more complex and probably more realistic Briet model: IRS has three effects, whos strength is calculated as a function of surviving insecticide content.

Proportion of Indoor residual spraying (IRS) interventions

→ scenario → interventions → human → component → IRS → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Indoor residual spraying (IRS) interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → IRS → initialInsecticide

<initialInsecticide
    mean=double
  [ SD=double ]
  [ distr=("const" or "normal") ] DEFAULT VALUE const
  />

Documentation (element)

Units: μg/cm² Min: 0

Documentation (type)

A parameter with optional heterogeneity.

Optionally, a distribution ("distr") and standard of deviation ("SD") may be specified.

Attributes

mean

mean=double

The mean value.

standard deviation

SD=double

The standard deviation of variates.

Distribution

distr=("const" or "normal")

Default value: const

Decay of insecticide

→ scenario → interventions → human → component → IRS → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</insecticideDecay>

decay

Documentation (element)

Units: none

Decay curve for insecticide content of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Per-mosquito species parameters

→ scenario → interventions → human → component → IRS → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → IRS → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied by exp(P×log(p)) where P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction

→ scenario → interventions → human → component → IRS → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

First, we calculate K = B + P×p where B is the base (without protection) probability of death, and P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Fecundity is multiplied by (1−K) / (1−B). It is not allowed to be greater than 1. To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Generic vector intervention

→ scenario → interventions → human → component → GVI

<GVI>
IN THIS ORDER:
| [ <usage ... /> ]
|   <decay ... /> 
| ( <anophelesParams ... /> )+
</GVI>

Documentation (element)

Note that all actions of this intervention component will decay according to a single decay function. If independant decay is wanted, a separate component can be used for each action.

Proportion of generic vector interventions

→ scenario → interventions → human → component → GVI → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Generic vector interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay

→ scenario → interventions → human → component → GVI → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ increasing=boolean ] DEFAULT VALUE false
  [ initialEfficacy=double ] DEFAULT VALUE 1
  [ rho=double ]
  [ halflife_short=string ]
  [ halflife_long=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
</decay>

decay

Documentation (element)

Description of decay of all intervention effects. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact" or "plus" or "minus" or "divides" or "multiplies")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

increasing=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

initialEfficacy

initialEfficacy=double

Default value: 1

biphasic: Efficacy between 0 and 1.

rho

rho=double

biphasic: Proportion between 0 and 1, proportion of the response that is short-lived.

halflife_short

halflife_short=string

biphasic: halflife of short lived component (default to years).

halflife_long

halflife_long=string

biphasic: halflife of long lived component (default to years).

Per-mosquito species parameters

→ scenario → interventions → human → component → GVI → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <deterrency ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → GVI → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of intervention on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied this factor times survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Fecundity reduction effect

→ scenario → interventions → human → component → GVI → anophelesParams → fecundityReduction

<fecundityReduction
    value=double
  />

Documentation (element)

Min: 0

Fertility is multiplied by 1 - (fecundityReduction * decay).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Recruitment only

→ scenario → interventions → human → component → recruitmentOnly

<recruitmentOnly/>

Documentation (element)

Recruitment of a host into a sub-population.

Clear Immunity

→ scenario → interventions → human → component → clearImmunity

<clearImmunity/>

Documentation (element)

Removes all exposure-related immunitsy gained over time by hosts without removing infections (or affecting the ability to gain immunity through exposure).

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

subPopRemoval

→ scenario → interventions → human → component → subPopRemoval

<subPopRemoval
  [ onFirstBout=boolean ] DEFAULT VALUE false
  [ onFirstTreatment=boolean ] DEFAULT VALUE false
  [ onFirstInfection=boolean ] DEFAULT VALUE false
  [ afterYears=double ]
  />

Documentation (type)

ITN attrition also removes humans from sub-populations.

Attributes

Time to first episode only

onFirstBout=boolean

Default value: false

Time to first treatment only

onFirstTreatment=boolean

Default value: false

Time to first infection only

onFirstInfection=boolean

Default value: false

Remove from sub-population after

afterYears=double

Units: Years Min: 0

Deployment

→ scenario → interventions → human → deployment

<deployment
  [ name=string ]
  >
IN THIS ORDER:
| ( <component ... /> )+
| ( <condition ... /> )*
| ( <continuous ... /> )*
| ( <timed ... /> )*
</deployment>

Documentation (element)

All components deployed by this intervention are deployed to the same people (each timed or continuous deployment selects recipients and then gives each recipient all components of the intervention).

Attributes

Intervention name

name=string

Name of intervention

component

→ scenario → interventions → human → deployment → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Condition

→ scenario → interventions → human → deployment → condition

<condition
    measure=string
  [ minValue=double ]
  [ maxValue=double ]
    initialState=boolean
  />

Documentation (element)

Conditions are evaluated for the whole population, not for individual age-groups or cohorts.

This affects all types of deployment.

Attributes

Measure

measure=string

The monitoring measure to test. Not all measures are available for use.

Minimum value

minValue=double

Minimum value. If specified, the measured variable must be greater than or equal to this value for the condition to be satisfied.

Maximum value

maxValue=double

Maximum value. If specified, the measured variable must be less than or equal to this value for the condition to be satisfied.

Initial state

initialState=boolean

Whether this condition is considered true or false before updated by a survey.

Age-based (continuous) deployment

→ scenario → interventions → human → deployment → continuous

<continuous>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| ( <deploy ... /> )+
</continuous>

Documentation (element)

List of ages at which deployment takes place (through EPI, post-natal and school-based programmes, etc.).

A sub-population restriction may be added as a property of the list of continuous deployments.

restrictToSubPop

→ scenario → interventions → human → deployment → continuous → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

deploy

→ scenario → interventions → human → deployment → continuous → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
  [ minAvailability=int ]
  [ maxAvailability=int ]
    targetAgeYrs=double
  [ begin=string ]
  [ end=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Minimum ento availability

minAvailability=int

Units: percent Min: 0

Maximum ento availability

maxAvailability=int

Units: percent Min: 0

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention. Input is rounded to the nearest time step.

First time active

begin=string

Units: User defined (defauls to steps)

End step

end=string

Units: User defined (defauls to steps)

Mass (timed) deployment

→ scenario → interventions → human → deployment → timed

<timed>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| [ <cumulativeCoverage ... /> ]
| ( <deploy ... /> )+
</timed>

Documentation (element)

List of timed deployments of the intervention (that is, of deployment campaigns).

Cumulative deployment mode can be specified for all deployments in a timed list. To allow multiple cumulative deployment descriptions, the entire timed list may be repeated.

restrictToSubPop

→ scenario → interventions → human → deployment → timed → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

Cumulative coverage

→ scenario → interventions → human → deployment → timed → cumulativeCoverage

<cumulativeCoverage
    component=string
  />

Documentation (element)

Attributes

Component identifier

component=string

The identifier (short name) of the component used when selecting people.

deploy

→ scenario → interventions → human → deployment → timed → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
  [ minAvailability=int ]
  [ maxAvailability=int ]
    time=string
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ repeatStep=string ]
  [ repeatEnd=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Minimum ento availability

minAvailability=int

Units: percent Min: 0

Maximum ento availability

maxAvailability=int

Units: percent Min: 0

Time

time=string

Units: User defined (defauls to steps) Min: 0

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0

Maximum age of eligible individuals (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible individuals (defaults to 0). Input is rounded to the nearest time step.

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Description of health system.

Documentation (type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("forced" or "dynamic")
  [ scaledAnnualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Description of entomological data

Attributes

Entomology dataset name

name=string

Name of entomology data

Transmission model mode

mode=("forced" or "dynamic")

Override annual EIR

scaledAnnualEIR=double

Units: Infectious bites per adult per year

If set, the annual EIR (for all species of vector) is scaled to this level; can be omitted if not needed.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters of the transmission model

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <seasonality ... /> 
|   <mosq ... /> 
| [ <lifeCycle ... /> ]
| [ <simpleMPD ... /> ]
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial estimate of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial estimate of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial estimate of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Seasonality of transmission

→ scenario → entomology → vector → anopheles → seasonality

<seasonality
    input=("EIR")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <fourierSeries ... /> 
| |   <monthlyValues ... /> 
| |   <dailyValues ... /> 
</seasonality>

Documentation (element)

Specifies the seasonality of transmission and optionally the level of annual transmission.

Attributes

Seasonality input

input=("EIR")

Annual EIR

annualEIR=double

Units: Inoculations per adult per annum Min: 0

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries

<fourierSeries
    EIRRotateAngle=double
  >
IN THIS ORDER:
| ( <coeffic ... /> )*
</fourierSeries>

coeffic

Documentation (element)

Units: Infectious bites per adult per day

Attributes

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: Radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Pair of Fourier coefficients

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries → coeffic

<coeffic
    a=double
    b=double
  />

Documentation (element)

A pair of Fourier series coefficients. The first element specifies a1 and b1, the second a2 and b2, etc. Any number (from 0 up) of pairs may be given.

Attributes

a_n parameter of Fourier approximation to ln(EIR)

a=double

a_n parameter of Fourier approximation to ln(EIR) for some natural number n.

b_n parameter of Fourier approximation to ln(EIR)

b=double

b_n parameter of Fourier approximation to ln(EIR) for some natural number n.

List of monthly values

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues

<monthlyValues
    smoothing=("none" or "fourier")
  >
IN THIS ORDER:
| ( <value ... /> ){12,12}
</monthlyValues>

value

Documentation (element)

Description of seasonality from monthly values. Multiple smoothing methods are possible (see smoothing attribute).

List should contain twelve entries: January to December.

Attributes

Smoothing function

smoothing=("none" or "fourier")

How the monthly values are converted into a daily sequence of values:

none: no smoothing (step function)
Fourier: a Fourier series (with terms up to a2/b2) is fit to the sequence of monthly values and used to generate a smoothed list of daily values.

Monthly value

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Monthly value

List of daily values

→ scenario → entomology → vector → anopheles → seasonality → dailyValues

<dailyValues>
IN THIS ORDER:
| ( <value ... /> )+
</dailyValues>

value

Documentation (element)

Description of seasonality from daily values.

List should contain 365 entries: 1st January to 31st December.

Daily value

→ scenario → entomology → vector → anopheles → seasonality → dailyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Daily value

Mosquito feeding cycle parameters

→ scenario → entomology → vector → anopheles → mosq

<mosq
    minInfectedThreshold=double
  >
IN ANY ORDER:
|   <mosqRestDuration ... /> 
|   <extrinsicIncubationPeriod ... /> 
|   <mosqLaidEggsSameDayProportion ... /> 
|   <mosqSeekingDuration ... /> 
|   <mosqSurvivalFeedingCycleProbability ... /> 
|   <availability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <mosqProbOvipositing ... /> 
|   <mosqHumanBloodIndex ... /> 
</mosq>

Documentation (element)

Parameters describing the feeding cycle and human mosquito interaction of a single species of anopheles mosquito.

Attributes

Mininum infected threshold for mosquitos

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

Duration of the resting period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqRestDuration

<mosqRestDuration
    value=int
  />

Documentation (element)

Units: Days

name:Duration of the resting period of the vector (days);

Attributes

Input parameter value

value=int

An integer value.

Extrinsic incubation period

→ scenario → entomology → vector → anopheles → mosq → extrinsicIncubationPeriod

<extrinsicIncubationPeriod
    value=int
  />

Documentation (element)

Units: Days

name:Extrinsic incubation period (days)

Attributes

Input parameter value

value=int

An integer value.

Proportion of mosquitoes host seeking on same day as ovipositing

→ scenario → entomology → vector → anopheles → mosq → mosqLaidEggsSameDayProportion

<mosqLaidEggsSameDayProportion
    value=double
  />

Documentation (element)

Units: Proportion

Proportion of mosquitoes host seeking on same day as ovipositing

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Duration of the host-seeking period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqSeekingDuration

<mosqSeekingDuration
    value=double
  />

Documentation (element)

Units: Days

Duration of the host-seeking period of the vector (days)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito survives the feeding cycle

→ scenario → entomology → vector → anopheles → mosq → mosqSurvivalFeedingCycleProbability

<mosqSurvivalFeedingCycleProbability
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito survives the feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human availability rate heterogeneity

→ scenario → entomology → vector → anopheles → mosq → availability

<availability
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
  />

Documentation (element)

If no attributes are specified or distr="const" or CV="0" then there will be no heterogeneity.

Documentation (type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

Probability that the mosquito succesfully bites chosen host

→ scenario → entomology → vector → anopheles → mosq → mosqProbBiting

<mosqProbBiting
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito succesfully bites chosen host

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → mosq → mosqProbFindRestSite

<mosqProbFindRestSite
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito escapes host and finds a resting place after biting

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → mosq → mosqProbResting

<mosqProbResting
    mean=double
    variance=double
  />

Documentation (element)

Probability of mosquito successfully resting after finding a resting site

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of a mosquito successfully laying eggs given that it has rested

→ scenario → entomology → vector → anopheles → mosq → mosqProbOvipositing

<mosqProbOvipositing
    value=double
  />

Documentation (element)

Probability of a mosquito successfully laying eggs given that it has rested

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human blood index

→ scenario → entomology → vector → anopheles → mosq → mosqHumanBloodIndex

<mosqHumanBloodIndex
    value=double
  />

Documentation (element)

Units: Proportion

The proportion of resting mosquitoes which fed on human blood during the last feed.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mosquito life cycle parameters

→ scenario → entomology → vector → anopheles → lifeCycle

<lifeCycle
  [ estimatedLarvalResources=double ] DEFAULT VALUE 1e8
  >
IN ANY ORDER:
|   <eggStage ... /> 
|   <larvalStage ... /> 
|   <pupalStage ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</lifeCycle>

Documentation (element)

Parameters describing the life-cycle of this species of mosquito

Attributes

Estimate of larval resources

estimatedLarvalResources=double

Units: X

Default value: 1e8

Egg stage

→ scenario → entomology → vector → anopheles → lifeCycle → eggStage

<eggStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the egg stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

larvalStage

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage

<larvalStage>
</larvalStage>

daily

Documentation (type)

Parameters for the larval stage of development

Documentation (base type)

Parameters associated with a mosquito development stage.

Daily development

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage → daily

<daily
    resourceUsage=double
    effectCompetition=double
  />

Documentation (element)

Attributes

Resource usage

resourceUsage=double

Units: X

Resource usage during larval stage of development. Units are arbitrary.

Effect of competition

effectCompetition=double

Units: none

Effect of competition over resources on development.

Pupal stage

→ scenario → entomology → vector → anopheles → lifeCycle → pupalStage

<pupalStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the pupal stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → lifeCycle → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Simple Mosq-Pop-Dynamics parameters

→ scenario → entomology → vector → anopheles → simpleMPD

<simpleMPD>
IN ANY ORDER:
|   <developmentDuration ... /> 
|   <developmentSurvival ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</simpleMPD>

Documentation (element)

Parameters describing the simple mosquito population dynamics model.

This is a simpler version of the life-cycle model, requiring less parameters and with much simpler initialisation.

Duration

→ scenario → entomology → vector → anopheles → simpleMPD → developmentDuration

<developmentDuration
    value=int
  />

Documentation (element)

Units: Days Min: 1

Duration from egg laying to emergence in days.

Attributes

Input parameter value

value=int

An integer value.

Probability of survival

→ scenario → entomology → vector → anopheles → simpleMPD → developmentSurvival

<developmentSurvival
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that mosquito survives from the egg being laid to emergence, given no resouce limitations (no density constraints).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → simpleMPD → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Alternative (non-human) host paramters

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN ANY ORDER:
|   <mosqRelativeEntoAvailability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
| [ <hostFecundityFactor ... /> ]
</nonHumanHosts>

Documentation (element)

Min: 0

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of non-human host (ξ_i)

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqRelativeEntoAvailability

<mosqRelativeEntoAvailability
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of the population of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative fecundity of biting mosquitoes

→ scenario → entomology → vector → anopheles → nonHumanHosts → hostFecundityFactor

<hostFecundityFactor
    value=double
  />

Documentation (element)

Units: Proportion

Multiplicative factor for the number of fertile eggs laid by a mosquito after biting this type of host, relative to an unprotected human.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Name of this species of non human hosts (must match up with those described per anopheles section).

Population size of non-human host species

number=double

Units: Animals

Parasite genetics

<parasiteGenetics
    samplingMode=("initial" or "tracking")
  >
IN THIS ORDER:
| ( <locus ... /> )+
</parasiteGenetics>

locus

Documentation (element)

A specification of genotypes of infection parasites.

May be omitted; in this case there is no modelling of genetic differences of infections (resistance, fitness).

Attributes

samplingMode

samplingMode=("initial" or "tracking")

Locus

→ scenario → parasiteGenetics → locus

<locus
    name=string
  >
IN THIS ORDER:
| ( <allele ... /> )+
</locus>

allele

Documentation (element)

Alleles at loci can affect fitness and resistance to any number of drugs.

Attributes

Name of locus

name=string

Name of the Locus

Allele

→ scenario → parasiteGenetics → locus → allele

<allele
    name=string
    initialFrequency=double
    fitness=double
  [ hrp2_deletion=boolean ] DEFAULT VALUE false
  />

Documentation (element)

Describes an allele, or one possible genetic option of multiple at one point of variance.

Attributes

Name

name=string

Name of the allele; used to refer to it elsewhere.

Initial frequency

initialFrequency=double

Fitness factor

fitness=double

HRP2 deletion

hrp2_deletion=boolean

Default value: false

Drug parameters (PK, PD and usage)

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
|   <treatments ... /> 
|   <drugs ... /> 
</pharmacology>

Documentation (element)

Drug model parameters and drug usage parameters

Documentation (type)

A library of drug related data for the PK/PD model.

Treatments library

→ scenario → pharmacology → treatments

<treatments>
IN THIS ORDER:
| ( <schedule ... /> )+
| ( <dosages ... /> )+
</treatments>

Documentation (element)

A library of drug deployment schedules and dosages.

schedule

→ scenario → pharmacology → treatments → schedule

<schedule
    name=string
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

A schedule for the administration of drugs in a course of treatment.

Note that dose sizes are multiplied by some multiplier (see dosages) and the times of all doses may be delayed.

Attributes

Name

name=string

Name for referring to this deployment schedule

medicate

→ scenario → pharmacology → treatments → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  />

Attributes

drug

drug=string

Abbreviated name of drug compound

Drug dose (mg with multiplier)

mg=double

Units: mg per something

Quantity of drug compound in mg per something. A separate dosage table must be used when medicating, which may specify multipliers of this number based on patient age or weight.

Time of administration

hour=double

Units: Hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

dosages

→ scenario → pharmacology → treatments → dosages

<dosages
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | ( <age ... /> )+
| | ( <bodymass ... /> )+
| |   <multiply ... /> 
</dosages>

Documentation (type)

A table for selecting a dose size. There are several ways this can work: using the patient's age or body mass in a look-up table to get a multplier, or directly using body mass as the multiplier.

The doses specified in "mg" in the treatment schedule are then multiplied by this multiplier.

Attributes

Name

name=string

Name for referring to this dosage table

Look-up table (age)

→ scenario → pharmacology → treatments → dosages → age

<age
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's age.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Look-up table (weight)

→ scenario → pharmacology → treatments → dosages → bodymass

<bodymass
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's body mass.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Multiply dose

→ scenario → pharmacology → treatments → dosages → multiply

<multiply
    by=("kg")
  />

Documentation (element)

Multiply the dose by some quantity, such as patient weight.

Attributes

By what?

by=("kg")

Quantity to multiply the dose by. Only option is "kg" (patient weight in kg).

Drug library

→ scenario → pharmacology → drugs

<drugs>
IN THIS ORDER:
| ( <drug ... /> )+
</drugs>

drug

Documentation (element)

A library of drug PK/PD data.

drug

→ scenario → pharmacology → drugs → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (type)

A drug description with PK/PD parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drugs → drug → PD

<PD
  [ locus=string ]
  >
IN THIS ORDER:
| ( <phenotype ... /> )+
</PD>

phenotype

Attributes

Locus

locus=string

PD parameters for some allele / resistance phenotype

→ scenario → pharmacology → drugs → drug → PD → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

Restrict phenotype applicability to certain alleles

→ scenario → pharmacology → drugs → drug → PD → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (element)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Maximal parasite killing rate

→ scenario → pharmacology → drugs → drug → PD → phenotype → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drugs → drug → PD → phenotype → IC50

<IC50
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

If CV > 0, the IC50 is sampled from a log-normal distribution.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Slope of effect curve

→ scenario → pharmacology → drugs → drug → PD → phenotype → slope

<slope>
    double
</slope>

Documentation (element)

Units: dimensionless

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drugs → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
| EXACTLY ONE OF:
| |   <half_life ... /> 
| | IN THIS ORDER:
| | |   <k ... /> 
| | |   <m_exponent ... /> 
| [ <k_a ... /> ]
| [ <conversion ... /> ]
|   <vol_dist ... /> 
| [ <compartment2 ... /> ]
| [ <compartment3 ... /> ]
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drugs → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drugs → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate λ, calculated as λ = ln(2) / half_life. The basic form of decay is C(t) = C0 * exp(-λ*t).

Alternatively, elimination rate can be specified via k and m_exponent.

Constant associated with elimination rate (k)

→ scenario → pharmacology → drugs → drug → PK → k

<k
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

If CV > 0, k is sampled per-human from the log-normal distribution: ln N( ln(mean) - σ^2 / 2, σ^2).

Alternatively, elimination rate can be specified via half_life.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Constant associated with elimination rate (m_exponent)

→ scenario → pharmacology → drugs → drug → PK → m_exponent

<m_exponent>
    double
</m_exponent>

Documentation (element)

Units: day^-1 Min: 0

Alternatively, elimination rate can be specified via half_life.

Note that in the case of a conversion model, this applies to both the elimination and the conversion rates.

Absorption rate constant (k_a)

→ scenario → pharmacology → drugs → drug → PK → k_a

<k_a
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Min: 0

Absorption rate parameter. Not allowed for one compartment models, but required for two and three compartment models and one compartment with conversion model (for the parent drug only).

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Conversion parameters (parent drug)

→ scenario → pharmacology → drugs → drug → PK → conversion

<conversion>
IN ANY ORDER:
|   <metabolite ... /> 
|   <rate ... /> 
|   <molRatio ... /> 
|   <IC50_log_correlation ... /> 
</conversion>

Documentation (element)

Configures the parent drug in a conversion model.

To use a conversion model, the parent drug should have this section defined as well as half-life or k (direct elimination; this may be zero) and k_a (absorption rate; this may be large).

Metabolite drug (abbreviation)

→ scenario → pharmacology → drugs → drug → PK → conversion → metabolite

<metabolite>
    string
</metabolite>

Documentation (element)

The abbreviation of the metabolite drug (e.g. "DHA" or "DHA_AR").

Rate of conversion

→ scenario → pharmacology → drugs → drug → PK → conversion → rate

<rate
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Rate of conversion of parent drug to metabolite.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Molecular weight ratio

→ scenario → pharmacology → drugs → drug → PK → conversion → molRatio

<molRatio>
    double
</molRatio>

Documentation (element)

Ratio of molecular weights: molecular weight of the metabolite divided by molecular weight of the parent.

IC50 log correlation

→ scenario → pharmacology → drugs → drug → PK → conversion → IC50_log_correlation

<IC50_log_correlation>
    double
</IC50_log_correlation>

Documentation (element)

Min: 0 Max: 1

If this value is 1, samples are fully correlated: a single z-score is used to calculate both samples. If this is 0, two independent samples are used.

Values between 0 and 1 (partial correlation) are supported; in this case IC50 values are sampled such that cor(log(x), log(y)) matches this value (where x, y are parent and metabolite IC50 values).

Volume of Distribution (Vd)

→ scenario → pharmacology → drugs → drug → PK → vol_dist

<vol_dist
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution.

If CV > 0 this is sampled from a log-normal distribution.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Second compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment2

<compartment2>
IN ANY ORDER:
|   <k12 ... /> 
|   <k21 ... /> 
</compartment2>

Documentation (element)

Optional element specifying conversion parameters to- and from- a second compartment.

Absorption rate to compartment 2 (k12)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → k12

<k12
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the first periphery compartment (2).

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Absorption rate from compartment 2 (k21)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → k21

<k21
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the first periphery compartment (2) to the central compartment.

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Third compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment3

<compartment3>
IN ANY ORDER:
|   <k13 ... /> 
|   <k31 ... /> 
</compartment3>

Documentation (element)

Optional element specifying conversion parameters to- and from- a third compartment.

Absorption rate to compartment 3 (k13)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → k13

<k13
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the second periphery compartment (3).

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Absorption rate from compartment 3 (k31)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → k31

<k31
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the second periphery compartment (3) to the central compartment.

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

Diagnostic parameters

→ scenario → diagnostics

<diagnostics>
IN THIS ORDER:
| ( <diagnostic ... /> )*
</diagnostics>

diagnostic

Documentation (element)

Diagnostic model parameters

diagnostic

→ scenario → diagnostics → diagnostic

<diagnostic
    name=string
  [ units=("Other" or "Garki" or "Malariatherapy") ]
  [ mechanism=("Other" or "HRP2") ] DEFAULT VALUE Other
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterministic ... /> 
| |   <stochastic ... /> 
</diagnostic>

Attributes

Name of diagnostic

name=string

Name of this diagnostic (parameterisation). May be used elsewhere in the XML document to refer to this set of diagnostic parameters.

Parasite density units / methodology

units=("Other" or "Garki" or "Malariatherapy")

Mechanism

mechanism=("Other" or "HRP2")

Default value: Other

Deterministic detection

→ scenario → diagnostics → diagnostic → deterministic

<deterministic
    minDensity=double
  />

Documentation (element)

Specify that an artificial deterministic test is used: outcome is positive if parasite density is at least the minimum given.

Attributes

Minimum detectible density

minDensity=double

Units: parasites/microlitre Min: 0

The minimum density at which parasites can be detected. If 0, the test outcome is always positive.

Non-deterministic detection

→ scenario → diagnostics → diagnostic → stochastic

<stochastic
    dens_50=double
    specificity=double
  />

Documentation (element)

An improved model of detection which is non-deterministic, including false positive results as well as false negatives.

Some parameterisations:

Microscopy sensitivity/specificity data in Africa; Source: expert opinion — Allan Schapira dens_50 = 20.0 specificity = .75

RDT sensitivity/specificity for Plasmodium falciparum in Africa Source: Murray et al (Clinical Microbiological Reviews, Jan. 2008) dens_50 = 50.0; specificity = .942;

Attributes

Density 50

dens_50=double

Units: parasites/microlitre Min: 0

The density at which the test outcome has a 50% chance of being positive.

Specificity

specificity=double

Units: Dimensionless Min: 0 Max: 1

The probability of a positive test outcome in the absense of parasites.

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
| [ <vivax ... /> ]
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: model/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=string
  >
IN ANY ORDER:
| [ <NeonatalMortality ... /> ]
| [ <NonMalariaFevers ... /> ]
</clinical>

Documentation (type)

Attributes

Follow-up period during which recurrence is considered a treatment failure

healthSystemMemory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

Neonatal mortality parameters

→ scenario → model → clinical → NeonatalMortality

<NeonatalMortality
    diagnostic=string
  />

Attributes

Diagnostic used to parameterise model

diagnostic=string

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
| [ <prNeedTreatmentNMF ... /> ]
| [ <prNeedTreatmentMF ... /> ]
</NonMalariaFevers>

Documentation (type)

Description of the incidence of non-malaria fever. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a non-malarial fever requires treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

Availability of humans to mosquitoes relative to an adult, categorized by age group

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ]
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

Vivax model parameters

→ scenario → model → vivax

<vivax>
IN ANY ORDER:
|   <probBloodStageInfectiousToMosq ... /> 
|   <hypnozoiteRelease ... /> 
|   <bloodStageProtectionLatency ... /> 
|   <bloodStageLengthDays ... /> 
|   <clinicalEvents ... /> 
</vivax>

Documentation (element)

This describes Vivax model parameters, and is required when using the VIVAX_SIMPLE_MODEL model option.

Probability of mosquito infection

→ scenario → model → vivax → probBloodStageInfectiousToMosq

<probBloodStageInfectiousToMosq
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

The chance of a feeding mosquito becoming infected, given that the host is patent. (This may be adjusted by transmission-blocking vaccines.)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Hypnozoite releases

→ scenario → model → vivax → hypnozoiteRelease

<hypnozoiteRelease
  [ pSecondRelease=double ] DEFAULT VALUE 0
  >
IN ANY ORDER:
|   <numberHypnozoites ... /> 
|   <firstReleaseDays ... /> 
| [ <secondReleaseDays ... /> ]
</hypnozoiteRelease>

Documentation (element)

Describes the number and times of hypnozoite releases.

Documentation (type)

This element defines probabilites when and how many hypnozoites are released from the liverstage into the blood.

The gap between the start of a new brood of hypnozoites and its release are defined as follows:

latentP + latentRelapse + randomReleaseDelay

randomReleaseDelay is based on one or two lognormal distributions, which are defined in firstRelease and optionally secondRelease.

You can define 2 release distributions, which get added together and represent the probability of hypnozoites which get released before winter (first release) or after (second release).

You can omit the secondRelease element if no release to the blood happens after winter.

Attributes

latent relapse days

pSecondRelease=double

Default value: 0

Probability of a second release. If undefined it is zero.

Number of Hypnozoites

→ scenario → model → vivax → hypnozoiteRelease → numberHypnozoites

<numberHypnozoites
    max=int
    base=double
  />

Documentation (element)

numberHypnozoites calculates the number of hypnozoites in the liver stage based on a base which is between 0 and 1.

This number is random based on the following distribution and normalized:

max ∑ (base ^ n) n = 0

Attributes

max

max=int

base

base=double

firstReleaseDays

→ scenario → model → vivax → hypnozoiteRelease → firstReleaseDays

<firstReleaseDays
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
    latentRelapse=double
  />

Documentation (type)

Hypnozoites are released after a delay, calculated as: roundToTSFromDays(delay + latentRelapse)

Here, roundToTSFromDays rounds the input (in days) to the nearest timestep, delay is sampled from a log-normal, and latentRelapse is the parameter specified here.

The delay is sampled from a log-normal distribution, parameterised via the (linear) mean and CV (coefficient of variation) given here.

Documentation (base type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

latent relapse days

latentRelapse=double

Usually between 10 and 15 days.

secondReleaseDays

→ scenario → model → vivax → hypnozoiteRelease → secondReleaseDays

<secondReleaseDays
  [ CV=double ]
  [ distr=("const" or "lognormal" or "gamma") ] DEFAULT VALUE const
  [ variance=double ]
    mean=double
    latentRelapse=double
  />

Documentation (type)

Hypnozoites are released after a delay, calculated as: roundToTSFromDays(delay + latentRelapse)

Here, roundToTSFromDays rounds the input (in days) to the nearest timestep, delay is sampled from a log-normal, and latentRelapse is the parameter specified here.

The delay is sampled from a log-normal distribution, parameterised via the (linear) mean and CV (coefficient of variation) given here.

Documentation (base type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal" or "gamma")

Default value: const

Coefficient of variation

variance=double

Units: unitless

mean

mean=double

The (linear) mean value.

latent relapse days

latentRelapse=double

Usually between 10 and 15 days.

Blood stage protection latency

→ scenario → model → vivax → bloodStageProtectionLatency

<bloodStageProtectionLatency
    value=double
  />

Documentation (element)

Min: 0

The length of time after expiry of a blood-stage infection during which relapses from the same brood are supressed by the immune system.

This is rounded to the nearest time-step.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Blood stage length

→ scenario → model → vivax → bloodStageLengthDays

<bloodStageLengthDays
    scale=double
    shape=double
    distr=("weibull")
  />

Documentation (element)

Units: Days

Parameters used to sample the length of blood-stage infections from a Weibull distribution (scale parameter lambda, shape parameter k).

Documentation (type)

Parameters of a Weibull distribution.

Attributes

Scale

scale=double

The Weibull scale parameter (λ).

shape

shape=double

The Weibull shape parameter (k).

Distribution

distr=("weibull")

To allow heterogeneity, a distribution must be specified. In this case, only "weibull" is allowed.

clinicalEvents

→ scenario → model → vivax → clinicalEvents

<clinicalEvents>
IN THIS ORDER:
|   <pPrimaryInfection ... /> 
|   <pRelapseOne ... /> 
|   <pRelapseTwoPlus ... /> 
|   <pEventIsSevere ... /> 
</clinicalEvents>

Documentation (type)

This elements holds all information about probabilites for clinical events from infections and relapses.

pPrimaryInfection

→ scenario → model → vivax → clinicalEvents → pPrimaryInfection

<pPrimaryInfection
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseOne

→ scenario → model → vivax → clinicalEvents → pRelapseOne

<pRelapseOne
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseTwoPlus

→ scenario → model → vivax → clinicalEvents → pRelapseTwoPlus

<pRelapseTwoPlus
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pEventIsSevere

→ scenario → model → vivax → clinicalEvents → pEventIsSevere

<pEventIsSevere
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=string
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=string

Units: User defined (default: steps) Min: 0 Max: 20

Pre-erythrocytic latent period Can be specified in steps (e.g. 3t) or days (e.g. 15d).

parameter

→ scenario → model → parameters → parameter

<parameter
  [ name=string ]
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 45 documentation

Generated from: scenario_45.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
  [ analysisNo=int ]
    name=string
  [ wuID=int ]
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:om="http://openmalaria.org/schema/scenario_45"
    xsi:schemaLocation="http://openmalaria.org/schema/scenario_45 scenario_45.xsd"
  >
IN ANY ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entomology ... /> 
| [ <parasiteGenetics ... /> ]
| [ <pharmacology ... /> ]
| [ <diagnostics ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Name of intervention

Work unit identifier

wuID=int

Units: Number

Work unit ID. Obselete and no longer required.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Description of demography

Attributes

Name of demography data

name=string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Years Min: 0 Max: 100

Maximum age of simulated humans in years

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

list of age groups included in demography

Documentation (type)

list of age groups included in demography or surveys

Attributes

Lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Units: Percentage Min: 0 Max: 100

Percentage of human population in age group

Upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ startDate=string ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
| [ <cohorts ... /> ]
</monitoring>

Documentation (element)

Description of surveys

Attributes

Name of monitoring settings

name=string

Name of monitoring settings

Start of monitoring

startDate=string

continuous

→ scenario → monitoring → continuous

<continuous
    period=string
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Delay between reports

period=string

Units: User defined (default: steps)

Delay between reports; typically one time step but can be greater. Can be specified in steps (e.g. 1t) or days (e.g. 5d).

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions
  [ onlyNewEpisode=boolean ] DEFAULT VALUE false
  >
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See model/mon/OutputMeasures.h for a list of supported outputs. Should also be on the wiki.

Attributes

Report only for new cases

onlyNewEpisode=boolean

Default value: false

option

→ scenario → monitoring → SurveyOptions → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  [ outputNumber=int ]
  [ byAge=boolean ]
  [ byCohort=boolean ]
  [ bySpecies=boolean ]
  [ byGenotype=boolean ]
  [ byDrugType=boolean ]
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Number identifying measure in output

outputNumber=int

Report by age category

byAge=boolean

Report by cohort

byCohort=boolean

Report by mosquito species

bySpecies=boolean

Report by parasite genotype

byGenotype=boolean

Report by drug type

byDrugType=boolean

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
  [ detectionLimit=double ]
  [ diagnostic=string ]
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/microlitre Min: 0

Deprecated: limit above which a human's infection is reported as patent. Alternative: do not specify this; instead specify "diagnostic".

Name of monitoring diagnostic

diagnostic=string

Name of a parameterised diagnostic to use in surveys (see scenario/diagnostics).

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime
  [ repeatStep=string ]
  [ repeatEnd=string ]
  [ reported=boolean ] DEFAULT VALUE true
  >
    string
</surveyTime>

Documentation (element)

Units: User defined (defaults to steps) Min: 0

The simulation ends immediately after the last survey is taken.

Attributes

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

reported

reported=boolean

Default value: true

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Cohorts

→ scenario → monitoring → cohorts

<cohorts>
IN THIS ORDER:
| ( <subPop ... /> )+
</cohorts>

subPop

Documentation (element)

Allows the configuration of multiple cohorts (output segregated according to membership within specific sub-populations).

If this element is omitted, monitoring surveys cover the entire simulated human population.

It does not affect the "continuous" outputs (these never take cohorts into account).

Sub-population

→ scenario → monitoring → cohorts → subPop

<subPop
    id=string
    number=integer
  />

Documentation (element)

In the output file, the output set is identified by multiplying this number by 1000 then adding it to the age group column.

Attributes

Sub-population identifier

id=string

Textual identifier for the sub-population (i.e. for an intervention component, since sub-populations are defined as the hosts an intervention component is deployed to).

Sub-population number

number=integer

Units: dimensionless Min: 1 Max: 2097152

Number identifying a sub-population; used to define identifiers of output sets. This number must be a power of 2 (i.e. 1, 2, 4, 8, ...). See documentation of subPop element.

Preventative interventions

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfections ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <vectorPop ... /> ]
| [ <vectorTrap ... /> ]
| [ <nonHumanHostsModifications ... /> ]
| [ <addNonHumanHosts ... /> ]
| [ <human ... /> ]
</interventions>

Documentation (element)

Attributes

Name of intervention set

name=string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeHS>

timedDeployment

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeHS → timedDeployment

<timedDeployment
    time=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timedDeployment>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</uncomplicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

multiple

→ scenario → interventions → human → component → decisionTree → multiple

<multiple
  [ name=string ]
  >
EXACTLY ONE OF:
| ( <caseType ... /> )*
| ( <diagnostic ... /> )*
| ( <fever ... /> )*
| ( <random ... /> )*
| ( <age ... /> )*
| ( <treatPKPD ... /> )*
| [ <treatSimple ... /> ]
| ( <deploy ... /> )*
| ( <report ... /> )*
</multiple>

Documentation (type)

A special node allowing multiple sub-trees to be evaluated.

This is different from an ordinary decision tree node in that:

a) multiple types of child can occur simultaneously (e.g. multiple types of treatment or treatment plus a 'random' sub-tree)

b) the 'noTreatment' and 'treatFailure' nodes are not allowed

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → multiple → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

firstLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → firstLine

<firstLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</firstLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

secondLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → secondLine

<secondLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</secondLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

positive

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

fever

→ scenario → interventions → human → component → decisionTree → fever

<fever
  [ name=string ]
    lookBack=string
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</fever>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Number of days to look back for fevers. This must be less than or equal to the healthsystem memory parameter. In general, this should be less than or equal to the repeatStep in MSAT with contiuous deployment

lookBack=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

positive

→ scenario → interventions → human → component → decisionTree → multiple → fever → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

outcome

→ scenario → interventions → human → component → decisionTree → multiple → random → outcome

<outcome
  [ name=string ]
    p=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</outcome>

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Probability

p=double

Units: None Min: 0 Max: 1

Probability of selecting this outcome. The sum of probabilities across all outcomes must be 1.

age

→ scenario → interventions → human → component → decisionTree → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Age range

→ scenario → interventions → human → component → decisionTree → multiple → age → age

<age
  [ name=string ]
    lb=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</age>

Documentation (element)

Describes a branch, selected for patients of a certain age.

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Lower bound (inclusive)

lb=double

Min: 0

noTreatment

→ scenario → interventions → human → component → decisionTree → noTreatment

<noTreatment
  [ name=string ]
  />

Documentation (type)

An end node doing nothing. This exists to explicitly state that no treatment happens and to prevent trees from accidentally being left incomplete.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

report

→ scenario → interventions → human → component → decisionTree → report

<report
  [ name=string ]
  [ outputNumber=int ] DEFAULT VALUE 0
  />

Documentation (type)

This increments measure 80 (nCMDTReport) by one every time this node is visited. This can be useful to report the results of mass test and treat interventions using the decision tree.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Delay (hours)

outputNumber=int

Default value: 0

treatFailure

→ scenario → interventions → human → component → decisionTree → treatFailure

<treatFailure
  [ name=string ]
  />

Documentation (type)

An end node which reports treatment but does not change parasitalogical status. This allows correct labelling of second-line cases.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → decisionTree → multiple → fever → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

negative

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

fever

→ scenario → interventions → human → component → decisionTree → multiple → fever

<fever
  [ name=string ]
    lookBack=string
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</fever>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Number of days to look back for fevers. This must be less than or equal to the healthsystem memory parameter. In general, this should be less than or equal to the repeatStep in MSAT with contiuous deployment

lookBack=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

random

→ scenario → interventions → human → component → decisionTree → multiple → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

age

→ scenario → interventions → human → component → decisionTree → multiple → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → multiple → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → multiple → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → multiple → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

report

→ scenario → interventions → human → component → decisionTree → multiple → report

<report
  [ name=string ]
  [ outputNumber=int ] DEFAULT VALUE 0
  />

Documentation (type)

This increments measure 80 (nCMDTReport) by one every time this node is visited. This can be useful to report the results of mass test and treat interventions using the decision tree.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Delay (hours)

outputNumber=int

Default value: 0

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</complicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: Days Min: 0 Max: unbounded

Maximum number of timesteps (including first day of case) that an individual with an uncomplicated case of malaria will remember he/she was sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial or non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of a complicated or severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
  [ name=string ]
  [ useDiagnosticUC=boolean ] DEFAULT VALUE false
  >
IN ANY ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <treatmentActions ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
</ImmediateOutcomes>

Documentation (type)

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Name of case management parameterisation

name=string

Name of health system

useDiagnosticUC

useDiagnosticUC=boolean

Default value: false

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Description of drug regimen.

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Artemisinine based combination therapy

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Quinine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0 Max: 1name:P(self-treat)

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Effectiveness of treatment for non-compliant patients

treatmentActions

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions

<treatmentActions>
IN ANY ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
</treatmentActions>

CQ
SP
AQ
SPAQ
ACT
QN

CQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ

<CQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</CQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

deploy

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy

<deploy
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ p=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| ( <component ... /> )+
</deploy>

component

Attributes

Maximum age of eligible humans

maxAge=double

Units: Years Min: 0

Maximum age of eligible humans (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible humans

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible humans (defaults to 0). Input is rounded to the nearest time step.

Probability of delivery to eligible humans

p=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Probability of this list of components being deployed, given that other constraints are met.

component

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Prophylactic treatment

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere → clearInfections

<clearInfections
    timesteps=string
    stage=("liver" or "blood" or "both")
  />

Documentation (element)

Attributes

Length of effect

timesteps=string

Units: User defined (defaults to steps)

Target stage

stage=("liver" or "blood" or "both")

SP

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SP

<SP
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SP>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

AQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → AQ

<AQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</AQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

SPAQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SPAQ

<SPAQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SPAQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

ACT

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → ACT

<ACT
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</ACT>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

QN

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → QN

<QN
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</QN>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

Probability that human is incompatible with liver-stage drug treatment

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pHumanCannotReceive

<pHumanCannotReceive
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that a human is determined to be unable to receive liver-stage drug treatment. Treatment is neither reported or given for such humans.

This is sampled once per human at birth.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Ignore liver-stage drug treatment incompatibility

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → ignoreCannotReceive

<ignoreCannotReceive
    value=boolean
  />

Documentation (element)

If true, ignore pHumanCannotReceive and consider all humans eligible for treatment; if false (or not specified), do not treat those demed incompatible with liver-stage drug treatment.

The point of this is that pHumanCannotReceive cannot be altered by changeHS interventions, but this property can be.

Attributes

Input parameter value

value=boolean

A boolean value.

Prob use in UC case

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pUseUncomplicated

<pUseUncomplicated
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

This feature is deprecated; it is suggested to use the "simple treatment" feature configured to clear liver-stage parasites, leaving this option unset or zero.

Chance of liver-stage drug treatment being used for routine treatment of an uncomplicated case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Effectiveness

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → effectivenessOnUse

<effectivenessOnUse
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that liver-stage drug treatment is effective.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

DecisionTree5Day

<DecisionTree5Day
  [ name=string ]
  >
IN ANY ORDER:
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
|   <treeUCOfficial ... /> 
|   <treeUCSelfTreat ... /> 
|   <cureRateSevere ... /> 
|   <treatmentSevere ... /> 
</DecisionTree5Day>

Documentation (type)

Besides greater flexibility, this allows treatment via PK/PD models.

Attributes

Name of case management parameterisation

name=string

Name of health system

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → DecisionTree5Day → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → DecisionTree5Day → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

treeUCOfficial

→ scenario → healthSystem → DecisionTree5Day → treeUCOfficial

<treeUCOfficial
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</treeUCOfficial>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treeUCSelfTreat

→ scenario → healthSystem → DecisionTree5Day → treeUCSelfTreat

<treeUCSelfTreat
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</treeUCSelfTreat>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Cure rate (severe cases)

→ scenario → healthSystem → DecisionTree5Day → cureRateSevere

<cureRateSevere
    value=double
  />

Documentation (element)

Min: 0 Max: 1

The probability of clearing parasites given access to appropriate (hospital) care, for a severe case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

treatmentSevere

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere

<treatmentSevere
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</treatmentSevere>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Case fatality rate for inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: Dimensionless

List of age-specific probabilities of sequelae in inpatients, during a severe bout of malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeEIR>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeEIR → timedDeployment

<timedDeployment
    eipDuration=int
    time=string
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timedDeployment>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Time

time=string

Units: User defined (defauls to steps) Min: 0

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=string ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=string

Units: User defined (default: steps) Min: 0

Default value: 0

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=string
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time of start

time=string

Units: User defined (defauls to steps) Min: 0

Insert R_0 case

<insertR_0Case
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</insertR_0Case>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → insertR_0Case → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Uninfect vectors

<uninfectVectors
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</uninfectVectors>

timedDeployment

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → uninfectVectors → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Vector population intervention

→ scenario → interventions → vectorPop

<vectorPop>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorPop>

intervention

Documentation (element)

Units: List of elements

A list of parameterisations of generic vector host-inspecific interventions.

intervention

→ scenario → interventions → vectorPop → intervention

<intervention
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

Units: List of elements

An intervention which may have various effects on the vector populations as a whole. (Not host specific.)

Multiple instances of this intervention class are allowed (multiple parameterisations, not just deployments).

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → vectorPop → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → vectorPop → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <seekingDeathRateIncrease ... /> ]
| [ <probDeathOvipositing ... /> ]
| [ <emergenceReduction ... /> ]
| [ <probAdditionalDeathSugarFeeding ... /> ]
</anopheles>

Documentation (type)

Units: dimensionless Min: 0 Max: 1

Descriptions of the effects of vector interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Proportional increase in deaths while host searching

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease

<seekingDeathRateIncrease
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</seekingDeathRateIncrease>

decay

Documentation (element)

Units: dimensionless

Describe an effect on the increase in the death rate while host seeking (mu_vA) due to this intervention.

Enter the rate increase (i.e. if rate increases to 120% of normal, give 0.2). New death rate while seeking is old × (1 + increase) where increase is this factor given. Must have increas ≥ -1.

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

complement=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

Proportion ovipositing mosquitoes killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing

<probDeathOvipositing
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probDeathOvipositing>

decay

Documentation (element)

Units: dimensionless

Describe an effect of increased mortality while ovipositing due to this intervention. Enter the probability of dying due to this intervention.

Attributes

Initial probability of killing

initial=double

Units: dimensionless Min: 0 Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

complement=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

Proportion of emerging pupa killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction

<emergenceReduction
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</emergenceReduction>

decay

Documentation (element)

Units: dimensionless

Describe an effect on emergence of pupa into adults: this value is the proportion of emerging pupa which are killed by this intervention.

Attributes

Initial proportion reduction

initial=double

Units: dimensionless Min: -inf Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

complement=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

Probability of death while host searching as a result of feeding on a sugar bait (used to dynamically adjust mu_vA)

→ scenario → interventions → vectorPop → intervention → description → anopheles → probAdditionalDeathSugarFeeding

<probAdditionalDeathSugarFeeding
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probAdditionalDeathSugarFeeding>

decay

Documentation (element)

Units: dimensionless

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probAdditionalDeathSugarFeeding → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

complement=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

Vector population intervention deployment

→ scenario → interventions → vectorPop → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

deploy

→ scenario → interventions → vectorPop → intervention → timed → deploy

<deploy
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Baited trap

→ scenario → interventions → vectorTrap

<vectorTrap>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorTrap>

intervention

Documentation (element)

intervention

→ scenario → interventions → vectorTrap → intervention

<intervention
  [ name=string ]
  >
IN THIS ORDER:
| ( <description ... /> )+
| [ <timed ... /> ]
</intervention>

Documentation (type)

Attributes

Descriptive name for type of trap

name=string

Optional name for this type of trap

Description

→ scenario → interventions → vectorTrap → intervention → description

<description
    mosquito=string
  >
IN THIS ORDER:
|   <relativeAvailability ... /> 
|   <decayOfAvailability ... /> 
</description>

Documentation (element)

Parameters associated with a vector trap intervention, per mosquito species.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Initial relative availability

→ scenario → interventions → vectorTrap → intervention → description → relativeAvailability

<relativeAvailability
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: inf

Describes the availiability of a trap to a host-seeking mosquito relative to an average unprotected adult.

I.e. if this parameter is 2, then each trap will on average attract twice as many mosquitoes as unprotected adults.

This is the initial availability; it may decay towards zero depending on the configured decay function.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay of availability

→ scenario → interventions → vectorTrap → intervention → description → decayOfAvailability

<decayOfAvailability
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (element)

Describes how availability decays to zero.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

complement=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

Vector trap intervention deployment

→ scenario → interventions → vectorTrap → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )*
</timed>

deploy

Documentation (element)

List of timed vector trap intervention deployment

deploy

→ scenario → interventions → vectorTrap → intervention → timed → deploy

<deploy
    time=string
    ratioToHumans=double
    lifespan=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Ratio to humans

ratioToHumans=double

Min: 0 Max: inf

The number of traps deployed, by this deployment, per adult human. E.g. if there are currently 100 traps and 1000 humans, then a ratio of 0.1 will increase the number of traps to 200.

Lifespan

lifespan=string

Units: Steps or Days or Years

nonHumanHostsModifications

→ scenario → interventions → nonHumanHostsModifications

<nonHumanHostsModifications>
IN THIS ORDER:
| ( <intervention ... /> )+
</nonHumanHostsModifications>

intervention

Documentation (element)

List of interventions that modify parameters of non-human hosts described in the .

intervention

→ scenario → interventions → nonHumanHostsModifications → intervention

<intervention
    name=string
    nonHumanHostsName=string
  >
IN THIS ORDER:
|   <decay ... /> 
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

This intervention modifies parameters of non-human hosts described in the section of the input scenario file.

The intervention is described by 5 parameters that define the change in each of non-human host parameters:

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

Name of intervention

nonHumanHostsName=string

Name of intervention (e.g. larviciding, sugar bait).

decay

→ scenario → interventions → nonHumanHostsModifications → intervention → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

complement=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

description

→ scenario → interventions → nonHumanHostsModifications → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <availabilityReduction ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
| [ <restingKillingEffect ... /> ]
| [ <fecundityReduction ... /> ]
</anopheles>

Documentation (type)

Descriptions of the effects of non human hosts interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

availabilityReduction

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → availabilityReduction

<availabilityReduction
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

preprandialKillingEffect

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

postprandialKillingEffect

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

restingKillingEffect

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → restingKillingEffect

<restingKillingEffect
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

fecundityReduction

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → fecundityReduction

<fecundityReduction
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

Vector population intervention deployment

→ scenario → interventions → nonHumanHostsModifications → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

addNonHumanHosts

<addNonHumanHosts>
IN THIS ORDER:
| ( <nonHumanHosts ... /> )+
</addNonHumanHosts>

nonHumanHosts

Documentation (element)

List of intervention that add new non-human hosts that have not been described in the .

nonHumanHosts

→ scenario → interventions → addNonHumanHosts → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</nonHumanHosts>

Documentation (type)

Describes a new non-human hosts that have not been described in the .

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
|   <mosqRelativeAvailabilityHuman ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <hostFecundityFactor ... /> 
</anopheles>

Documentation (type)

Descriptions of the effects of new non human hosts with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Relative availability of non-human host (ξ_i)

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqRelativeAvailabilityHuman

<mosqRelativeAvailabilityHuman
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of the population of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → hostFecundityFactor

<hostFecundityFactor
    value=double
  />

Documentation (element)

Units: Proportion

Multiplicative factor for the number of fertile eggs laid by a mosquito after biting this type of host, relative to an unprotected human.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vector trap intervention deployment

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )*
</timed>

deploy

Documentation (element)

List of timed vector trap intervention deployment

deploy

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → timed → deploy

<deploy
    time=string
    lifespan=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Lifespan

lifespan=string

Units: Steps or Days or Years

Human-specific interventions

→ scenario → interventions → human

<human>
IN THIS ORDER:
| ( <component ... /> )+
| ( <deployment ... /> )*
</human>

Documentation (element)

Encapsulates all interventions whose effects are specific to the human host: any interventions where target humans may be selected via population-coverage, age limits and sub-population membership.

Component

→ scenario → interventions → human → component

<component
    id=string
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <screen ... /> 
| |   <treatSimple ... /> 
| |   <treatPKPD ... /> 
| |   <decisionTree ... /> 
| |   <PEV ... /> 
| |   <BSV ... /> 
| |   <TBV ... /> 
| |   <ITN ... /> 
| |   <IRS ... /> 
| |   <GVI ... /> 
| | [ <recruitmentOnly ... /> ]
| |   <clearImmunity ... /> 
| [ <subPopRemoval ... /> ]
</component>

Documentation (element)

Each element describes one component: its effects, decay of the(se) effect(s), and related stuff (e.g. description of indirect decay and of usage levels).

Attributes

Component identifier

id=string

Name of component

name=string

An informal name/description for the component

screen

→ scenario → interventions → human → component → screen

<screen
    diagnostic=string
  >
IN THIS ORDER:
| ( <positive ... /> )*
| ( <negative ... /> )*
</screen>

Documentation (type)

This can be combined with MDA to achieve mass screen and treat (MSAT) or other types of mass screening intervention.

The use of the screening itself is reported (if enabled), but not the outcome. Deployment of interventions triggered by the screening may be reported, however.

Attributes

Name of diagnostic

diagnostic=string

Name of a parameterised diagnostic (see scenario/diagnostics).

positive

→ scenario → interventions → human → component → screen → positive

<positive
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → screen → negative

<negative
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

treatSimple

→ scenario → interventions → human → component → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

treatPKPD

→ scenario → interventions → human → component → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

decisionTree

→ scenario → interventions → human → component → decisionTree

<decisionTree
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <fever ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
| ( <report ... /> )+
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
| ( <treatSimple ... /> )+
| ( <deploy ... /> )+
</decisionTree>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Vaccines

→ scenario → interventions → human → component → PEV

<PEV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )*
| ( <phenotype ... /> )*
</PEV>

Documentation (element)

Pre-erythrocytic vaccine (PEV): prevents a proportion of infections from commencing.

Documentation (type)

Description of a vaccine's effect

Decay of effect

→ scenario → interventions → human → component → PEV → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (element)

Specification of decay of efficacy. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

complement=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

Variance parameter for vaccine efficacy

→ scenario → interventions → human → component → PEV → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

PD parameters for some allele / resistance phenotype

→ scenario → interventions → human → component → PEV → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
| ( <initialEfficacy ... /> )+
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

restriction

→ scenario → interventions → human → component → PEV → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (type)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → phenotype → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vaccines

→ scenario → interventions → human → component → BSV

<BSV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )*
| ( <phenotype ... /> )*
</BSV>

Documentation (element)

Blood-stage vaccine (BSV): acts as a killing factor on blood-stage parasites. Exact action depends on the within host model.

Documentation (type)

Description of a vaccine's effect

Vaccines

→ scenario → interventions → human → component → TBV

<TBV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )*
| ( <phenotype ... /> )*
</TBV>

Documentation (element)

Transmission-blocking vaccine (TBV): one minus this scales the probability of transmission to mosquitoes

Documentation (type)

Description of a vaccine's effect

Bed nets

→ scenario → interventions → human → component → ITN

<ITN>
IN THIS ORDER:
| [ <usage ... /> ]
|   <holeRate ... /> 
|   <ripRate ... /> 
|   <ripFactor ... /> 
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
|   <attritionOfNets ... /> 
| ( <anophelesParams ... /> )+
</ITN>

Documentation (element)

Description of bed-net interventions (ITNs, LLINs).

Proportion of time nets are used by humans

→ scenario → interventions → human → component → ITN → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of nets by humans, from 0 to 1.

At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing.

See also "propActing" (proportion of bits for which net acts).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Rate at which holes are made

→ scenario → interventions → human → component → ITN → holeRate

<holeRate
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: Holes per annum Min: 0

The rate at which new holes are made in nets.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

The (linear) coefficient of variation. This value must be specified when a (non-constant) distribution is used. Note that specifying CV="0" has the same effect as distr="const" and disables sampling of this parameter, even if distr is not "const".

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Rate at which holes are enlarged

→ scenario → interventions → human → component → ITN → ripRate

<ripRate
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: Rips per existing hole per annum Min: 0

Each existing hole has a probability of being ripped bigger according to a Poisson process with this rate as (only) parameter.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Rip factor

→ scenario → interventions → human → component → ITN → ripFactor

<ripFactor
    value=double
  />

Documentation (element)

Units: none Min: 0

This factor expresses how important rips are in increasing the hole.

The hole index of a net is h + F×x where h and x are the total numbers of holes and rips respectively and F is the rip factor.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → ITN → initialInsecticide

<initialInsecticide
    mean=double
  [ SD=double ]
  [ distr=("const" or "normal") ] DEFAULT VALUE const
  />

Documentation (element)

Units: mg/m² Min: 0

Documentation (type)

A parameter with optional heterogeneity.

Optionally, a distribution ("distr") and standard of deviation ("SD") may be specified.

Attributes

mean

mean=double

The mean value.

standard deviation

SD=double

The standard deviation of variates.

Distribution

distr=("const" or "normal")

Default value: const

Decay of insecticide

→ scenario → interventions → human → component → ITN → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (element)

Units: none

Decay curve for insecticide content of nets. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

complement=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

Attrition of nets

→ scenario → interventions → human → component → ITN → attritionOfNets

<attritionOfNets
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (element)

Units: dimensionless

Specifies the rate at which nets are disposed of over time. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Humans are removed from the intervention component's sub-population on disposal (attrition) of their nets. Currently this event is not reported.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

complement=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

anophelesParams

→ scenario → interventions → human → component → ITN → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <holeIndexMax ... /> ]
| EXACTLY ONE OF:
| |   <deterrency ... /> 
| |   <twoStageDeterrency ... /> 
| EXACTLY ONE OF:
| |   <preprandialKillingEffect ... /> 
| |   <preprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| |   <postprandialKillingEffect ... /> 
| |   <postprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| | [ <fecundityReduction ... /> ]
| | [ <fecundityReductionLogit ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which net acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

maximum of holed surface area that has an effect (comparable to no net)

→ scenario → interventions → human → component → ITN → anophelesParams → holeIndexMax

<holeIndexMax
    value=double
  />

Documentation (element)

Units: in same unit as holeIndex

Used by logit attacking and killing models only, holeIndexMax is a user defined maximum hole index (typically, the total surface area of a net).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency

<twoStageDeterrency>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <entering ... /> 
| |   <enteringLogit ... /> 
| EXACTLY ONE OF:
| |   <attacking ... /> 
| |   <attackingLogit ... /> 
</twoStageDeterrency>

Documentation (element)

Units: dimensionless

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

This deterrency model multiplies human attractiveness by pEnt×pAtt.

Deterrency: entering

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → entering

<entering
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless

pEnt represents the relative probability of entering due to ITNs: pEnt = exp(log(P)×p) where P is the insecticide factor and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Deterrency: entering (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → enteringLogit

<enteringLogit
    baseFactor=double
    insecticideFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: none

See parent element documentation

Insecticide factor

insecticideFactor=double

Units: none

See parent element documentation

Deterrency: attacking

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attacking

<attacking
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Deterrency: attacking (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attackingLogit

<attackingLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Pre-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Pre-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffectLogit

<preprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Post-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffectLogit

<postprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Fecundity reduction

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-B), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReductionLogit

<fecundityReductionLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-K0), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Indoor residual spraying

→ scenario → interventions → human → component → IRS

<IRS>
IN THIS ORDER:
| [ <usage ... /> ]
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
| ( <anophelesParams ... /> )+
</IRS>

Documentation (element)

Description of indoor residual spraying interventions.

Documentation (type)

Description of effect for the more complex and probably more realistic Briet model: IRS has three effects, whos strength is calculated as a function of surviving insecticide content.

Proportion of Indoor residual spraying (IRS) interventions

→ scenario → interventions → human → component → IRS → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Indoor residual spraying (IRS) interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → IRS → initialInsecticide

<initialInsecticide
    mean=double
  [ SD=double ]
  [ distr=("const" or "normal") ] DEFAULT VALUE const
  />

Documentation (element)

Units: μg/cm² Min: 0

Documentation (type)

A parameter with optional heterogeneity.

Optionally, a distribution ("distr") and standard of deviation ("SD") may be specified.

Attributes

mean

mean=double

The mean value.

standard deviation

SD=double

The standard deviation of variates.

Distribution

distr=("const" or "normal")

Default value: const

Decay of insecticide

→ scenario → interventions → human → component → IRS → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (element)

Units: none

Decay curve for insecticide content of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

complement=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

Per-mosquito species parameters

→ scenario → interventions → human → component → IRS → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → IRS → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied by exp(P×log(p)) where P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction

→ scenario → interventions → human → component → IRS → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

First, we calculate K = B + P×p where B is the base (without protection) probability of death, and P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Fecundity is multiplied by (1−K) / (1−B). It is not allowed to be greater than 1. To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Generic vector intervention

→ scenario → interventions → human → component → GVI

<GVI>
IN THIS ORDER:
| [ <usage ... /> ]
|   <decay ... /> 
| ( <anophelesParams ... /> )+
</GVI>

Documentation (element)

Note that all actions of this intervention component will decay according to a single decay function. If independant decay is wanted, a separate component can be used for each action.

Proportion of generic vector interventions

→ scenario → interventions → human → component → GVI → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Generic vector interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay

→ scenario → interventions → human → component → GVI → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (element)

Description of decay of all intervention effects. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

L

complement=boolean

Units: User-defined (defaults to years) Min: 0

Default value: false

Per-mosquito species parameters

→ scenario → interventions → human → component → GVI → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <deterrency ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → GVI → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of intervention on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied this factor times survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Fecundity reduction effect

→ scenario → interventions → human → component → GVI → anophelesParams → fecundityReduction

<fecundityReduction
    value=double
  />

Documentation (element)

Min: 0

Fertility is multiplied by 1 - (fecundityReduction * decay).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Recruitment only

→ scenario → interventions → human → component → recruitmentOnly

<recruitmentOnly/>

Documentation (element)

Recruitment of a host into a sub-population.

Clear Immunity

→ scenario → interventions → human → component → clearImmunity

<clearImmunity/>

Documentation (element)

Removes all exposure-related immunitsy gained over time by hosts without removing infections (or affecting the ability to gain immunity through exposure).

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

subPopRemoval

→ scenario → interventions → human → component → subPopRemoval

<subPopRemoval
  [ onFirstBout=boolean ] DEFAULT VALUE false
  [ onFirstTreatment=boolean ] DEFAULT VALUE false
  [ onFirstInfection=boolean ] DEFAULT VALUE false
  [ afterYears=double ]
  />

Documentation (type)

ITN attrition also removes humans from sub-populations.

Attributes

Time to first episode only

onFirstBout=boolean

Default value: false

Time to first treatment only

onFirstTreatment=boolean

Default value: false

Time to first infection only

onFirstInfection=boolean

Default value: false

Remove from sub-population after

afterYears=double

Units: Years Min: 0

Deployment

→ scenario → interventions → human → deployment

<deployment
  [ name=string ]
  >
IN THIS ORDER:
| ( <component ... /> )+
| ( <condition ... /> )*
| ( <continuous ... /> )*
| ( <timed ... /> )*
</deployment>

Documentation (element)

All components deployed by this intervention are deployed to the same people (each timed or continuous deployment selects recipients and then gives each recipient all components of the intervention).

Attributes

Intervention name

name=string

Name of intervention

component

→ scenario → interventions → human → deployment → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Condition

→ scenario → interventions → human → deployment → condition

<condition
    measure=string
  [ minValue=double ]
  [ maxValue=double ]
    initialState=boolean
  />

Documentation (element)

Conditions are evaluated for the whole population, not for individual age-groups or cohorts.

This affects all types of deployment.

Attributes

Measure

measure=string

The monitoring measure to test. Not all measures are available for use.

Minimum value

minValue=double

Minimum value. If specified, the measured variable must be greater than or equal to this value for the condition to be satisfied.

Maximum value

maxValue=double

Maximum value. If specified, the measured variable must be less than or equal to this value for the condition to be satisfied.

Initial state

initialState=boolean

Whether this condition is considered true or false before updated by a survey.

Age-based (continuous) deployment

→ scenario → interventions → human → deployment → continuous

<continuous>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| ( <deploy ... /> )+
</continuous>

Documentation (element)

List of ages at which deployment takes place (through EPI, post-natal and school-based programmes, etc.).

A sub-population restriction may be added as a property of the list of continuous deployments.

restrictToSubPop

→ scenario → interventions → human → deployment → continuous → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

deploy

→ scenario → interventions → human → deployment → continuous → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    targetAgeYrs=double
  [ begin=string ]
  [ end=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention. Input is rounded to the nearest time step.

First time active

begin=string

Units: User defined (defauls to steps)

End step

end=string

Units: User defined (defauls to steps)

Mass (timed) deployment

→ scenario → interventions → human → deployment → timed

<timed>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| [ <cumulativeCoverage ... /> ]
| ( <deploy ... /> )+
</timed>

Documentation (element)

List of timed deployments of the intervention (that is, of deployment campaigns).

Cumulative deployment mode can be specified for all deployments in a timed list. To allow multiple cumulative deployment descriptions, the entire timed list may be repeated.

restrictToSubPop

→ scenario → interventions → human → deployment → timed → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

Cumulative coverage

→ scenario → interventions → human → deployment → timed → cumulativeCoverage

<cumulativeCoverage
    component=string
  />

Documentation (element)

Attributes

Component identifier

component=string

The identifier (short name) of the component used when selecting people.

deploy

→ scenario → interventions → human → deployment → timed → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    time=string
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ repeatStep=string ]
  [ repeatEnd=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Time

time=string

Units: User defined (defauls to steps) Min: 0

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0

Maximum age of eligible individuals (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible individuals (defaults to 0). Input is rounded to the nearest time step.

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Description of health system.

Documentation (type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("forced" or "dynamic")
  [ scaledAnnualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Description of entomological data

Attributes

Entomology dataset name

name=string

Name of entomology data

Transmission model mode

mode=("forced" or "dynamic")

Override annual EIR

scaledAnnualEIR=double

Units: Infectious bites per adult per year

If set, the annual EIR (for all species of vector) is scaled to this level; can be omitted if not needed.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters of the transmission model

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <seasonality ... /> 
|   <mosq ... /> 
| [ <lifeCycle ... /> ]
| [ <simpleMPD ... /> ]
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial estimate of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial estimate of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial estimate of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Seasonality of transmission

→ scenario → entomology → vector → anopheles → seasonality

<seasonality
    input=("EIR")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <fourierSeries ... /> 
| |   <monthlyValues ... /> 
| |   <dailyValues ... /> 
</seasonality>

Documentation (element)

Specifies the seasonality of transmission and optionally the level of annual transmission.

Attributes

Seasonality input

input=("EIR")

Annual EIR

annualEIR=double

Units: Inoculations per adult per annum Min: 0

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries

<fourierSeries
    EIRRotateAngle=double
  >
IN THIS ORDER:
| ( <coeffic ... /> )*
</fourierSeries>

coeffic

Documentation (element)

Units: Infectious bites per adult per day

Attributes

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: Radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Pair of Fourier coefficients

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries → coeffic

<coeffic
    a=double
    b=double
  />

Documentation (element)

A pair of Fourier series coefficients. The first element specifies a1 and b1, the second a2 and b2, etc. Any number (from 0 up) of pairs may be given.

Attributes

a_n parameter of Fourier approximation to ln(EIR)

a=double

a_n parameter of Fourier approximation to ln(EIR) for some natural number n.

b_n parameter of Fourier approximation to ln(EIR)

b=double

b_n parameter of Fourier approximation to ln(EIR) for some natural number n.

List of monthly values

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues

<monthlyValues
    smoothing=("none" or "fourier")
  >
IN THIS ORDER:
| ( <value ... /> ){12,12}
</monthlyValues>

value

Documentation (element)

Description of seasonality from monthly values. Multiple smoothing methods are possible (see smoothing attribute).

List should contain twelve entries: January to December.

Attributes

Smoothing function

smoothing=("none" or "fourier")

How the monthly values are converted into a daily sequence of values:

none: no smoothing (step function)
Fourier: a Fourier series (with terms up to a2/b2) is fit to the sequence of monthly values and used to generate a smoothed list of daily values.

Monthly value

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Monthly value

List of daily values

→ scenario → entomology → vector → anopheles → seasonality → dailyValues

<dailyValues>
IN THIS ORDER:
| ( <value ... /> )+
</dailyValues>

value

Documentation (element)

Description of seasonality from daily values.

List should contain 365 entries: 1st January to 31st December.

Daily value

→ scenario → entomology → vector → anopheles → seasonality → dailyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Daily value

Mosquito feeding cycle parameters

→ scenario → entomology → vector → anopheles → mosq

<mosq
    minInfectedThreshold=double
  >
IN ANY ORDER:
|   <mosqRestDuration ... /> 
|   <extrinsicIncubationPeriod ... /> 
|   <mosqLaidEggsSameDayProportion ... /> 
|   <mosqSeekingDuration ... /> 
|   <mosqSurvivalFeedingCycleProbability ... /> 
|   <availability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <mosqProbOvipositing ... /> 
|   <mosqHumanBloodIndex ... /> 
</mosq>

Documentation (element)

Parameters describing the feeding cycle and human mosquito interaction of a single species of anopheles mosquito.

Attributes

Mininum infected threshold for mosquitos

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

Duration of the resting period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqRestDuration

<mosqRestDuration
    value=int
  />

Documentation (element)

Units: Days

name:Duration of the resting period of the vector (days);

Attributes

Input parameter value

value=int

An integer value.

Extrinsic incubation period

→ scenario → entomology → vector → anopheles → mosq → extrinsicIncubationPeriod

<extrinsicIncubationPeriod
    value=int
  />

Documentation (element)

Units: Days

name:Extrinsic incubation period (days)

Attributes

Input parameter value

value=int

An integer value.

Proportion of mosquitoes host seeking on same day as ovipositing

→ scenario → entomology → vector → anopheles → mosq → mosqLaidEggsSameDayProportion

<mosqLaidEggsSameDayProportion
    value=double
  />

Documentation (element)

Units: Proportion

Proportion of mosquitoes host seeking on same day as ovipositing

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Duration of the host-seeking period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqSeekingDuration

<mosqSeekingDuration
    value=double
  />

Documentation (element)

Units: Days

Duration of the host-seeking period of the vector (days)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito survives the feeding cycle

→ scenario → entomology → vector → anopheles → mosq → mosqSurvivalFeedingCycleProbability

<mosqSurvivalFeedingCycleProbability
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito survives the feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human availability rate heterogeneity

→ scenario → entomology → vector → anopheles → mosq → availability

<availability
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
  />

Documentation (element)

If no attributes are specified or distr="const" or CV="0" then there will be no heterogeneity.

Documentation (type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

Probability that the mosquito succesfully bites chosen host

→ scenario → entomology → vector → anopheles → mosq → mosqProbBiting

<mosqProbBiting
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito succesfully bites chosen host

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → mosq → mosqProbFindRestSite

<mosqProbFindRestSite
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito escapes host and finds a resting place after biting

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → mosq → mosqProbResting

<mosqProbResting
    mean=double
    variance=double
  />

Documentation (element)

Probability of mosquito successfully resting after finding a resting site

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of a mosquito successfully laying eggs given that it has rested

→ scenario → entomology → vector → anopheles → mosq → mosqProbOvipositing

<mosqProbOvipositing
    value=double
  />

Documentation (element)

Probability of a mosquito successfully laying eggs given that it has rested

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human blood index

→ scenario → entomology → vector → anopheles → mosq → mosqHumanBloodIndex

<mosqHumanBloodIndex
    value=double
  />

Documentation (element)

Units: Proportion

The proportion of resting mosquitoes which fed on human blood during the last feed.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mosquito life cycle parameters

→ scenario → entomology → vector → anopheles → lifeCycle

<lifeCycle
  [ estimatedLarvalResources=double ] DEFAULT VALUE 1e8
  >
IN ANY ORDER:
|   <eggStage ... /> 
|   <larvalStage ... /> 
|   <pupalStage ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</lifeCycle>

Documentation (element)

Parameters describing the life-cycle of this species of mosquito

Attributes

Estimate of larval resources

estimatedLarvalResources=double

Units: X

Default value: 1e8

Egg stage

→ scenario → entomology → vector → anopheles → lifeCycle → eggStage

<eggStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the egg stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

larvalStage

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage

<larvalStage>
</larvalStage>

daily

Documentation (type)

Parameters for the larval stage of development

Documentation (base type)

Parameters associated with a mosquito development stage.

Daily development

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage → daily

<daily
    resourceUsage=double
    effectCompetition=double
  />

Documentation (element)

Attributes

Resource usage

resourceUsage=double

Units: X

Resource usage during larval stage of development. Units are arbitrary.

Effect of competition

effectCompetition=double

Units: none

Effect of competition over resources on development.

Pupal stage

→ scenario → entomology → vector → anopheles → lifeCycle → pupalStage

<pupalStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the pupal stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → lifeCycle → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Simple Mosq-Pop-Dynamics parameters

→ scenario → entomology → vector → anopheles → simpleMPD

<simpleMPD>
IN ANY ORDER:
|   <developmentDuration ... /> 
|   <developmentSurvival ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</simpleMPD>

Documentation (element)

Parameters describing the simple mosquito population dynamics model.

This is a simpler version of the life-cycle model, requiring less parameters and with much simpler initialisation.

Duration

→ scenario → entomology → vector → anopheles → simpleMPD → developmentDuration

<developmentDuration
    value=int
  />

Documentation (element)

Units: Days Min: 1

Duration from egg laying to emergence in days.

Attributes

Input parameter value

value=int

An integer value.

Probability of survival

→ scenario → entomology → vector → anopheles → simpleMPD → developmentSurvival

<developmentSurvival
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that mosquito survives from the egg being laid to emergence, given no resouce limitations (no density constraints).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → simpleMPD → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Alternative (non-human) host paramters

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN ANY ORDER:
|   <mosqRelativeEntoAvailability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
| [ <hostFecundityFactor ... /> ]
</nonHumanHosts>

Documentation (element)

Min: 0

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of non-human host (ξ_i)

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqRelativeEntoAvailability

<mosqRelativeEntoAvailability
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of the population of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative fecundity of biting mosquitoes

→ scenario → entomology → vector → anopheles → nonHumanHosts → hostFecundityFactor

<hostFecundityFactor
    value=double
  />

Documentation (element)

Units: Proportion

Multiplicative factor for the number of fertile eggs laid by a mosquito after biting this type of host, relative to an unprotected human.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Name of this species of non human hosts (must match up with those described per anopheles section).

Population size of non-human host species

number=double

Units: Animals

Parasite genetics

<parasiteGenetics
    samplingMode=("initial" or "tracking")
  >
IN THIS ORDER:
| ( <locus ... /> )+
</parasiteGenetics>

locus

Documentation (element)

A specification of genotypes of infection parasites.

May be omitted; in this case there is no modelling of genetic differences of infections (resistance, fitness).

Attributes

samplingMode

samplingMode=("initial" or "tracking")

Locus

→ scenario → parasiteGenetics → locus

<locus
    name=string
  >
IN THIS ORDER:
| ( <allele ... /> )+
</locus>

allele

Documentation (element)

Alleles at loci can affect fitness and resistance to any number of drugs.

Attributes

Name of locus

name=string

Name of the Locus

Allele

→ scenario → parasiteGenetics → locus → allele

<allele
    name=string
    initialFrequency=double
    fitness=double
  [ hrp2_deletion=boolean ] DEFAULT VALUE false
  />

Documentation (element)

Describes an allele, or one possible genetic option of multiple at one point of variance.

Attributes

Name

name=string

Name of the allele; used to refer to it elsewhere.

Initial frequency

initialFrequency=double

Fitness factor

fitness=double

HRP2 deletion

hrp2_deletion=boolean

Default value: false

Drug parameters (PK, PD and usage)

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
|   <treatments ... /> 
|   <drugs ... /> 
</pharmacology>

Documentation (element)

Drug model parameters and drug usage parameters

Documentation (type)

A library of drug related data for the PK/PD model.

Treatments library

→ scenario → pharmacology → treatments

<treatments>
IN THIS ORDER:
| ( <schedule ... /> )+
| ( <dosages ... /> )+
</treatments>

Documentation (element)

A library of drug deployment schedules and dosages.

schedule

→ scenario → pharmacology → treatments → schedule

<schedule
    name=string
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

A schedule for the administration of drugs in a course of treatment.

Note that dose sizes are multiplied by some multiplier (see dosages) and the times of all doses may be delayed.

Attributes

Name

name=string

Name for referring to this deployment schedule

medicate

→ scenario → pharmacology → treatments → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  />

Attributes

drug

drug=string

Abbreviated name of drug compound

Drug dose (mg with multiplier)

mg=double

Units: mg per something

Quantity of drug compound in mg per something. A separate dosage table must be used when medicating, which may specify multipliers of this number based on patient age or weight.

Time of administration

hour=double

Units: Hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

dosages

→ scenario → pharmacology → treatments → dosages

<dosages
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | ( <age ... /> )+
| | ( <bodymass ... /> )+
| |   <multiply ... /> 
</dosages>

Documentation (type)

A table for selecting a dose size. There are several ways this can work: using the patient's age or body mass in a look-up table to get a multplier, or directly using body mass as the multiplier.

The doses specified in "mg" in the treatment schedule are then multiplied by this multiplier.

Attributes

Name

name=string

Name for referring to this dosage table

Look-up table (age)

→ scenario → pharmacology → treatments → dosages → age

<age
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's age.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Look-up table (weight)

→ scenario → pharmacology → treatments → dosages → bodymass

<bodymass
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's body mass.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Multiply dose

→ scenario → pharmacology → treatments → dosages → multiply

<multiply
    by=("kg")
  />

Documentation (element)

Multiply the dose by some quantity, such as patient weight.

Attributes

By what?

by=("kg")

Quantity to multiply the dose by. Only option is "kg" (patient weight in kg).

Drug library

→ scenario → pharmacology → drugs

<drugs>
IN THIS ORDER:
| ( <drug ... /> )+
</drugs>

drug

Documentation (element)

A library of drug PK/PD data.

drug

→ scenario → pharmacology → drugs → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (type)

A drug description with PK/PD parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drugs → drug → PD

<PD
  [ locus=string ]
  >
IN THIS ORDER:
| ( <phenotype ... /> )+
</PD>

phenotype

Attributes

Locus

locus=string

PD parameters for some allele / resistance phenotype

→ scenario → pharmacology → drugs → drug → PD → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

Restrict phenotype applicability to certain alleles

→ scenario → pharmacology → drugs → drug → PD → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (element)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Maximal parasite killing rate

→ scenario → pharmacology → drugs → drug → PD → phenotype → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drugs → drug → PD → phenotype → IC50

<IC50
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

If CV > 0, the IC50 is sampled from a log-normal distribution.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Slope of effect curve

→ scenario → pharmacology → drugs → drug → PD → phenotype → slope

<slope>
    double
</slope>

Documentation (element)

Units: dimensionless

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drugs → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
| EXACTLY ONE OF:
| |   <half_life ... /> 
| | IN THIS ORDER:
| | |   <k ... /> 
| | |   <m_exponent ... /> 
| [ <k_a ... /> ]
| [ <conversion ... /> ]
|   <vol_dist ... /> 
| [ <compartment2 ... /> ]
| [ <compartment3 ... /> ]
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drugs → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drugs → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate λ, calculated as λ = ln(2) / half_life. The basic form of decay is C(t) = C0 * exp(-λ*t).

Alternatively, elimination rate can be specified via k and m_exponent.

Constant associated with elimination rate (k)

→ scenario → pharmacology → drugs → drug → PK → k

<k
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

If CV > 0, k is sampled per-human from the log-normal distribution: ln N( ln(mean) - σ^2 / 2, σ^2).

Alternatively, elimination rate can be specified via half_life.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Constant associated with elimination rate (m_exponent)

→ scenario → pharmacology → drugs → drug → PK → m_exponent

<m_exponent>
    double
</m_exponent>

Documentation (element)

Units: day^-1 Min: 0

Alternatively, elimination rate can be specified via half_life.

Note that in the case of a conversion model, this applies to both the elimination and the conversion rates.

Absorption rate constant (k_a)

→ scenario → pharmacology → drugs → drug → PK → k_a

<k_a
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Min: 0

Absorption rate parameter. Not allowed for one compartment models, but required for two and three compartment models and one compartment with conversion model (for the parent drug only).

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Conversion parameters (parent drug)

→ scenario → pharmacology → drugs → drug → PK → conversion

<conversion>
IN ANY ORDER:
|   <metabolite ... /> 
|   <rate ... /> 
|   <molRatio ... /> 
|   <IC50_log_correlation ... /> 
</conversion>

Documentation (element)

Configures the parent drug in a conversion model.

To use a conversion model, the parent drug should have this section defined as well as half-life or k (direct elimination; this may be zero) and k_a (absorption rate; this may be large).

Metabolite drug (abbreviation)

→ scenario → pharmacology → drugs → drug → PK → conversion → metabolite

<metabolite>
    string
</metabolite>

Documentation (element)

The abbreviation of the metabolite drug (e.g. "DHA" or "DHA_AR").

Rate of conversion

→ scenario → pharmacology → drugs → drug → PK → conversion → rate

<rate
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Rate of conversion of parent drug to metabolite.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Molecular weight ratio

→ scenario → pharmacology → drugs → drug → PK → conversion → molRatio

<molRatio>
    double
</molRatio>

Documentation (element)

Ratio of molecular weights: molecular weight of the metabolite divided by molecular weight of the parent.

IC50 log correlation

→ scenario → pharmacology → drugs → drug → PK → conversion → IC50_log_correlation

<IC50_log_correlation>
    double
</IC50_log_correlation>

Documentation (element)

Min: 0 Max: 1

If this value is 1, samples are fully correlated: a single z-score is used to calculate both samples. If this is 0, two independent samples are used.

Values between 0 and 1 (partial correlation) are supported; in this case IC50 values are sampled such that cor(log(x), log(y)) matches this value (where x, y are parent and metabolite IC50 values).

Volume of Distribution (Vd)

→ scenario → pharmacology → drugs → drug → PK → vol_dist

<vol_dist
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution.

If CV > 0 this is sampled from a log-normal distribution.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Second compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment2

<compartment2>
IN ANY ORDER:
|   <k12 ... /> 
|   <k21 ... /> 
</compartment2>

Documentation (element)

Optional element specifying conversion parameters to- and from- a second compartment.

Absorption rate to compartment 2 (k12)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → k12

<k12
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the first periphery compartment (2).

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Absorption rate from compartment 2 (k21)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → k21

<k21
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the first periphery compartment (2) to the central compartment.

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Third compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment3

<compartment3>
IN ANY ORDER:
|   <k13 ... /> 
|   <k31 ... /> 
</compartment3>

Documentation (element)

Optional element specifying conversion parameters to- and from- a third compartment.

Absorption rate to compartment 3 (k13)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → k13

<k13
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the second periphery compartment (3).

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Absorption rate from compartment 3 (k31)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → k31

<k31
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the second periphery compartment (3) to the central compartment.

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Diagnostic parameters

→ scenario → diagnostics

<diagnostics>
IN THIS ORDER:
| ( <diagnostic ... /> )*
</diagnostics>

diagnostic

Documentation (element)

Diagnostic model parameters

diagnostic

→ scenario → diagnostics → diagnostic

<diagnostic
    name=string
  [ units=("Other" or "Garki" or "Malariatherapy") ]
  [ mechanism=("Other" or "HRP2") ] DEFAULT VALUE Other
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterministic ... /> 
| |   <stochastic ... /> 
</diagnostic>

Attributes

Name of diagnostic

name=string

Name of this diagnostic (parameterisation). May be used elsewhere in the XML document to refer to this set of diagnostic parameters.

Parasite density units / methodology

units=("Other" or "Garki" or "Malariatherapy")

Mechanism

mechanism=("Other" or "HRP2")

Default value: Other

Deterministic detection

→ scenario → diagnostics → diagnostic → deterministic

<deterministic
    minDensity=double
  />

Documentation (element)

Specify that an artificial deterministic test is used: outcome is positive if parasite density is at least the minimum given.

Attributes

Minimum detectible density

minDensity=double

Units: parasites/microlitre Min: 0

The minimum density at which parasites can be detected. If 0, the test outcome is always positive.

Non-deterministic detection

→ scenario → diagnostics → diagnostic → stochastic

<stochastic
    dens_50=double
    specificity=double
  />

Documentation (element)

An improved model of detection which is non-deterministic, including false positive results as well as false negatives.

Some parameterisations:

Microscopy sensitivity/specificity data in Africa; Source: expert opinion — Allan Schapira dens_50 = 20.0 specificity = .75

RDT sensitivity/specificity for Plasmodium falciparum in Africa Source: Murray et al (Clinical Microbiological Reviews, Jan. 2008) dens_50 = 50.0; specificity = .942;

Attributes

Density 50

dens_50=double

Units: parasites/microlitre Min: 0

The density at which the test outcome has a 50% chance of being positive.

Specificity

specificity=double

Units: Dimensionless Min: 0 Max: 1

The probability of a positive test outcome in the absense of parasites.

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
| [ <vivax ... /> ]
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: model/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=string
  >
IN ANY ORDER:
| [ <NeonatalMortality ... /> ]
| [ <NonMalariaFevers ... /> ]
</clinical>

Documentation (type)

Attributes

Follow-up period during which recurrence is considered a treatment failure

healthSystemMemory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

Neonatal mortality parameters

→ scenario → model → clinical → NeonatalMortality

<NeonatalMortality
    diagnostic=string
  />

Attributes

Diagnostic used to parameterise model

diagnostic=string

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
| [ <prNeedTreatmentNMF ... /> ]
| [ <prNeedTreatmentMF ... /> ]
</NonMalariaFevers>

Documentation (type)

Description of the incidence of non-malaria fever. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a non-malarial fever requires treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

Availability of humans to mosquitoes relative to an adult, categorized by age group

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ]
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

Vivax model parameters

→ scenario → model → vivax

<vivax>
IN ANY ORDER:
|   <probBloodStageInfectiousToMosq ... /> 
|   <hypnozoiteRelease ... /> 
|   <bloodStageProtectionLatency ... /> 
|   <bloodStageLengthDays ... /> 
|   <clinicalEvents ... /> 
</vivax>

Documentation (element)

This describes Vivax model parameters, and is required when using the VIVAX_SIMPLE_MODEL model option.

Probability of mosquito infection

→ scenario → model → vivax → probBloodStageInfectiousToMosq

<probBloodStageInfectiousToMosq
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

The chance of a feeding mosquito becoming infected, given that the host is patent. (This may be adjusted by transmission-blocking vaccines.)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Hypnozoite releases

→ scenario → model → vivax → hypnozoiteRelease

<hypnozoiteRelease
  [ pSecondRelease=double ] DEFAULT VALUE 0
  >
IN ANY ORDER:
|   <numberHypnozoites ... /> 
|   <firstReleaseDays ... /> 
| [ <secondReleaseDays ... /> ]
</hypnozoiteRelease>

Documentation (element)

Describes the number and times of hypnozoite releases.

Documentation (type)

This element defines probabilites when and how many hypnozoites are released from the liverstage into the blood.

The gap between the start of a new brood of hypnozoites and its release are defined as follows:

latentP + latentRelapse + randomReleaseDelay

randomReleaseDelay is based on one or two lognormal distributions, which are defined in firstRelease and optionally secondRelease.

You can define 2 release distributions, which get added together and represent the probability of hypnozoites which get released before winter (first release) or after (second release).

You can omit the secondRelease element if no release to the blood happens after winter.

Attributes

latent relapse days

pSecondRelease=double

Default value: 0

Probability of a second release. If undefined it is zero.

Number of Hypnozoites

→ scenario → model → vivax → hypnozoiteRelease → numberHypnozoites

<numberHypnozoites
    max=int
    base=double
  />

Documentation (element)

numberHypnozoites calculates the number of hypnozoites in the liver stage based on a base which is between 0 and 1.

This number is random based on the following distribution and normalized:

max ∑ (base ^ n) n = 0

Attributes

max

max=int

base

base=double

firstReleaseDays

→ scenario → model → vivax → hypnozoiteRelease → firstReleaseDays

<firstReleaseDays
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
    latentRelapse=double
  />

Documentation (type)

Hypnozoites are released after a delay, calculated as: roundToTSFromDays(delay + latentRelapse)

Here, roundToTSFromDays rounds the input (in days) to the nearest timestep, delay is sampled from a log-normal, and latentRelapse is the parameter specified here.

The delay is sampled from a log-normal distribution, parameterised via the (linear) mean and CV (coefficient of variation) given here.

Documentation (base type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

latent relapse days

latentRelapse=double

Usually between 10 and 15 days.

secondReleaseDays

→ scenario → model → vivax → hypnozoiteRelease → secondReleaseDays

<secondReleaseDays
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
    latentRelapse=double
  />

Documentation (type)

Hypnozoites are released after a delay, calculated as: roundToTSFromDays(delay + latentRelapse)

Here, roundToTSFromDays rounds the input (in days) to the nearest timestep, delay is sampled from a log-normal, and latentRelapse is the parameter specified here.

The delay is sampled from a log-normal distribution, parameterised via the (linear) mean and CV (coefficient of variation) given here.

Documentation (base type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

latent relapse days

latentRelapse=double

Usually between 10 and 15 days.

Blood stage protection latency

→ scenario → model → vivax → bloodStageProtectionLatency

<bloodStageProtectionLatency
    value=double
  />

Documentation (element)

Min: 0

The length of time after expiry of a blood-stage infection during which relapses from the same brood are supressed by the immune system.

This is rounded to the nearest time-step.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Blood stage length

→ scenario → model → vivax → bloodStageLengthDays

<bloodStageLengthDays
    scale=double
    shape=double
    distr=("weibull")
  />

Documentation (element)

Units: Days

Parameters used to sample the length of blood-stage infections from a Weibull distribution (scale parameter lambda, shape parameter k).

Documentation (type)

Parameters of a Weibull distribution.

Attributes

Scale

scale=double

The Weibull scale parameter (λ).

shape

shape=double

The Weibull shape parameter (k).

Distribution

distr=("weibull")

To allow heterogeneity, a distribution must be specified. In this case, only "weibull" is allowed.

clinicalEvents

→ scenario → model → vivax → clinicalEvents

<clinicalEvents>
IN THIS ORDER:
|   <pPrimaryInfection ... /> 
|   <pRelapseOne ... /> 
|   <pRelapseTwoPlus ... /> 
|   <pEventIsSevere ... /> 
</clinicalEvents>

Documentation (type)

This elements holds all information about probabilites for clinical events from infections and relapses.

pPrimaryInfection

→ scenario → model → vivax → clinicalEvents → pPrimaryInfection

<pPrimaryInfection
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseOne

→ scenario → model → vivax → clinicalEvents → pRelapseOne

<pRelapseOne
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseTwoPlus

→ scenario → model → vivax → clinicalEvents → pRelapseTwoPlus

<pRelapseTwoPlus
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pEventIsSevere

→ scenario → model → vivax → clinicalEvents → pEventIsSevere

<pEventIsSevere
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=string
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=string

Units: User defined (default: steps) Min: 0 Max: 20

Pre-erythrocytic latent period Can be specified in steps (e.g. 3t) or days (e.g. 15d).

parameter

→ scenario → model → parameters → parameter

<parameter
  [ name=string ]
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 44 documentation

Generated from: scenario_44.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
  [ analysisNo=int ]
    name=string
  [ wuID=int ]
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:om="http://openmalaria.org/schema/scenario_44"
    xsi:schemaLocation="http://openmalaria.org/schema/scenario_44 scenario_44.xsd"
  >
IN ANY ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entomology ... /> 
| [ <parasiteGenetics ... /> ]
| [ <pharmacology ... /> ]
| [ <diagnostics ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Name of intervention

Work unit identifier

wuID=int

Units: Number

Work unit ID. Obselete and no longer required.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Description of demography

Attributes

Name of demography data

name=string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Years Min: 0 Max: 100

Maximum age of simulated humans in years

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

list of age groups included in demography

Documentation (type)

list of age groups included in demography or surveys

Attributes

Lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Units: Percentage Min: 0 Max: 100

Percentage of human population in age group

Upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ startDate=string ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
| [ <cohorts ... /> ]
</monitoring>

Documentation (element)

Description of surveys

Attributes

Name of monitoring settings

name=string

Name of monitoring settings

Start of monitoring

startDate=string

continuous

→ scenario → monitoring → continuous

<continuous
    period=string
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Delay between reports

period=string

Units: User defined (default: steps)

Delay between reports; typically one time step but can be greater. Can be specified in steps (e.g. 1t) or days (e.g. 5d).

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions
  [ onlyNewEpisode=boolean ] DEFAULT VALUE false
  >
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See model/mon/OutputMeasures.h for a list of supported outputs. Should also be on the wiki.

Attributes

Report only for new cases

onlyNewEpisode=boolean

Default value: false

option

→ scenario → monitoring → SurveyOptions → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  [ outputNumber=int ]
  [ byAge=boolean ]
  [ byCohort=boolean ]
  [ bySpecies=boolean ]
  [ byGenotype=boolean ]
  [ byDrugType=boolean ]
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Number identifying measure in output

outputNumber=int

Report by age category

byAge=boolean

Report by cohort

byCohort=boolean

Report by mosquito species

bySpecies=boolean

Report by parasite genotype

byGenotype=boolean

Report by drug type

byDrugType=boolean

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
  [ detectionLimit=double ]
  [ diagnostic=string ]
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/microlitre Min: 0

Deprecated: limit above which a human's infection is reported as patent. Alternative: do not specify this; instead specify "diagnostic".

Name of monitoring diagnostic

diagnostic=string

Name of a parameterised diagnostic to use in surveys (see scenario/diagnostics).

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime
  [ repeatStep=string ]
  [ repeatEnd=string ]
  [ reported=boolean ] DEFAULT VALUE true
  >
    string
</surveyTime>

Documentation (element)

Units: User defined (defaults to steps) Min: 0

The simulation ends immediately after the last survey is taken.

Attributes

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

reported

reported=boolean

Default value: true

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Cohorts

→ scenario → monitoring → cohorts

<cohorts>
IN THIS ORDER:
| ( <subPop ... /> )+
</cohorts>

subPop

Documentation (element)

Allows the configuration of multiple cohorts (output segregated according to membership within specific sub-populations).

If this element is omitted, monitoring surveys cover the entire simulated human population.

It does not affect the "continuous" outputs (these never take cohorts into account).

Sub-population

→ scenario → monitoring → cohorts → subPop

<subPop
    id=string
    number=integer
  />

Documentation (element)

In the output file, the output set is identified by multiplying this number by 1000 then adding it to the age group column.

Attributes

Sub-population identifier

id=string

Textual identifier for the sub-population (i.e. for an intervention component, since sub-populations are defined as the hosts an intervention component is deployed to).

Sub-population number

number=integer

Units: dimensionless Min: 1 Max: 2097152

Number identifying a sub-population; used to define identifiers of output sets. This number must be a power of 2 (i.e. 1, 2, 4, 8, ...). See documentation of subPop element.

Preventative interventions

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfections ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <vectorPop ... /> ]
| [ <vectorTrap ... /> ]
| [ <nonHumanHostsModifications ... /> ]
| [ <addNonHumanHosts ... /> ]
| [ <human ... /> ]
</interventions>

Documentation (element)

Attributes

Name of intervention set

name=string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeHS>

timedDeployment

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeHS → timedDeployment

<timedDeployment
    time=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timedDeployment>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</uncomplicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

multiple

→ scenario → interventions → human → component → decisionTree → multiple

<multiple
  [ name=string ]
  >
IN THIS ORDER:
| ( <caseType ... /> )*
| ( <diagnostic ... /> )*
| ( <random ... /> )*
| ( <age ... /> )*
| ( <treatPKPD ... /> )*
| [ <treatSimple ... /> ]
| ( <deploy ... /> )*
</multiple>

Documentation (type)

A special node allowing multiple sub-trees to be evaluated.

This is different from an ordinary decision tree node in that:

a) multiple types of child can occur simultaneously (e.g. multiple types of treatment or treatment plus a 'random' sub-tree)

b) the 'noTreatment' and 'treatFailure' nodes are not allowed

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → multiple → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

firstLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → firstLine

<firstLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</firstLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

secondLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → secondLine

<secondLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</secondLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

positive

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

outcome

→ scenario → interventions → human → component → decisionTree → multiple → random → outcome

<outcome
  [ name=string ]
    p=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</outcome>

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Probability

p=double

Units: None Min: 0 Max: 1

Probability of selecting this outcome. The sum of probabilities across all outcomes must be 1.

age

→ scenario → interventions → human → component → decisionTree → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Age range

→ scenario → interventions → human → component → decisionTree → multiple → age → age

<age
  [ name=string ]
    lb=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</age>

Documentation (element)

Describes a branch, selected for patients of a certain age.

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Lower bound (inclusive)

lb=double

Min: 0

noTreatment

→ scenario → interventions → human → component → decisionTree → noTreatment

<noTreatment
  [ name=string ]
  />

Documentation (type)

An end node doing nothing. This exists to explicitly state that no treatment happens and to prevent trees from accidentally being left incomplete.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatFailure

→ scenario → interventions → human → component → decisionTree → treatFailure

<treatFailure
  [ name=string ]
  />

Documentation (type)

An end node which reports treatment but does not change parasitalogical status. This allows correct labelling of second-line cases.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → multiple → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

age

→ scenario → interventions → human → component → decisionTree → multiple → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → multiple → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → multiple → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → multiple → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</complicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: Days Min: 0 Max: unbounded

Maximum number of timesteps (including first day of case) that an individual with an uncomplicated case of malaria will remember he/she was sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial or non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of a complicated or severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
  [ name=string ]
  [ useDiagnosticUC=boolean ] DEFAULT VALUE false
  >
IN ANY ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <treatmentActions ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
</ImmediateOutcomes>

Documentation (type)

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Name of case management parameterisation

name=string

Name of health system

useDiagnosticUC

useDiagnosticUC=boolean

Default value: false

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Description of drug regimen.

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Artemisinine based combination therapy

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Quinine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0 Max: 1name:P(self-treat)

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Effectiveness of treatment for non-compliant patients

treatmentActions

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions

<treatmentActions>
IN ANY ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
</treatmentActions>

CQ
SP
AQ
SPAQ
ACT
QN

CQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ

<CQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</CQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

deploy

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy

<deploy
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ p=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| ( <component ... /> )+
</deploy>

component

Attributes

Maximum age of eligible humans

maxAge=double

Units: Years Min: 0

Maximum age of eligible humans (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible humans

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible humans (defaults to 0). Input is rounded to the nearest time step.

Probability of delivery to eligible humans

p=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Probability of this list of components being deployed, given that other constraints are met.

component

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Prophylactic treatment

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere → clearInfections

<clearInfections
    timesteps=string
    stage=("liver" or "blood" or "both")
  />

Documentation (element)

Attributes

Length of effect

timesteps=string

Units: User defined (defaults to steps)

Target stage

stage=("liver" or "blood" or "both")

SP

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SP

<SP
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SP>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

AQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → AQ

<AQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</AQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

SPAQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SPAQ

<SPAQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SPAQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

ACT

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → ACT

<ACT
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</ACT>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

QN

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → QN

<QN
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</QN>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

Probability that human is incompatible with liver-stage drug treatment

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pHumanCannotReceive

<pHumanCannotReceive
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that a human is determined to be unable to receive liver-stage drug treatment. Treatment is neither reported or given for such humans.

This is sampled once per human at birth.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Ignore liver-stage drug treatment incompatibility

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → ignoreCannotReceive

<ignoreCannotReceive
    value=boolean
  />

Documentation (element)

If true, ignore pHumanCannotReceive and consider all humans eligible for treatment; if false (or not specified), do not treat those demed incompatible with liver-stage drug treatment.

The point of this is that pHumanCannotReceive cannot be altered by changeHS interventions, but this property can be.

Attributes

Input parameter value

value=boolean

A boolean value.

Prob use in UC case

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pUseUncomplicated

<pUseUncomplicated
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

This feature is deprecated; it is suggested to use the "simple treatment" feature configured to clear liver-stage parasites, leaving this option unset or zero.

Chance of liver-stage drug treatment being used for routine treatment of an uncomplicated case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Effectiveness

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → effectivenessOnUse

<effectivenessOnUse
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that liver-stage drug treatment is effective.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

DecisionTree5Day

<DecisionTree5Day
  [ name=string ]
  >
IN ANY ORDER:
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
|   <treeUCOfficial ... /> 
|   <treeUCSelfTreat ... /> 
|   <cureRateSevere ... /> 
|   <treatmentSevere ... /> 
</DecisionTree5Day>

Documentation (type)

Besides greater flexibility, this allows treatment via PK/PD models.

Attributes

Name of case management parameterisation

name=string

Name of health system

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → DecisionTree5Day → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → DecisionTree5Day → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

treeUCOfficial

→ scenario → healthSystem → DecisionTree5Day → treeUCOfficial

<treeUCOfficial
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCOfficial>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treeUCSelfTreat

→ scenario → healthSystem → DecisionTree5Day → treeUCSelfTreat

<treeUCSelfTreat
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCSelfTreat>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Cure rate (severe cases)

→ scenario → healthSystem → DecisionTree5Day → cureRateSevere

<cureRateSevere
    value=double
  />

Documentation (element)

Min: 0 Max: 1

The probability of clearing parasites given access to appropriate (hospital) care, for a severe case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

treatmentSevere

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere

<treatmentSevere
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</treatmentSevere>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Case fatality rate for inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: Dimensionless

List of age-specific probabilities of sequelae in inpatients, during a severe bout of malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeEIR>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeEIR → timedDeployment

<timedDeployment
    eipDuration=int
    time=string
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timedDeployment>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Time

time=string

Units: User defined (defauls to steps) Min: 0

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=string ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=string

Units: User defined (default: steps) Min: 0

Default value: 0

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=string
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time of start

time=string

Units: User defined (defauls to steps) Min: 0

Insert R_0 case

<insertR_0Case
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</insertR_0Case>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → insertR_0Case → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Uninfect vectors

<uninfectVectors
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</uninfectVectors>

timedDeployment

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → uninfectVectors → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Vector population intervention

→ scenario → interventions → vectorPop

<vectorPop>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorPop>

intervention

Documentation (element)

Units: List of elements

A list of parameterisations of generic vector host-inspecific interventions.

intervention

→ scenario → interventions → vectorPop → intervention

<intervention
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

Units: List of elements

An intervention which may have various effects on the vector populations as a whole. (Not host specific.)

Multiple instances of this intervention class are allowed (multiple parameterisations, not just deployments).

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → vectorPop → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → vectorPop → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <seekingDeathRateIncrease ... /> ]
| [ <probDeathOvipositing ... /> ]
| [ <emergenceReduction ... /> ]
</anopheles>

Documentation (type)

Units: dimensionless Min: 0 Max: 1

Descriptions of the effects of vector interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Proportional increase in deaths while host searching

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease

<seekingDeathRateIncrease
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</seekingDeathRateIncrease>

decay

Documentation (element)

Units: dimensionless

Describe an effect on the increase in the death rate while host seeking (mu_vA) due to this intervention.

Enter the rate increase (i.e. if rate increases to 120% of normal, give 0.2). New death rate while seeking is old × (1 + increase) where increase is this factor given. Must have increas ≥ -1.

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Proportion ovipositing mosquitoes killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing

<probDeathOvipositing
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probDeathOvipositing>

decay

Documentation (element)

Units: dimensionless

Describe an effect of increased mortality while ovipositing due to this intervention. Enter the probability of dying due to this intervention.

Attributes

Initial probability of killing

initial=double

Units: dimensionless Min: 0 Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Proportion of emerging pupa killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction

<emergenceReduction
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</emergenceReduction>

decay

Documentation (element)

Units: dimensionless

Describe an effect on emergence of pupa into adults: this value is the proportion of emerging pupa which are killed by this intervention.

Attributes

Initial proportion reduction

initial=double

Units: dimensionless Min: -inf Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Vector population intervention deployment

→ scenario → interventions → vectorPop → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

deploy

→ scenario → interventions → vectorPop → intervention → timed → deploy

<deploy
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Baited trap

→ scenario → interventions → vectorTrap

<vectorTrap>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorTrap>

intervention

Documentation (element)

intervention

→ scenario → interventions → vectorTrap → intervention

<intervention
  [ name=string ]
  >
IN THIS ORDER:
| ( <description ... /> )+
| [ <timed ... /> ]
</intervention>

Documentation (type)

Attributes

Descriptive name for type of trap

name=string

Optional name for this type of trap

Description

→ scenario → interventions → vectorTrap → intervention → description

<description
    mosquito=string
  >
IN THIS ORDER:
|   <relativeAvailability ... /> 
|   <decayOfAvailability ... /> 
</description>

Documentation (element)

Parameters associated with a vector trap intervention, per mosquito species.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Initial relative availability

→ scenario → interventions → vectorTrap → intervention → description → relativeAvailability

<relativeAvailability
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: inf

Describes the availiability of a trap to a host-seeking mosquito relative to an average unprotected adult.

I.e. if this parameter is 2, then each trap will on average attract twice as many mosquitoes as unprotected adults.

This is the initial availability; it may decay towards zero depending on the configured decay function.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay of availability

→ scenario → interventions → vectorTrap → intervention → description → decayOfAvailability

<decayOfAvailability
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Describes how availability decays to zero.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Vector trap intervention deployment

→ scenario → interventions → vectorTrap → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )*
</timed>

deploy

Documentation (element)

List of timed vector trap intervention deployment

deploy

→ scenario → interventions → vectorTrap → intervention → timed → deploy

<deploy
    time=string
    ratioToHumans=double
    lifespan=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Ratio to humans

ratioToHumans=double

Min: 0 Max: inf

The number of traps deployed, by this deployment, per adult human. E.g. if there are currently 100 traps and 1000 humans, then a ratio of 0.1 will increase the number of traps to 200.

Lifespan

lifespan=string

Units: Steps or Days or Years

nonHumanHostsModifications

→ scenario → interventions → nonHumanHostsModifications

<nonHumanHostsModifications>
IN THIS ORDER:
| ( <intervention ... /> )+
</nonHumanHostsModifications>

intervention

Documentation (element)

List of interventions that modify parameters of non-human hosts described in the .

intervention

→ scenario → interventions → nonHumanHostsModifications → intervention

<intervention
    name=string
    nonHumanHostsName=string
  >
IN THIS ORDER:
|   <decay ... /> 
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

This intervention modifies parameters of non-human hosts described in the section of the input scenario file.

The intervention is described by 5 parameters that define the change in each of non-human host parameters:

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

Name of intervention

nonHumanHostsName=string

Name of intervention (e.g. larviciding, sugar bait).

decay

→ scenario → interventions → nonHumanHostsModifications → intervention → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

description

→ scenario → interventions → nonHumanHostsModifications → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <availabilityReduction ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
| [ <restingKillingEffect ... /> ]
| [ <fecundityReduction ... /> ]
</anopheles>

Documentation (type)

Descriptions of the effects of non human hosts interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

availabilityReduction

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → availabilityReduction

<availabilityReduction
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

preprandialKillingEffect

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

postprandialKillingEffect

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

restingKillingEffect

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → restingKillingEffect

<restingKillingEffect
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

fecundityReduction

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → fecundityReduction

<fecundityReduction
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

Vector population intervention deployment

→ scenario → interventions → nonHumanHostsModifications → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

addNonHumanHosts

<addNonHumanHosts>
IN THIS ORDER:
| ( <nonHumanHosts ... /> )+
</addNonHumanHosts>

nonHumanHosts

Documentation (element)

List of intervention that add new non-human hosts that have not been described in the .

nonHumanHosts

→ scenario → interventions → addNonHumanHosts → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</nonHumanHosts>

Documentation (type)

Describes a new non-human hosts that have not been described in the .

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
|   <mosqRelativeAvailabilityHuman ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <hostFecundityFactor ... /> 
</anopheles>

Documentation (type)

Descriptions of the effects of new non human hosts with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Relative availability of non-human host (ξ_i)

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqRelativeAvailabilityHuman

<mosqRelativeAvailabilityHuman
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of the population of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → hostFecundityFactor

<hostFecundityFactor
    value=double
  />

Documentation (element)

Units: Proportion

Multiplicative factor for the number of fertile eggs laid by a mosquito after biting this type of host, relative to an unprotected human.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vector trap intervention deployment

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )*
</timed>

deploy

Documentation (element)

List of timed vector trap intervention deployment

deploy

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → timed → deploy

<deploy
    time=string
    lifespan=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Lifespan

lifespan=string

Units: Steps or Days or Years

Human-specific interventions

→ scenario → interventions → human

<human>
IN THIS ORDER:
| ( <component ... /> )+
| ( <deployment ... /> )*
</human>

Documentation (element)

Encapsulates all interventions whose effects are specific to the human host: any interventions where target humans may be selected via population-coverage, age limits and sub-population membership.

Component

→ scenario → interventions → human → component

<component
    id=string
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <screen ... /> 
| |   <treatSimple ... /> 
| |   <treatPKPD ... /> 
| |   <decisionTree ... /> 
| |   <PEV ... /> 
| |   <BSV ... /> 
| |   <TBV ... /> 
| |   <ITN ... /> 
| |   <IRS ... /> 
| |   <GVI ... /> 
| | [ <recruitmentOnly ... /> ]
| |   <clearImmunity ... /> 
| [ <subPopRemoval ... /> ]
</component>

Documentation (element)

Each element describes one component: its effects, decay of the(se) effect(s), and related stuff (e.g. description of indirect decay and of usage levels).

Attributes

Component identifier

id=string

Name of component

name=string

An informal name/description for the component

screen

→ scenario → interventions → human → component → screen

<screen
    diagnostic=string
  >
IN THIS ORDER:
| ( <positive ... /> )*
| ( <negative ... /> )*
</screen>

Documentation (type)

This can be combined with MDA to achieve mass screen and treat (MSAT) or other types of mass screening intervention.

The use of the screening itself is reported (if enabled), but not the outcome. Deployment of interventions triggered by the screening may be reported, however.

Attributes

Name of diagnostic

diagnostic=string

Name of a parameterised diagnostic (see scenario/diagnostics).

positive

→ scenario → interventions → human → component → screen → positive

<positive
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → screen → negative

<negative
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

treatSimple

→ scenario → interventions → human → component → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

treatPKPD

→ scenario → interventions → human → component → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

decisionTree

→ scenario → interventions → human → component → decisionTree

<decisionTree
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</decisionTree>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Vaccines

→ scenario → interventions → human → component → PEV

<PEV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )*
| ( <phenotype ... /> )*
</PEV>

Documentation (element)

Pre-erythrocytic vaccine (PEV): prevents a proportion of infections from commencing.

Documentation (type)

Description of a vaccine's effect

Decay of effect

→ scenario → interventions → human → component → PEV → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Specification of decay of efficacy. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Variance parameter for vaccine efficacy

→ scenario → interventions → human → component → PEV → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

PD parameters for some allele / resistance phenotype

→ scenario → interventions → human → component → PEV → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
| ( <initialEfficacy ... /> )+
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

restriction

→ scenario → interventions → human → component → PEV → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (type)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → phenotype → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vaccines

→ scenario → interventions → human → component → BSV

<BSV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )*
| ( <phenotype ... /> )*
</BSV>

Documentation (element)

Blood-stage vaccine (BSV): acts as a killing factor on blood-stage parasites. Exact action depends on the within host model.

Documentation (type)

Description of a vaccine's effect

Vaccines

→ scenario → interventions → human → component → TBV

<TBV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )*
| ( <phenotype ... /> )*
</TBV>

Documentation (element)

Transmission-blocking vaccine (TBV): one minus this scales the probability of transmission to mosquitoes

Documentation (type)

Description of a vaccine's effect

Bed nets

→ scenario → interventions → human → component → ITN

<ITN>
IN THIS ORDER:
| [ <usage ... /> ]
|   <holeRate ... /> 
|   <ripRate ... /> 
|   <ripFactor ... /> 
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
|   <attritionOfNets ... /> 
| ( <anophelesParams ... /> )+
</ITN>

Documentation (element)

Description of bed-net interventions (ITNs, LLINs).

Proportion of time nets are used by humans

→ scenario → interventions → human → component → ITN → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of nets by humans, from 0 to 1.

At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing.

See also "propActing" (proportion of bits for which net acts).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Rate at which holes are made

→ scenario → interventions → human → component → ITN → holeRate

<holeRate
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: Holes per annum Min: 0

The rate at which new holes are made in nets.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Rate at which holes are enlarged

→ scenario → interventions → human → component → ITN → ripRate

<ripRate
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: Rips per existing hole per annum Min: 0

Each existing hole has a probability of being ripped bigger according to a Poisson process with this rate as (only) parameter.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Rip factor

→ scenario → interventions → human → component → ITN → ripFactor

<ripFactor
    value=double
  />

Documentation (element)

Units: none Min: 0

This factor expresses how important rips are in increasing the hole.

The hole index of a net is h + F×x where h and x are the total numbers of holes and rips respectively and F is the rip factor.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → ITN → initialInsecticide

<initialInsecticide
    mean=double
  [ SD=double ]
  [ distr=("const" or "normal") ] DEFAULT VALUE const
  />

Documentation (element)

Units: mg/m² Min: 0

Documentation (type)

A parameter with optional heterogeneity.

Optionally, a distribution ("distr") and standard of deviation ("SD") may be specified.

Attributes

mean

mean=double

The mean value.

standard deviation

SD=double

The standard deviation of variates.

Distribution

distr=("const" or "normal")

Default value: const

Decay of insecticide

→ scenario → interventions → human → component → ITN → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of nets. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Attrition of nets

→ scenario → interventions → human → component → ITN → attritionOfNets

<attritionOfNets
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: dimensionless

Specifies the rate at which nets are disposed of over time. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Humans are removed from the intervention component's sub-population on disposal (attrition) of their nets. Currently this event is not reported.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → human → component → ITN → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <holeIndexMax ... /> ]
| EXACTLY ONE OF:
| |   <deterrency ... /> 
| |   <twoStageDeterrency ... /> 
| EXACTLY ONE OF:
| |   <preprandialKillingEffect ... /> 
| |   <preprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| |   <postprandialKillingEffect ... /> 
| |   <postprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| | [ <fecundityReduction ... /> ]
| | [ <fecundityReductionLogit ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which net acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

maximum of holed surface area that has an effect (comparable to no net)

→ scenario → interventions → human → component → ITN → anophelesParams → holeIndexMax

<holeIndexMax
    value=double
  />

Documentation (element)

Units: in same unit as holeIndex

Used by logit attacking and killing models only, holeIndexMax is a user defined maximum hole index (typically, the total surface area of a net).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency

<twoStageDeterrency>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <entering ... /> 
| |   <enteringLogit ... /> 
| EXACTLY ONE OF:
| |   <attacking ... /> 
| |   <attackingLogit ... /> 
</twoStageDeterrency>

Documentation (element)

Units: dimensionless

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

This deterrency model multiplies human attractiveness by pEnt×pAtt.

Deterrency: entering

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → entering

<entering
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless

pEnt represents the relative probability of entering due to ITNs: pEnt = exp(log(P)×p) where P is the insecticide factor and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Deterrency: entering (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → enteringLogit

<enteringLogit
    baseFactor=double
    insecticideFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: none

See parent element documentation

Insecticide factor

insecticideFactor=double

Units: none

See parent element documentation

Deterrency: attacking

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attacking

<attacking
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Deterrency: attacking (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attackingLogit

<attackingLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Pre-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Pre-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffectLogit

<preprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Post-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffectLogit

<postprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Fecundity reduction

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-B), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReductionLogit

<fecundityReductionLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-K0), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Indoor residual spraying

→ scenario → interventions → human → component → IRS

<IRS>
IN THIS ORDER:
| [ <usage ... /> ]
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
| ( <anophelesParams ... /> )+
</IRS>

Documentation (element)

Description of indoor residual spraying interventions.

Documentation (type)

Description of effect for the more complex and probably more realistic Briet model: IRS has three effects, whos strength is calculated as a function of surviving insecticide content.

Proportion of Indoor residual spraying (IRS) interventions

→ scenario → interventions → human → component → IRS → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Indoor residual spraying (IRS) interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → IRS → initialInsecticide

<initialInsecticide
    mean=double
  [ SD=double ]
  [ distr=("const" or "normal") ] DEFAULT VALUE const
  />

Documentation (element)

Units: μg/cm² Min: 0

Documentation (type)

A parameter with optional heterogeneity.

Optionally, a distribution ("distr") and standard of deviation ("SD") may be specified.

Attributes

mean

mean=double

The mean value.

standard deviation

SD=double

The standard deviation of variates.

Distribution

distr=("const" or "normal")

Default value: const

Decay of insecticide

→ scenario → interventions → human → component → IRS → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → IRS → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → IRS → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied by exp(P×log(p)) where P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction

→ scenario → interventions → human → component → IRS → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

First, we calculate K = B + P×p where B is the base (without protection) probability of death, and P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Fecundity is multiplied by (1−K) / (1−B). It is not allowed to be greater than 1. To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Generic vector intervention

→ scenario → interventions → human → component → GVI

<GVI>
IN THIS ORDER:
| [ <usage ... /> ]
|   <decay ... /> 
| ( <anophelesParams ... /> )+
</GVI>

Documentation (element)

Note that all actions of this intervention component will decay according to a single decay function. If independant decay is wanted, a separate component can be used for each action.

Proportion of generic vector interventions

→ scenario → interventions → human → component → GVI → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Generic vector interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay

→ scenario → interventions → human → component → GVI → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Description of decay of all intervention effects. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → GVI → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <deterrency ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → GVI → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of intervention on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied this factor times survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Fecundity reduction effect

→ scenario → interventions → human → component → GVI → anophelesParams → fecundityReduction

<fecundityReduction
    value=double
  />

Documentation (element)

Min: 0

Fertility is multiplied by 1 - (fecundityReduction * decay).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Recruitment only

→ scenario → interventions → human → component → recruitmentOnly

<recruitmentOnly/>

Documentation (element)

Recruitment of a host into a sub-population.

Clear Immunity

→ scenario → interventions → human → component → clearImmunity

<clearImmunity/>

Documentation (element)

Removes all exposure-related immunitsy gained over time by hosts without removing infections (or affecting the ability to gain immunity through exposure).

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

subPopRemoval

→ scenario → interventions → human → component → subPopRemoval

<subPopRemoval
  [ onFirstBout=boolean ] DEFAULT VALUE false
  [ onFirstTreatment=boolean ] DEFAULT VALUE false
  [ onFirstInfection=boolean ] DEFAULT VALUE false
  [ afterYears=double ]
  />

Documentation (type)

ITN attrition also removes humans from sub-populations.

Attributes

Time to first episode only

onFirstBout=boolean

Default value: false

Time to first treatment only

onFirstTreatment=boolean

Default value: false

Time to first infection only

onFirstInfection=boolean

Default value: false

Remove from sub-population after

afterYears=double

Units: Years Min: 0

Deployment

→ scenario → interventions → human → deployment

<deployment
  [ name=string ]
  >
IN THIS ORDER:
| ( <component ... /> )+
| ( <condition ... /> )*
| ( <continuous ... /> )*
| ( <timed ... /> )*
</deployment>

Documentation (element)

All components deployed by this intervention are deployed to the same people (each timed or continuous deployment selects recipients and then gives each recipient all components of the intervention).

Attributes

Intervention name

name=string

Name of intervention

component

→ scenario → interventions → human → deployment → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Condition

→ scenario → interventions → human → deployment → condition

<condition
    measure=string
  [ minValue=double ]
  [ maxValue=double ]
    initialState=boolean
  />

Documentation (element)

Conditions are evaluated for the whole population, not for individual age-groups or cohorts.

This affects all types of deployment.

Attributes

Measure

measure=string

The monitoring measure to test. Not all measures are available for use.

Minimum value

minValue=double

Minimum value. If specified, the measured variable must be greater than or equal to this value for the condition to be satisfied.

Maximum value

maxValue=double

Maximum value. If specified, the measured variable must be less than or equal to this value for the condition to be satisfied.

Initial state

initialState=boolean

Whether this condition is considered true or false before updated by a survey.

Age-based (continuous) deployment

→ scenario → interventions → human → deployment → continuous

<continuous>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| ( <deploy ... /> )+
</continuous>

Documentation (element)

List of ages at which deployment takes place (through EPI, post-natal and school-based programmes, etc.).

A sub-population restriction may be added as a property of the list of continuous deployments.

restrictToSubPop

→ scenario → interventions → human → deployment → continuous → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

deploy

→ scenario → interventions → human → deployment → continuous → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    targetAgeYrs=double
  [ begin=string ]
  [ end=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention. Input is rounded to the nearest time step.

First time active

begin=string

Units: User defined (defauls to steps)

End step

end=string

Units: User defined (defauls to steps)

Mass (timed) deployment

→ scenario → interventions → human → deployment → timed

<timed>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| [ <cumulativeCoverage ... /> ]
| ( <deploy ... /> )+
</timed>

Documentation (element)

List of timed deployments of the intervention (that is, of deployment campaigns).

Cumulative deployment mode can be specified for all deployments in a timed list. To allow multiple cumulative deployment descriptions, the entire timed list may be repeated.

restrictToSubPop

→ scenario → interventions → human → deployment → timed → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

Cumulative coverage

→ scenario → interventions → human → deployment → timed → cumulativeCoverage

<cumulativeCoverage
    component=string
  />

Documentation (element)

Attributes

Component identifier

component=string

The identifier (short name) of the component used when selecting people.

deploy

→ scenario → interventions → human → deployment → timed → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    time=string
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ repeatStep=string ]
  [ repeatEnd=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Time

time=string

Units: User defined (defauls to steps) Min: 0

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0

Maximum age of eligible individuals (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible individuals (defaults to 0). Input is rounded to the nearest time step.

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Description of health system.

Documentation (type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("forced" or "dynamic")
  [ scaledAnnualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Description of entomological data

Attributes

Entomology dataset name

name=string

Name of entomology data

Transmission model mode

mode=("forced" or "dynamic")

Override annual EIR

scaledAnnualEIR=double

Units: Infectious bites per adult per year

If set, the annual EIR (for all species of vector) is scaled to this level; can be omitted if not needed.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters of the transmission model

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <seasonality ... /> 
|   <mosq ... /> 
| [ <lifeCycle ... /> ]
| [ <simpleMPD ... /> ]
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial estimate of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial estimate of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial estimate of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Seasonality of transmission

→ scenario → entomology → vector → anopheles → seasonality

<seasonality
    input=("EIR")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <fourierSeries ... /> 
| |   <monthlyValues ... /> 
| |   <dailyValues ... /> 
</seasonality>

Documentation (element)

Specifies the seasonality of transmission and optionally the level of annual transmission.

Attributes

Seasonality input

input=("EIR")

Annual EIR

annualEIR=double

Units: Inoculations per adult per annum Min: 0

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries

<fourierSeries
    EIRRotateAngle=double
  >
IN THIS ORDER:
| ( <coeffic ... /> )*
</fourierSeries>

coeffic

Documentation (element)

Units: Infectious bites per adult per day

Attributes

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: Radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Pair of Fourier coefficients

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries → coeffic

<coeffic
    a=double
    b=double
  />

Documentation (element)

A pair of Fourier series coefficients. The first element specifies a1 and b1, the second a2 and b2, etc. Any number (from 0 up) of pairs may be given.

Attributes

a_n parameter of Fourier approximation to ln(EIR)

a=double

a_n parameter of Fourier approximation to ln(EIR) for some natural number n.

b_n parameter of Fourier approximation to ln(EIR)

b=double

b_n parameter of Fourier approximation to ln(EIR) for some natural number n.

List of monthly values

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues

<monthlyValues
    smoothing=("none" or "fourier")
  >
IN THIS ORDER:
| ( <value ... /> ){12,12}
</monthlyValues>

value

Documentation (element)

Description of seasonality from monthly values. Multiple smoothing methods are possible (see smoothing attribute).

List should contain twelve entries: January to December.

Attributes

Smoothing function

smoothing=("none" or "fourier")

How the monthly values are converted into a daily sequence of values:

none: no smoothing (step function)
Fourier: a Fourier series (with terms up to a2/b2) is fit to the sequence of monthly values and used to generate a smoothed list of daily values.

Monthly value

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Monthly value

List of daily values

→ scenario → entomology → vector → anopheles → seasonality → dailyValues

<dailyValues>
IN THIS ORDER:
| ( <value ... /> ){365,365}
</dailyValues>

value

Documentation (element)

Description of seasonality from daily values.

List should contain 365 entries: 1st January to 31st December.

Daily value

→ scenario → entomology → vector → anopheles → seasonality → dailyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Daily value

Mosquito feeding cycle parameters

→ scenario → entomology → vector → anopheles → mosq

<mosq
    minInfectedThreshold=double
  >
IN ANY ORDER:
|   <mosqRestDuration ... /> 
|   <extrinsicIncubationPeriod ... /> 
|   <mosqLaidEggsSameDayProportion ... /> 
|   <mosqSeekingDuration ... /> 
|   <mosqSurvivalFeedingCycleProbability ... /> 
|   <availability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <mosqProbOvipositing ... /> 
|   <mosqHumanBloodIndex ... /> 
</mosq>

Documentation (element)

Parameters describing the feeding cycle and human mosquito interaction of a single species of anopheles mosquito.

Attributes

Mininum infected threshold for mosquitos

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

Duration of the resting period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqRestDuration

<mosqRestDuration
    value=int
  />

Documentation (element)

Units: Days

name:Duration of the resting period of the vector (days);

Attributes

Input parameter value

value=int

An integer value.

Extrinsic incubation period

→ scenario → entomology → vector → anopheles → mosq → extrinsicIncubationPeriod

<extrinsicIncubationPeriod
    value=int
  />

Documentation (element)

Units: Days

name:Extrinsic incubation period (days)

Attributes

Input parameter value

value=int

An integer value.

Proportion of mosquitoes host seeking on same day as ovipositing

→ scenario → entomology → vector → anopheles → mosq → mosqLaidEggsSameDayProportion

<mosqLaidEggsSameDayProportion
    value=double
  />

Documentation (element)

Units: Proportion

Proportion of mosquitoes host seeking on same day as ovipositing

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Duration of the host-seeking period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqSeekingDuration

<mosqSeekingDuration
    value=double
  />

Documentation (element)

Units: Days

Duration of the host-seeking period of the vector (days)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito survives the feeding cycle

→ scenario → entomology → vector → anopheles → mosq → mosqSurvivalFeedingCycleProbability

<mosqSurvivalFeedingCycleProbability
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito survives the feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human availability rate heterogeneity

→ scenario → entomology → vector → anopheles → mosq → availability

<availability
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
  />

Documentation (element)

If no attributes are specified or distr="const" or CV="0" then there will be no heterogeneity.

Documentation (type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

Probability that the mosquito succesfully bites chosen host

→ scenario → entomology → vector → anopheles → mosq → mosqProbBiting

<mosqProbBiting
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito succesfully bites chosen host

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → mosq → mosqProbFindRestSite

<mosqProbFindRestSite
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito escapes host and finds a resting place after biting

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → mosq → mosqProbResting

<mosqProbResting
    mean=double
    variance=double
  />

Documentation (element)

Probability of mosquito successfully resting after finding a resting site

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of a mosquito successfully laying eggs given that it has rested

→ scenario → entomology → vector → anopheles → mosq → mosqProbOvipositing

<mosqProbOvipositing
    value=double
  />

Documentation (element)

Probability of a mosquito successfully laying eggs given that it has rested

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human blood index

→ scenario → entomology → vector → anopheles → mosq → mosqHumanBloodIndex

<mosqHumanBloodIndex
    value=double
  />

Documentation (element)

Units: Proportion

The proportion of resting mosquitoes which fed on human blood during the last feed.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mosquito life cycle parameters

→ scenario → entomology → vector → anopheles → lifeCycle

<lifeCycle
  [ estimatedLarvalResources=double ] DEFAULT VALUE 1e8
  >
IN ANY ORDER:
|   <eggStage ... /> 
|   <larvalStage ... /> 
|   <pupalStage ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</lifeCycle>

Documentation (element)

Parameters describing the life-cycle of this species of mosquito

Attributes

Estimate of larval resources

estimatedLarvalResources=double

Units: X

Default value: 1e8

Egg stage

→ scenario → entomology → vector → anopheles → lifeCycle → eggStage

<eggStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the egg stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

larvalStage

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage

<larvalStage>
</larvalStage>

daily

Documentation (type)

Parameters for the larval stage of development

Documentation (base type)

Parameters associated with a mosquito development stage.

Daily development

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage → daily

<daily
    resourceUsage=double
    effectCompetition=double
  />

Documentation (element)

Attributes

Resource usage

resourceUsage=double

Units: X

Resource usage during larval stage of development. Units are arbitrary.

Effect of competition

effectCompetition=double

Units: none

Effect of competition over resources on development.

Pupal stage

→ scenario → entomology → vector → anopheles → lifeCycle → pupalStage

<pupalStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the pupal stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → lifeCycle → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Simple Mosq-Pop-Dynamics parameters

→ scenario → entomology → vector → anopheles → simpleMPD

<simpleMPD>
IN ANY ORDER:
|   <developmentDuration ... /> 
|   <developmentSurvival ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</simpleMPD>

Documentation (element)

Parameters describing the simple mosquito population dynamics model.

This is a simpler version of the life-cycle model, requiring less parameters and with much simpler initialisation.

Duration

→ scenario → entomology → vector → anopheles → simpleMPD → developmentDuration

<developmentDuration
    value=int
  />

Documentation (element)

Units: Days Min: 1

Duration from egg laying to emergence in days.

Attributes

Input parameter value

value=int

An integer value.

Probability of survival

→ scenario → entomology → vector → anopheles → simpleMPD → developmentSurvival

<developmentSurvival
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that mosquito survives from the egg being laid to emergence, given no resouce limitations (no density constraints).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → simpleMPD → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Alternative (non-human) host paramters

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN ANY ORDER:
|   <mosqRelativeEntoAvailability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
| [ <hostFecundityFactor ... /> ]
</nonHumanHosts>

Documentation (element)

Min: 0

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of non-human host (ξ_i)

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqRelativeEntoAvailability

<mosqRelativeEntoAvailability
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of the population of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative fecundity of biting mosquitoes

→ scenario → entomology → vector → anopheles → nonHumanHosts → hostFecundityFactor

<hostFecundityFactor
    value=double
  />

Documentation (element)

Units: Proportion

Multiplicative factor for the number of fertile eggs laid by a mosquito after biting this type of host, relative to an unprotected human.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Name of this species of non human hosts (must match up with those described per anopheles section).

Population size of non-human host species

number=double

Units: Animals

Parasite genetics

<parasiteGenetics
    samplingMode=("initial" or "tracking")
  >
IN THIS ORDER:
| ( <locus ... /> )+
</parasiteGenetics>

locus

Documentation (element)

A specification of genotypes of infection parasites.

May be omitted; in this case there is no modelling of genetic differences of infections (resistance, fitness).

Attributes

samplingMode

samplingMode=("initial" or "tracking")

Locus

→ scenario → parasiteGenetics → locus

<locus
    name=string
  >
IN THIS ORDER:
| ( <allele ... /> )+
</locus>

allele

Documentation (element)

Alleles at loci can affect fitness and resistance to any number of drugs.

Attributes

Name of locus

name=string

Name of the Locus

Allele

→ scenario → parasiteGenetics → locus → allele

<allele
    name=string
    initialFrequency=double
    fitness=double
  [ hrp2_deletion=boolean ] DEFAULT VALUE false
  />

Documentation (element)

Describes an allele, or one possible genetic option of multiple at one point of variance.

Attributes

Name

name=string

Name of the allele; used to refer to it elsewhere.

Initial frequency

initialFrequency=double

Fitness factor

fitness=double

HRP2 deletion

hrp2_deletion=boolean

Default value: false

Drug parameters (PK, PD and usage)

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
|   <treatments ... /> 
|   <drugs ... /> 
</pharmacology>

Documentation (element)

Drug model parameters and drug usage parameters

Documentation (type)

A library of drug related data for the PK/PD model.

Treatments library

→ scenario → pharmacology → treatments

<treatments>
IN THIS ORDER:
| ( <schedule ... /> )+
| ( <dosages ... /> )+
</treatments>

Documentation (element)

A library of drug deployment schedules and dosages.

schedule

→ scenario → pharmacology → treatments → schedule

<schedule
    name=string
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

A schedule for the administration of drugs in a course of treatment.

Note that dose sizes are multiplied by some multiplier (see dosages) and the times of all doses may be delayed.

Attributes

Name

name=string

Name for referring to this deployment schedule

medicate

→ scenario → pharmacology → treatments → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  />

Attributes

drug

drug=string

Abbreviated name of drug compound

Drug dose (mg with multiplier)

mg=double

Units: mg per something

Quantity of drug compound in mg per something. A separate dosage table must be used when medicating, which may specify multipliers of this number based on patient age or weight.

Time of administration

hour=double

Units: Hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

dosages

→ scenario → pharmacology → treatments → dosages

<dosages
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | ( <age ... /> )+
| | ( <bodymass ... /> )+
| |   <multiply ... /> 
</dosages>

Documentation (type)

A table for selecting a dose size. There are several ways this can work: using the patient's age or body mass in a look-up table to get a multplier, or directly using body mass as the multiplier.

The doses specified in "mg" in the treatment schedule are then multiplied by this multiplier.

Attributes

Name

name=string

Name for referring to this dosage table

Look-up table (age)

→ scenario → pharmacology → treatments → dosages → age

<age
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's age.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Look-up table (weight)

→ scenario → pharmacology → treatments → dosages → bodymass

<bodymass
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's body mass.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Multiply dose

→ scenario → pharmacology → treatments → dosages → multiply

<multiply
    by=("kg")
  />

Documentation (element)

Multiply the dose by some quantity, such as patient weight.

Attributes

By what?

by=("kg")

Quantity to multiply the dose by. Only option is "kg" (patient weight in kg).

Drug library

→ scenario → pharmacology → drugs

<drugs>
IN THIS ORDER:
| ( <drug ... /> )+
</drugs>

drug

Documentation (element)

A library of drug PK/PD data.

drug

→ scenario → pharmacology → drugs → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (type)

A drug description with PK/PD parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drugs → drug → PD

<PD
  [ locus=string ]
  >
IN THIS ORDER:
| ( <phenotype ... /> )+
</PD>

phenotype

Attributes

Locus

locus=string

PD parameters for some allele / resistance phenotype

→ scenario → pharmacology → drugs → drug → PD → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

Restrict phenotype applicability to certain alleles

→ scenario → pharmacology → drugs → drug → PD → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (element)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Maximal parasite killing rate

→ scenario → pharmacology → drugs → drug → PD → phenotype → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drugs → drug → PD → phenotype → IC50

<IC50
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

If CV > 0, the IC50 is sampled from a log-normal distribution.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Slope of effect curve

→ scenario → pharmacology → drugs → drug → PD → phenotype → slope

<slope>
    double
</slope>

Documentation (element)

Units: dimensionless

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drugs → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
| EXACTLY ONE OF:
| |   <half_life ... /> 
| | IN THIS ORDER:
| | |   <k ... /> 
| | |   <m_exponent ... /> 
| [ <k_a ... /> ]
| [ <conversion ... /> ]
|   <vol_dist ... /> 
| [ <compartment2 ... /> ]
| [ <compartment3 ... /> ]
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drugs → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drugs → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate λ, calculated as λ = ln(2) / half_life. The basic form of decay is C(t) = C0 * exp(-λ*t).

Alternatively, elimination rate can be specified via k and m_exponent.

Constant associated with elimination rate (k)

→ scenario → pharmacology → drugs → drug → PK → k

<k
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

If CV > 0, k is sampled per-human from the log-normal distribution: ln N( ln(mean) - σ^2 / 2, σ^2).

Alternatively, elimination rate can be specified via half_life.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Constant associated with elimination rate (m_exponent)

→ scenario → pharmacology → drugs → drug → PK → m_exponent

<m_exponent>
    double
</m_exponent>

Documentation (element)

Units: day^-1 Min: 0

Alternatively, elimination rate can be specified via half_life.

Note that in the case of a conversion model, this applies to both the elimination and the conversion rates.

Absorption rate constant (k_a)

→ scenario → pharmacology → drugs → drug → PK → k_a

<k_a
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Min: 0

Absorption rate parameter. Not allowed for one compartment models, but required for two and three compartment models and one compartment with conversion model (for the parent drug only).

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Conversion parameters (parent drug)

→ scenario → pharmacology → drugs → drug → PK → conversion

<conversion>
IN ANY ORDER:
|   <metabolite ... /> 
|   <rate ... /> 
|   <molRatio ... /> 
|   <IC50_log_correlation ... /> 
</conversion>

Documentation (element)

Configures the parent drug in a conversion model.

To use a conversion model, the parent drug should have this section defined as well as half-life or k (direct elimination; this may be zero) and k_a (absorption rate; this may be large).

Metabolite drug (abbreviation)

→ scenario → pharmacology → drugs → drug → PK → conversion → metabolite

<metabolite>
    string
</metabolite>

Documentation (element)

The abbreviation of the metabolite drug (e.g. "DHA" or "DHA_AR").

Rate of conversion

→ scenario → pharmacology → drugs → drug → PK → conversion → rate

<rate
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Rate of conversion of parent drug to metabolite.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Molecular weight ratio

→ scenario → pharmacology → drugs → drug → PK → conversion → molRatio

<molRatio>
    double
</molRatio>

Documentation (element)

Ratio of molecular weights: molecular weight of the metabolite divided by molecular weight of the parent.

IC50 log correlation

→ scenario → pharmacology → drugs → drug → PK → conversion → IC50_log_correlation

<IC50_log_correlation>
    double
</IC50_log_correlation>

Documentation (element)

Min: 0 Max: 1

If this value is 1, samples are fully correlated: a single z-score is used to calculate both samples. If this is 0, two independent samples are used.

Values between 0 and 1 (partial correlation) are supported; in this case IC50 values are sampled such that cor(log(x), log(y)) matches this value (where x, y are parent and metabolite IC50 values).

Volume of Distribution (Vd)

→ scenario → pharmacology → drugs → drug → PK → vol_dist

<vol_dist
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution.

If CV > 0 this is sampled from a log-normal distribution.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Second compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment2

<compartment2>
IN ANY ORDER:
|   <k12 ... /> 
|   <k21 ... /> 
</compartment2>

Documentation (element)

Optional element specifying conversion parameters to- and from- a second compartment.

Absorption rate to compartment 2 (k12)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → k12

<k12
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the first periphery compartment (2).

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Absorption rate from compartment 2 (k21)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → k21

<k21
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the first periphery compartment (2) to the central compartment.

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Third compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment3

<compartment3>
IN ANY ORDER:
|   <k13 ... /> 
|   <k31 ... /> 
</compartment3>

Documentation (element)

Optional element specifying conversion parameters to- and from- a third compartment.

Absorption rate to compartment 3 (k13)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → k13

<k13
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the second periphery compartment (3).

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Absorption rate from compartment 3 (k31)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → k31

<k31
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the second periphery compartment (3) to the central compartment.

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Diagnostic parameters

→ scenario → diagnostics

<diagnostics>
IN THIS ORDER:
| ( <diagnostic ... /> )*
</diagnostics>

diagnostic

Documentation (element)

Diagnostic model parameters

diagnostic

→ scenario → diagnostics → diagnostic

<diagnostic
    name=string
  [ units=("Other" or "Garki" or "Malariatherapy") ]
  [ mechanism=("Other" or "HRP2") ] DEFAULT VALUE Other
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterministic ... /> 
| |   <stochastic ... /> 
</diagnostic>

Attributes

Name of diagnostic

name=string

Name of this diagnostic (parameterisation). May be used elsewhere in the XML document to refer to this set of diagnostic parameters.

Parasite density units / methodology

units=("Other" or "Garki" or "Malariatherapy")

Mechanism

mechanism=("Other" or "HRP2")

Default value: Other

Deterministic detection

→ scenario → diagnostics → diagnostic → deterministic

<deterministic
    minDensity=double
  />

Documentation (element)

Specify that an artificial deterministic test is used: outcome is positive if parasite density is at least the minimum given.

Attributes

Minimum detectible density

minDensity=double

Units: parasites/microlitre Min: 0

The minimum density at which parasites can be detected. If 0, the test outcome is always positive.

Non-deterministic detection

→ scenario → diagnostics → diagnostic → stochastic

<stochastic
    dens_50=double
    specificity=double
  />

Documentation (element)

An improved model of detection which is non-deterministic, including false positive results as well as false negatives.

Some parameterisations:

Microscopy sensitivity/specificity data in Africa; Source: expert opinion — Allan Schapira dens_50 = 20.0 specificity = .75

RDT sensitivity/specificity for Plasmodium falciparum in Africa Source: Murray et al (Clinical Microbiological Reviews, Jan. 2008) dens_50 = 50.0; specificity = .942;

Attributes

Density 50

dens_50=double

Units: parasites/microlitre Min: 0

The density at which the test outcome has a 50% chance of being positive.

Specificity

specificity=double

Units: Dimensionless Min: 0 Max: 1

The probability of a positive test outcome in the absense of parasites.

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
| [ <vivax ... /> ]
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: model/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=string
  >
IN ANY ORDER:
| [ <NeonatalMortality ... /> ]
| [ <NonMalariaFevers ... /> ]
</clinical>

Documentation (type)

Attributes

Follow-up period during which recurrence is considered a treatment failure

healthSystemMemory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

Neonatal mortality parameters

→ scenario → model → clinical → NeonatalMortality

<NeonatalMortality
    diagnostic=string
  />

Attributes

Diagnostic used to parameterise model

diagnostic=string

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
| [ <prNeedTreatmentNMF ... /> ]
| [ <prNeedTreatmentMF ... /> ]
</NonMalariaFevers>

Documentation (type)

Description of the incidence of non-malaria fever. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a non-malarial fever requires treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

Availability of humans to mosquitoes relative to an adult, categorized by age group

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ]
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

Vivax model parameters

→ scenario → model → vivax

<vivax>
IN ANY ORDER:
|   <probBloodStageInfectiousToMosq ... /> 
|   <hypnozoiteRelease ... /> 
|   <bloodStageProtectionLatency ... /> 
|   <bloodStageLengthDays ... /> 
|   <clinicalEvents ... /> 
</vivax>

Documentation (element)

This describes Vivax model parameters, and is required when using the VIVAX_SIMPLE_MODEL model option.

Probability of mosquito infection

→ scenario → model → vivax → probBloodStageInfectiousToMosq

<probBloodStageInfectiousToMosq
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

The chance of a feeding mosquito becoming infected, given that the host is patent. (This may be adjusted by transmission-blocking vaccines.)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Hypnozoite releases

→ scenario → model → vivax → hypnozoiteRelease

<hypnozoiteRelease
  [ pSecondRelease=double ] DEFAULT VALUE 0
  >
IN ANY ORDER:
|   <numberHypnozoites ... /> 
|   <firstReleaseDays ... /> 
| [ <secondReleaseDays ... /> ]
</hypnozoiteRelease>

Documentation (element)

Describes the number and times of hypnozoite releases.

Documentation (type)

This element defines probabilites when and how many hypnozoites are released from the liverstage into the blood.

The gap between the start of a new brood of hypnozoites and its release are defined as follows:

latentP + latentRelapse + randomReleaseDelay

randomReleaseDelay is based on one or two lognormal distributions, which are defined in firstRelease and optionally secondRelease.

You can define 2 release distributions, which get added together and represent the probability of hypnozoites which get released before winter (first release) or after (second release).

You can omit the secondRelease element if no release to the blood happens after winter.

Attributes

latent relapse days

pSecondRelease=double

Default value: 0

Probability of a second release. If undefined it is zero.

Number of Hypnozoites

→ scenario → model → vivax → hypnozoiteRelease → numberHypnozoites

<numberHypnozoites
    max=int
    base=double
  />

Documentation (element)

numberHypnozoites calculates the number of hypnozoites in the liver stage based on a base which is between 0 and 1.

This number is random based on the following distribution and normalized:

max ∑ (base ^ n) n = 0

Attributes

max

max=int

base

base=double

firstReleaseDays

→ scenario → model → vivax → hypnozoiteRelease → firstReleaseDays

<firstReleaseDays
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
    latentRelapse=double
  />

Documentation (type)

Hypnozoites are released after a delay, calculated as: roundToTSFromDays(delay + latentRelapse)

Here, roundToTSFromDays rounds the input (in days) to the nearest timestep, delay is sampled from a log-normal, and latentRelapse is the parameter specified here.

The delay is sampled from a log-normal distribution, parameterised via the (linear) mean and CV (coefficient of variation) given here.

Documentation (base type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

latent relapse days

latentRelapse=double

Usually between 10 and 15 days.

secondReleaseDays

→ scenario → model → vivax → hypnozoiteRelease → secondReleaseDays

<secondReleaseDays
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
    latentRelapse=double
  />

Documentation (type)

Hypnozoites are released after a delay, calculated as: roundToTSFromDays(delay + latentRelapse)

Here, roundToTSFromDays rounds the input (in days) to the nearest timestep, delay is sampled from a log-normal, and latentRelapse is the parameter specified here.

The delay is sampled from a log-normal distribution, parameterised via the (linear) mean and CV (coefficient of variation) given here.

Documentation (base type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

latent relapse days

latentRelapse=double

Usually between 10 and 15 days.

Blood stage protection latency

→ scenario → model → vivax → bloodStageProtectionLatency

<bloodStageProtectionLatency
    value=double
  />

Documentation (element)

Min: 0

The length of time after expiry of a blood-stage infection during which relapses from the same brood are supressed by the immune system.

This is rounded to the nearest time-step.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Blood stage length

→ scenario → model → vivax → bloodStageLengthDays

<bloodStageLengthDays
    scale=double
    shape=double
    distr=("weibull")
  />

Documentation (element)

Units: Days

Parameters used to sample the length of blood-stage infections from a Weibull distribution (scale parameter lambda, shape parameter k).

Documentation (type)

Parameters of a Weibull distribution.

Attributes

Scale

scale=double

The Weibull scale parameter (λ).

shape

shape=double

The Weibull shape parameter (k).

Distribution

distr=("weibull")

To allow heterogeneity, a distribution must be specified. In this case, only "weibull" is allowed.

clinicalEvents

→ scenario → model → vivax → clinicalEvents

<clinicalEvents>
IN THIS ORDER:
|   <pPrimaryInfection ... /> 
|   <pRelapseOne ... /> 
|   <pRelapseTwoPlus ... /> 
|   <pEventIsSevere ... /> 
</clinicalEvents>

Documentation (type)

This elements holds all information about probabilites for clinical events from infections and relapses.

pPrimaryInfection

→ scenario → model → vivax → clinicalEvents → pPrimaryInfection

<pPrimaryInfection
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseOne

→ scenario → model → vivax → clinicalEvents → pRelapseOne

<pRelapseOne
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseTwoPlus

→ scenario → model → vivax → clinicalEvents → pRelapseTwoPlus

<pRelapseTwoPlus
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pEventIsSevere

→ scenario → model → vivax → clinicalEvents → pEventIsSevere

<pEventIsSevere
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=string
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=string

Units: User defined (default: steps) Min: 0 Max: 20

Pre-erythrocytic latent period Can be specified in steps (e.g. 3t) or days (e.g. 15d).

parameter

→ scenario → model → parameters → parameter

<parameter
  [ name=string ]
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 43 documentation

Generated from: scenario_43.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
  [ analysisNo=int ]
    name=string
  [ wuID=int ]
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:om="http://openmalaria.org/schema/scenario_43"
    xsi:schemaLocation="http://openmalaria.org/schema/scenario_43 scenario_43.xsd"
  >
IN ANY ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entomology ... /> 
| [ <parasiteGenetics ... /> ]
| [ <pharmacology ... /> ]
| [ <diagnostics ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Name of intervention

Work unit identifier

wuID=int

Units: Number

Work unit ID. Obselete and no longer required.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Description of demography

Attributes

Name of demography data

name=string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Years Min: 0 Max: 100

Maximum age of simulated humans in years

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

list of age groups included in demography

Documentation (type)

list of age groups included in demography or surveys

Attributes

Lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Units: Percentage Min: 0 Max: 100

Percentage of human population in age group

Upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ startDate=string ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
| [ <cohorts ... /> ]
</monitoring>

Documentation (element)

Description of surveys

Attributes

Name of monitoring settings

name=string

Name of monitoring settings

Start of monitoring

startDate=string

continuous

→ scenario → monitoring → continuous

<continuous
    period=string
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Delay between reports

period=string

Units: User defined (default: steps)

Delay between reports; typically one time step but can be greater. Can be specified in steps (e.g. 1t) or days (e.g. 5d).

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions
  [ onlyNewEpisode=boolean ] DEFAULT VALUE false
  >
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See model/mon/OutputMeasures.h for a list of supported outputs. Should also be on the wiki.

Attributes

Report only for new cases

onlyNewEpisode=boolean

Default value: false

option

→ scenario → monitoring → SurveyOptions → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  [ outputNumber=int ]
  [ byAge=boolean ]
  [ byCohort=boolean ]
  [ bySpecies=boolean ]
  [ byGenotype=boolean ]
  [ byDrugType=boolean ]
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Number identifying measure in output

outputNumber=int

Report by age category

byAge=boolean

Report by cohort

byCohort=boolean

Report by mosquito species

bySpecies=boolean

Report by parasite genotype

byGenotype=boolean

Report by drug type

byDrugType=boolean

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
  [ detectionLimit=double ]
  [ diagnostic=string ]
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/microlitre Min: 0

Deprecated: limit above which a human's infection is reported as patent. Alternative: do not specify this; instead specify "diagnostic".

Name of monitoring diagnostic

diagnostic=string

Name of a parameterised diagnostic to use in surveys (see scenario/diagnostics).

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime
  [ repeatStep=string ]
  [ repeatEnd=string ]
  [ reported=boolean ] DEFAULT VALUE true
  >
    string
</surveyTime>

Documentation (element)

Units: User defined (defaults to steps) Min: 0

The simulation ends immediately after the last survey is taken.

Attributes

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

reported

reported=boolean

Default value: true

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Cohorts

→ scenario → monitoring → cohorts

<cohorts>
IN THIS ORDER:
| ( <subPop ... /> )+
</cohorts>

subPop

Documentation (element)

Allows the configuration of multiple cohorts (output segregated according to membership within specific sub-populations).

If this element is omitted, monitoring surveys cover the entire simulated human population.

It does not affect the "continuous" outputs (these never take cohorts into account).

Sub-population

→ scenario → monitoring → cohorts → subPop

<subPop
    id=string
    number=integer
  />

Documentation (element)

In the output file, the output set is identified by multiplying this number by 1000 then adding it to the age group column.

Attributes

Sub-population identifier

id=string

Textual identifier for the sub-population (i.e. for an intervention component, since sub-populations are defined as the hosts an intervention component is deployed to).

Sub-population number

number=integer

Units: dimensionless Min: 1 Max: 2097152

Number identifying a sub-population; used to define identifiers of output sets. This number must be a power of 2 (i.e. 1, 2, 4, 8, ...). See documentation of subPop element.

Preventative interventions

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfections ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <vectorPop ... /> ]
| [ <vectorTrap ... /> ]
| [ <nonHumanHostsModifications ... /> ]
| [ <addNonHumanHosts ... /> ]
| [ <human ... /> ]
</interventions>

Documentation (element)

Attributes

Name of intervention set

name=string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeHS>

timedDeployment

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeHS → timedDeployment

<timedDeployment
    time=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timedDeployment>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</uncomplicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

multiple

→ scenario → interventions → human → component → decisionTree → multiple

<multiple
  [ name=string ]
  >
IN THIS ORDER:
| ( <caseType ... /> )*
| ( <diagnostic ... /> )*
| ( <random ... /> )*
| ( <age ... /> )*
| ( <treatPKPD ... /> )*
| [ <treatSimple ... /> ]
| ( <deploy ... /> )*
</multiple>

Documentation (type)

A special node allowing multiple sub-trees to be evaluated.

This is different from an ordinary decision tree node in that:

a) multiple types of child can occur simultaneously (e.g. multiple types of treatment or treatment plus a 'random' sub-tree)

b) the 'noTreatment' and 'treatFailure' nodes are not allowed

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → multiple → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

firstLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → firstLine

<firstLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</firstLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

secondLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → secondLine

<secondLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</secondLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

positive

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

outcome

→ scenario → interventions → human → component → decisionTree → multiple → random → outcome

<outcome
  [ name=string ]
    p=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</outcome>

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Probability

p=double

Units: None Min: 0 Max: 1

Probability of selecting this outcome. The sum of probabilities across all outcomes must be 1.

age

→ scenario → interventions → human → component → decisionTree → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Age range

→ scenario → interventions → human → component → decisionTree → multiple → age → age

<age
  [ name=string ]
    lb=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</age>

Documentation (element)

Describes a branch, selected for patients of a certain age.

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Lower bound (inclusive)

lb=double

Min: 0

noTreatment

→ scenario → interventions → human → component → decisionTree → noTreatment

<noTreatment
  [ name=string ]
  />

Documentation (type)

An end node doing nothing. This exists to explicitly state that no treatment happens and to prevent trees from accidentally being left incomplete.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatFailure

→ scenario → interventions → human → component → decisionTree → treatFailure

<treatFailure
  [ name=string ]
  />

Documentation (type)

An end node which reports treatment but does not change parasitalogical status. This allows correct labelling of second-line cases.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → multiple → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

age

→ scenario → interventions → human → component → decisionTree → multiple → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → multiple → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → multiple → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → multiple → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</complicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: Days Min: 0 Max: unbounded

Maximum number of timesteps (including first day of case) that an individual with an uncomplicated case of malaria will remember he/she was sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial or non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of a complicated or severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
  [ name=string ]
  [ useDiagnosticUC=boolean ] DEFAULT VALUE false
  >
IN ANY ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <treatmentActions ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
</ImmediateOutcomes>

Documentation (type)

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Name of case management parameterisation

name=string

Name of health system

useDiagnosticUC

useDiagnosticUC=boolean

Default value: false

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Description of drug regimen.

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Artemisinine based combination therapy

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Quinine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0 Max: 1name:P(self-treat)

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Effectiveness of treatment for non-compliant patients

treatmentActions

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions

<treatmentActions>
IN ANY ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
</treatmentActions>

CQ
SP
AQ
SPAQ
ACT
QN

CQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ

<CQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</CQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

deploy

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy

<deploy
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ p=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| ( <component ... /> )+
</deploy>

component

Attributes

Maximum age of eligible humans

maxAge=double

Units: Years Min: 0

Maximum age of eligible humans (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible humans

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible humans (defaults to 0). Input is rounded to the nearest time step.

Probability of delivery to eligible humans

p=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Probability of this list of components being deployed, given that other constraints are met.

component

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Prophylactic treatment

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere → clearInfections

<clearInfections
    timesteps=string
    stage=("liver" or "blood" or "both")
  />

Documentation (element)

Attributes

Length of effect

timesteps=string

Units: User defined (defaults to steps)

Target stage

stage=("liver" or "blood" or "both")

SP

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SP

<SP
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SP>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

AQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → AQ

<AQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</AQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

SPAQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SPAQ

<SPAQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SPAQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

ACT

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → ACT

<ACT
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</ACT>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

QN

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → QN

<QN
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</QN>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

Probability that human is incompatible with liver-stage drug treatment

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pHumanCannotReceive

<pHumanCannotReceive
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that a human is determined to be unable to receive liver-stage drug treatment. Treatment is neither reported or given for such humans.

This is sampled once per human at birth.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Ignore liver-stage drug treatment incompatibility

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → ignoreCannotReceive

<ignoreCannotReceive
    value=boolean
  />

Documentation (element)

If true, ignore pHumanCannotReceive and consider all humans eligible for treatment; if false (or not specified), do not treat those demed incompatible with liver-stage drug treatment.

The point of this is that pHumanCannotReceive cannot be altered by changeHS interventions, but this property can be.

Attributes

Input parameter value

value=boolean

A boolean value.

Prob use in UC case

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pUseUncomplicated

<pUseUncomplicated
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

This feature is deprecated; it is suggested to use the "simple treatment" feature configured to clear liver-stage parasites, leaving this option unset or zero.

Chance of liver-stage drug treatment being used for routine treatment of an uncomplicated case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Effectiveness

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → effectivenessOnUse

<effectivenessOnUse
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that liver-stage drug treatment is effective.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

DecisionTree5Day

<DecisionTree5Day
  [ name=string ]
  >
IN ANY ORDER:
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
|   <treeUCOfficial ... /> 
|   <treeUCSelfTreat ... /> 
|   <cureRateSevere ... /> 
|   <treatmentSevere ... /> 
</DecisionTree5Day>

Documentation (type)

Besides greater flexibility, this allows treatment via PK/PD models.

Attributes

Name of case management parameterisation

name=string

Name of health system

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → DecisionTree5Day → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → DecisionTree5Day → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

treeUCOfficial

→ scenario → healthSystem → DecisionTree5Day → treeUCOfficial

<treeUCOfficial
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCOfficial>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treeUCSelfTreat

→ scenario → healthSystem → DecisionTree5Day → treeUCSelfTreat

<treeUCSelfTreat
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCSelfTreat>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Cure rate (severe cases)

→ scenario → healthSystem → DecisionTree5Day → cureRateSevere

<cureRateSevere
    value=double
  />

Documentation (element)

Min: 0 Max: 1

The probability of clearing parasites given access to appropriate (hospital) care, for a severe case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

treatmentSevere

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere

<treatmentSevere
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</treatmentSevere>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Case fatality rate for inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: Dimensionless

List of age-specific probabilities of sequelae in inpatients, during a severe bout of malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeEIR>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeEIR → timedDeployment

<timedDeployment
    eipDuration=int
    time=string
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timedDeployment>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Time

time=string

Units: User defined (defauls to steps) Min: 0

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=string ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=string

Units: User defined (default: steps) Min: 0

Default value: 0

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=string
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time of start

time=string

Units: User defined (defauls to steps) Min: 0

Insert R_0 case

<insertR_0Case
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</insertR_0Case>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → insertR_0Case → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Uninfect vectors

<uninfectVectors
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</uninfectVectors>

timedDeployment

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → uninfectVectors → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Vector population intervention

→ scenario → interventions → vectorPop

<vectorPop>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorPop>

intervention

Documentation (element)

Units: List of elements

A list of parameterisations of generic vector host-inspecific interventions.

intervention

→ scenario → interventions → vectorPop → intervention

<intervention
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

Units: List of elements

An intervention which may have various effects on the vector populations as a whole. (Not host specific.)

Multiple instances of this intervention class are allowed (multiple parameterisations, not just deployments).

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → vectorPop → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → vectorPop → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <seekingDeathRateIncrease ... /> ]
| [ <probDeathOvipositing ... /> ]
| [ <emergenceReduction ... /> ]
</anopheles>

Documentation (type)

Units: dimensionless Min: 0 Max: 1

Descriptions of the effects of vector interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Proportional increase in deaths while host searching

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease

<seekingDeathRateIncrease
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</seekingDeathRateIncrease>

decay

Documentation (element)

Units: dimensionless

Describe an effect on the increase in the death rate while host seeking (mu_vA) due to this intervention.

Enter the rate increase (i.e. if rate increases to 120% of normal, give 0.2). New death rate while seeking is old × (1 + increase) where increase is this factor given. Must have increas ≥ -1.

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Proportion ovipositing mosquitoes killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing

<probDeathOvipositing
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probDeathOvipositing>

decay

Documentation (element)

Units: dimensionless

Describe an effect of increased mortality while ovipositing due to this intervention. Enter the probability of dying due to this intervention.

Attributes

Initial probability of killing

initial=double

Units: dimensionless Min: 0 Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Proportion of emerging pupa killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction

<emergenceReduction
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</emergenceReduction>

decay

Documentation (element)

Units: dimensionless

Describe an effect on emergence of pupa into adults: this value is the proportion of emerging pupa which are killed by this intervention.

Attributes

Initial proportion reduction

initial=double

Units: dimensionless Min: -inf Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Vector population intervention deployment

→ scenario → interventions → vectorPop → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

deploy

→ scenario → interventions → vectorPop → intervention → timed → deploy

<deploy
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Baited trap

→ scenario → interventions → vectorTrap

<vectorTrap>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorTrap>

intervention

Documentation (element)

intervention

→ scenario → interventions → vectorTrap → intervention

<intervention
  [ name=string ]
  >
IN THIS ORDER:
| ( <description ... /> )+
| [ <timed ... /> ]
</intervention>

Documentation (type)

Attributes

Descriptive name for type of trap

name=string

Optional name for this type of trap

Description

→ scenario → interventions → vectorTrap → intervention → description

<description
    mosquito=string
  >
IN THIS ORDER:
|   <relativeAvailability ... /> 
|   <decayOfAvailability ... /> 
</description>

Documentation (element)

Parameters associated with a vector trap intervention, per mosquito species.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Initial relative availability

→ scenario → interventions → vectorTrap → intervention → description → relativeAvailability

<relativeAvailability
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: inf

Describes the availiability of a trap to a host-seeking mosquito relative to an average unprotected adult.

I.e. if this parameter is 2, then each trap will on average attract twice as many mosquitoes as unprotected adults.

This is the initial availability; it may decay towards zero depending on the configured decay function.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay of availability

→ scenario → interventions → vectorTrap → intervention → description → decayOfAvailability

<decayOfAvailability
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Describes how availability decays to zero.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Vector trap intervention deployment

→ scenario → interventions → vectorTrap → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )*
</timed>

deploy

Documentation (element)

List of timed vector trap intervention deployment

deploy

→ scenario → interventions → vectorTrap → intervention → timed → deploy

<deploy
    time=string
    ratioToHumans=double
    lifespan=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Ratio to humans

ratioToHumans=double

Min: 0 Max: inf

The number of traps deployed, by this deployment, per adult human. E.g. if there are currently 100 traps and 1000 humans, then a ratio of 0.1 will increase the number of traps to 200.

Lifespan

lifespan=string

Units: Steps or Days or Years

nonHumanHostsModifications

→ scenario → interventions → nonHumanHostsModifications

<nonHumanHostsModifications>
IN THIS ORDER:
| ( <intervention ... /> )+
</nonHumanHostsModifications>

intervention

Documentation (element)

List of interventions that modify parameters of non-human hosts described in the .

intervention

→ scenario → interventions → nonHumanHostsModifications → intervention

<intervention
    name=string
    nonHumanHostsName=string
  >
IN THIS ORDER:
|   <decay ... /> 
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

This intervention modifies parameters of non-human hosts described in the section of the input scenario file.

The intervention is described by 5 parameters that define the change in each of non-human host parameters:

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

Name of intervention

nonHumanHostsName=string

Name of intervention (e.g. larviciding, sugar bait).

decay

→ scenario → interventions → nonHumanHostsModifications → intervention → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

description

→ scenario → interventions → nonHumanHostsModifications → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <availabilityReduction ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
| [ <restingKillingEffect ... /> ]
| [ <fecundityReduction ... /> ]
</anopheles>

Documentation (type)

Descriptions of the effects of non human hosts interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

availabilityReduction

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → availabilityReduction

<availabilityReduction
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

preprandialKillingEffect

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

postprandialKillingEffect

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

restingKillingEffect

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → restingKillingEffect

<restingKillingEffect
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

fecundityReduction

→ scenario → interventions → nonHumanHostsModifications → intervention → description → anopheles → fecundityReduction

<fecundityReduction
    initial=double
  />

Documentation (element)

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

Vector population intervention deployment

→ scenario → interventions → nonHumanHostsModifications → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

addNonHumanHosts

<addNonHumanHosts>
IN THIS ORDER:
| ( <nonHumanHosts ... /> )+
</addNonHumanHosts>

nonHumanHosts

Documentation (element)

List of intervention that add new non-human hosts that have not been described in the .

nonHumanHosts

→ scenario → interventions → addNonHumanHosts → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</nonHumanHosts>

Documentation (type)

Describes a new non-human hosts that have not been described in the .

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
|   <mosqRelativeAvailabilityHuman ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <hostFecundityFactor ... /> 
</anopheles>

Documentation (type)

Descriptions of the effects of new non human hosts with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Relative availability of non-human host (ξ_i)

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqRelativeAvailabilityHuman

<mosqRelativeAvailabilityHuman
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of the population of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → description → anopheles → hostFecundityFactor

<hostFecundityFactor
    value=double
  />

Documentation (element)

Units: Proportion

Multiplicative factor for the number of fertile eggs laid by a mosquito after biting this type of host, relative to an unprotected human.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vector trap intervention deployment

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )*
</timed>

deploy

Documentation (element)

List of timed vector trap intervention deployment

deploy

→ scenario → interventions → addNonHumanHosts → nonHumanHosts → timed → deploy

<deploy
    time=string
    lifespan=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Lifespan

lifespan=string

Units: Steps or Days or Years

Human-specific interventions

→ scenario → interventions → human

<human>
IN THIS ORDER:
| ( <component ... /> )+
| ( <deployment ... /> )*
</human>

Documentation (element)

Encapsulates all interventions whose effects are specific to the human host: any interventions where target humans may be selected via population-coverage, age limits and sub-population membership.

Component

→ scenario → interventions → human → component

<component
    id=string
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <screen ... /> 
| |   <treatSimple ... /> 
| |   <treatPKPD ... /> 
| |   <decisionTree ... /> 
| |   <PEV ... /> 
| |   <BSV ... /> 
| |   <TBV ... /> 
| |   <ITN ... /> 
| |   <IRS ... /> 
| |   <GVI ... /> 
| | [ <recruitmentOnly ... /> ]
| |   <clearImmunity ... /> 
| [ <subPopRemoval ... /> ]
</component>

Documentation (element)

Each element describes one component: its effects, decay of the(se) effect(s), and related stuff (e.g. description of indirect decay and of usage levels).

Attributes

Component identifier

id=string

Name of component

name=string

An informal name/description for the component

screen

→ scenario → interventions → human → component → screen

<screen
    diagnostic=string
  >
IN THIS ORDER:
| ( <positive ... /> )*
| ( <negative ... /> )*
</screen>

Documentation (type)

This can be combined with MDA to achieve mass screen and treat (MSAT) or other types of mass screening intervention.

The use of the screening itself is reported (if enabled), but not the outcome. Deployment of interventions triggered by the screening may be reported, however.

Attributes

Name of diagnostic

diagnostic=string

Name of a parameterised diagnostic (see scenario/diagnostics).

positive

→ scenario → interventions → human → component → screen → positive

<positive
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → screen → negative

<negative
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

treatSimple

→ scenario → interventions → human → component → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

treatPKPD

→ scenario → interventions → human → component → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

decisionTree

→ scenario → interventions → human → component → decisionTree

<decisionTree
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</decisionTree>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Vaccines

→ scenario → interventions → human → component → PEV

<PEV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</PEV>

Documentation (element)

Pre-erythrocytic vaccine (PEV): prevents a proportion of infections from commencing.

Documentation (type)

Description of a vaccine's effect

Decay of effect

→ scenario → interventions → human → component → PEV → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Specification of decay of efficacy. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Variance parameter for vaccine efficacy

→ scenario → interventions → human → component → PEV → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vaccines

→ scenario → interventions → human → component → BSV

<BSV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</BSV>

Documentation (element)

Blood-stage vaccine (BSV): acts as a killing factor on blood-stage parasites. Exact action depends on the within host model.

Documentation (type)

Description of a vaccine's effect

Vaccines

→ scenario → interventions → human → component → TBV

<TBV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</TBV>

Documentation (element)

Transmission-blocking vaccine (TBV): one minus this scales the probability of transmission to mosquitoes

Documentation (type)

Description of a vaccine's effect

Bed nets

→ scenario → interventions → human → component → ITN

<ITN>
IN THIS ORDER:
| [ <usage ... /> ]
|   <holeRate ... /> 
|   <ripRate ... /> 
|   <ripFactor ... /> 
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
|   <attritionOfNets ... /> 
| ( <anophelesParams ... /> )+
</ITN>

Documentation (element)

Description of bed-net interventions (ITNs, LLINs).

Proportion of time nets are used by humans

→ scenario → interventions → human → component → ITN → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of nets by humans, from 0 to 1.

At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing.

See also "propActing" (proportion of bits for which net acts).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Rate at which holes are made

→ scenario → interventions → human → component → ITN → holeRate

<holeRate
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: Holes per annum Min: 0

The rate at which new holes are made in nets.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Rate at which holes are enlarged

→ scenario → interventions → human → component → ITN → ripRate

<ripRate
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: Rips per existing hole per annum Min: 0

Each existing hole has a probability of being ripped bigger according to a Poisson process with this rate as (only) parameter.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Rip factor

→ scenario → interventions → human → component → ITN → ripFactor

<ripFactor
    value=double
  />

Documentation (element)

Units: none Min: 0

This factor expresses how important rips are in increasing the hole.

The hole index of a net is h + F×x where h and x are the total numbers of holes and rips respectively and F is the rip factor.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → ITN → initialInsecticide

<initialInsecticide
    mean=double
  [ SD=double ]
  [ distr=("const" or "normal") ] DEFAULT VALUE const
  />

Documentation (element)

Units: mg/m² Min: 0

Documentation (type)

A parameter with optional heterogeneity.

Optionally, a distribution ("distr") and standard of deviation ("SD") may be specified.

Attributes

mean

mean=double

The mean value.

standard deviation

SD=double

The standard deviation of variates.

Distribution

distr=("const" or "normal")

Default value: const

Decay of insecticide

→ scenario → interventions → human → component → ITN → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of nets. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Attrition of nets

→ scenario → interventions → human → component → ITN → attritionOfNets

<attritionOfNets
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: dimensionless

Specifies the rate at which nets are disposed of over time. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Humans are removed from the intervention component's sub-population on disposal (attrition) of their nets. Currently this event is not reported.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → human → component → ITN → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <holeIndexMax ... /> ]
| EXACTLY ONE OF:
| |   <deterrency ... /> 
| |   <twoStageDeterrency ... /> 
| EXACTLY ONE OF:
| |   <preprandialKillingEffect ... /> 
| |   <preprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| |   <postprandialKillingEffect ... /> 
| |   <postprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| | [ <fecundityReduction ... /> ]
| | [ <fecundityReductionLogit ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which net acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

maximum of holed surface area that has an effect (comparable to no net)

→ scenario → interventions → human → component → ITN → anophelesParams → holeIndexMax

<holeIndexMax
    value=double
  />

Documentation (element)

Units: in same unit as holeIndex

Used by logit attacking and killing models only, holeIndexMax is a user defined maximum hole index (typically, the total surface area of a net).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency

<twoStageDeterrency>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <entering ... /> 
| |   <enteringLogit ... /> 
| EXACTLY ONE OF:
| |   <attacking ... /> 
| |   <attackingLogit ... /> 
</twoStageDeterrency>

Documentation (element)

Units: dimensionless

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

This deterrency model multiplies human attractiveness by pEnt×pAtt.

Deterrency: entering

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → entering

<entering
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless

pEnt represents the relative probability of entering due to ITNs: pEnt = exp(log(P)×p) where P is the insecticide factor and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Deterrency: entering (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → enteringLogit

<enteringLogit
    baseFactor=double
    insecticideFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: none

See parent element documentation

Insecticide factor

insecticideFactor=double

Units: none

See parent element documentation

Deterrency: attacking

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attacking

<attacking
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Deterrency: attacking (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attackingLogit

<attackingLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Pre-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Pre-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffectLogit

<preprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Post-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffectLogit

<postprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Fecundity reduction

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-B), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReductionLogit

<fecundityReductionLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-K0), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Indoor residual spraying

→ scenario → interventions → human → component → IRS

<IRS>
IN THIS ORDER:
| [ <usage ... /> ]
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
| ( <anophelesParams ... /> )+
</IRS>

Documentation (element)

Description of indoor residual spraying interventions.

Documentation (type)

Description of effect for the more complex and probably more realistic Briet model: IRS has three effects, whos strength is calculated as a function of surviving insecticide content.

Proportion of Indoor residual spraying (IRS) interventions

→ scenario → interventions → human → component → IRS → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Indoor residual spraying (IRS) interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → IRS → initialInsecticide

<initialInsecticide
    mean=double
  [ SD=double ]
  [ distr=("const" or "normal") ] DEFAULT VALUE const
  />

Documentation (element)

Units: μg/cm² Min: 0

Documentation (type)

A parameter with optional heterogeneity.

Optionally, a distribution ("distr") and standard of deviation ("SD") may be specified.

Attributes

mean

mean=double

The mean value.

standard deviation

SD=double

The standard deviation of variates.

Distribution

distr=("const" or "normal")

Default value: const

Decay of insecticide

→ scenario → interventions → human → component → IRS → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → IRS → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → IRS → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied by exp(P×log(p)) where P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction

→ scenario → interventions → human → component → IRS → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

First, we calculate K = B + P×p where B is the base (without protection) probability of death, and P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Fecundity is multiplied by (1−K) / (1−B). It is not allowed to be greater than 1. To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Generic vector intervention

→ scenario → interventions → human → component → GVI

<GVI>
IN THIS ORDER:
| [ <usage ... /> ]
|   <decay ... /> 
| ( <anophelesParams ... /> )+
</GVI>

Documentation (element)

Note that all actions of this intervention component will decay according to a single decay function. If independant decay is wanted, a separate component can be used for each action.

Proportion of generic vector interventions

→ scenario → interventions → human → component → GVI → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Generic vector interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay

→ scenario → interventions → human → component → GVI → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Description of decay of all intervention effects. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → GVI → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <deterrency ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → GVI → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of intervention on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied this factor times survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Fecundity reduction effect

→ scenario → interventions → human → component → GVI → anophelesParams → fecundityReduction

<fecundityReduction
    value=double
  />

Documentation (element)

Min: 0

Fertility is multiplied by 1 - (fecundityReduction * decay).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Recruitment only

→ scenario → interventions → human → component → recruitmentOnly

<recruitmentOnly/>

Documentation (element)

Recruitment of a host into a sub-population.

Clear Immunity

→ scenario → interventions → human → component → clearImmunity

<clearImmunity/>

Documentation (element)

Removes all exposure-related immunitsy gained over time by hosts without removing infections (or affecting the ability to gain immunity through exposure).

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

subPopRemoval

→ scenario → interventions → human → component → subPopRemoval

<subPopRemoval
  [ onFirstBout=boolean ] DEFAULT VALUE false
  [ onFirstTreatment=boolean ] DEFAULT VALUE false
  [ onFirstInfection=boolean ] DEFAULT VALUE false
  [ afterYears=double ]
  />

Documentation (type)

ITN attrition also removes humans from sub-populations.

Attributes

Time to first episode only

onFirstBout=boolean

Default value: false

Time to first treatment only

onFirstTreatment=boolean

Default value: false

Time to first infection only

onFirstInfection=boolean

Default value: false

Remove from sub-population after

afterYears=double

Units: Years Min: 0

Deployment

→ scenario → interventions → human → deployment

<deployment
  [ name=string ]
  >
IN THIS ORDER:
| ( <component ... /> )+
| ( <condition ... /> )*
| ( <continuous ... /> )*
| ( <timed ... /> )*
</deployment>

Documentation (element)

All components deployed by this intervention are deployed to the same people (each timed or continuous deployment selects recipients and then gives each recipient all components of the intervention).

Attributes

Intervention name

name=string

Name of intervention

component

→ scenario → interventions → human → deployment → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Condition

→ scenario → interventions → human → deployment → condition

<condition
    measure=string
  [ minValue=double ]
  [ maxValue=double ]
    initialState=boolean
  />

Documentation (element)

Conditions are evaluated for the whole population, not for individual age-groups or cohorts.

This affects all types of deployment.

Attributes

Measure

measure=string

The monitoring measure to test. Not all measures are available for use.

Minimum value

minValue=double

Minimum value. If specified, the measured variable must be greater than or equal to this value for the condition to be satisfied.

Maximum value

maxValue=double

Maximum value. If specified, the measured variable must be less than or equal to this value for the condition to be satisfied.

Initial state

initialState=boolean

Whether this condition is considered true or false before updated by a survey.

Age-based (continuous) deployment

→ scenario → interventions → human → deployment → continuous

<continuous>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| ( <deploy ... /> )+
</continuous>

Documentation (element)

List of ages at which deployment takes place (through EPI, post-natal and school-based programmes, etc.).

A sub-population restriction may be added as a property of the list of continuous deployments.

restrictToSubPop

→ scenario → interventions → human → deployment → continuous → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

deploy

→ scenario → interventions → human → deployment → continuous → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    targetAgeYrs=double
  [ begin=string ]
  [ end=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention. Input is rounded to the nearest time step.

First time active

begin=string

Units: User defined (defauls to steps)

End step

end=string

Units: User defined (defauls to steps)

Mass (timed) deployment

→ scenario → interventions → human → deployment → timed

<timed>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| [ <cumulativeCoverage ... /> ]
| ( <deploy ... /> )+
</timed>

Documentation (element)

List of timed deployments of the intervention (that is, of deployment campaigns).

Cumulative deployment mode can be specified for all deployments in a timed list. To allow multiple cumulative deployment descriptions, the entire timed list may be repeated.

restrictToSubPop

→ scenario → interventions → human → deployment → timed → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

Cumulative coverage

→ scenario → interventions → human → deployment → timed → cumulativeCoverage

<cumulativeCoverage
    component=string
  />

Documentation (element)

Attributes

Component identifier

component=string

The identifier (short name) of the component used when selecting people.

deploy

→ scenario → interventions → human → deployment → timed → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    time=string
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ repeatStep=string ]
  [ repeatEnd=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Time

time=string

Units: User defined (defauls to steps) Min: 0

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0

Maximum age of eligible individuals (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible individuals (defaults to 0). Input is rounded to the nearest time step.

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Description of health system.

Documentation (type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("forced" or "dynamic")
  [ scaledAnnualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Description of entomological data

Attributes

Entomology dataset name

name=string

Name of entomology data

Transmission model mode

mode=("forced" or "dynamic")

Override annual EIR

scaledAnnualEIR=double

Units: Infectious bites per adult per year

If set, the annual EIR (for all species of vector) is scaled to this level; can be omitted if not needed.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters of the transmission model

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <seasonality ... /> 
|   <mosq ... /> 
| [ <lifeCycle ... /> ]
| [ <simpleMPD ... /> ]
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial estimate of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial estimate of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial estimate of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Seasonality of transmission

→ scenario → entomology → vector → anopheles → seasonality

<seasonality
    input=("EIR")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <fourierSeries ... /> 
| |   <monthlyValues ... /> 
| |   <dailyValues ... /> 
</seasonality>

Documentation (element)

Specifies the seasonality of transmission and optionally the level of annual transmission.

Attributes

Seasonality input

input=("EIR")

Annual EIR

annualEIR=double

Units: Inoculations per adult per annum Min: 0

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries

<fourierSeries
    EIRRotateAngle=double
  >
IN THIS ORDER:
| ( <coeffic ... /> )*
</fourierSeries>

coeffic

Documentation (element)

Units: Infectious bites per adult per day

Attributes

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: Radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Pair of Fourier coefficients

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries → coeffic

<coeffic
    a=double
    b=double
  />

Documentation (element)

A pair of Fourier series coefficients. The first element specifies a1 and b1, the second a2 and b2, etc. Any number (from 0 up) of pairs may be given.

Attributes

a_n parameter of Fourier approximation to ln(EIR)

a=double

a_n parameter of Fourier approximation to ln(EIR) for some natural number n.

b_n parameter of Fourier approximation to ln(EIR)

b=double

b_n parameter of Fourier approximation to ln(EIR) for some natural number n.

List of monthly values

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues

<monthlyValues
    smoothing=("none" or "fourier")
  >
IN THIS ORDER:
| ( <value ... /> ){12,12}
</monthlyValues>

value

Documentation (element)

Description of seasonality from monthly values. Multiple smoothing methods are possible (see smoothing attribute).

List should contain twelve entries: January to December.

Attributes

Smoothing function

smoothing=("none" or "fourier")

How the monthly values are converted into a daily sequence of values:

none: no smoothing (step function)
Fourier: a Fourier series (with terms up to a2/b2) is fit to the sequence of monthly values and used to generate a smoothed list of daily values.

Monthly value

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Monthly value

List of daily values

→ scenario → entomology → vector → anopheles → seasonality → dailyValues

<dailyValues>
IN THIS ORDER:
| ( <value ... /> ){365,365}
</dailyValues>

value

Documentation (element)

Description of seasonality from daily values.

List should contain 365 entries: 1st January to 31st December.

Daily value

→ scenario → entomology → vector → anopheles → seasonality → dailyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Daily value

Mosquito feeding cycle parameters

→ scenario → entomology → vector → anopheles → mosq

<mosq
    minInfectedThreshold=double
  >
IN ANY ORDER:
|   <mosqRestDuration ... /> 
|   <extrinsicIncubationPeriod ... /> 
|   <mosqLaidEggsSameDayProportion ... /> 
|   <mosqSeekingDuration ... /> 
|   <mosqSurvivalFeedingCycleProbability ... /> 
|   <availability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <mosqProbOvipositing ... /> 
|   <mosqHumanBloodIndex ... /> 
</mosq>

Documentation (element)

Parameters describing the feeding cycle and human mosquito interaction of a single species of anopheles mosquito.

Attributes

Mininum infected threshold for mosquitos

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

Duration of the resting period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqRestDuration

<mosqRestDuration
    value=int
  />

Documentation (element)

Units: Days

name:Duration of the resting period of the vector (days);

Attributes

Input parameter value

value=int

An integer value.

Extrinsic incubation period

→ scenario → entomology → vector → anopheles → mosq → extrinsicIncubationPeriod

<extrinsicIncubationPeriod
    value=int
  />

Documentation (element)

Units: Days

name:Extrinsic incubation period (days)

Attributes

Input parameter value

value=int

An integer value.

Proportion of mosquitoes host seeking on same day as ovipositing

→ scenario → entomology → vector → anopheles → mosq → mosqLaidEggsSameDayProportion

<mosqLaidEggsSameDayProportion
    value=double
  />

Documentation (element)

Units: Proportion

Proportion of mosquitoes host seeking on same day as ovipositing

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Duration of the host-seeking period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqSeekingDuration

<mosqSeekingDuration
    value=double
  />

Documentation (element)

Units: Days

Duration of the host-seeking period of the vector (days)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito survives the feeding cycle

→ scenario → entomology → vector → anopheles → mosq → mosqSurvivalFeedingCycleProbability

<mosqSurvivalFeedingCycleProbability
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito survives the feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human availability rate heterogeneity

→ scenario → entomology → vector → anopheles → mosq → availability

<availability
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
  />

Documentation (element)

If no attributes are specified or distr="const" or CV="0" then there will be no heterogeneity.

Documentation (type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

Probability that the mosquito succesfully bites chosen host

→ scenario → entomology → vector → anopheles → mosq → mosqProbBiting

<mosqProbBiting
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito succesfully bites chosen host

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → mosq → mosqProbFindRestSite

<mosqProbFindRestSite
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito escapes host and finds a resting place after biting

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → mosq → mosqProbResting

<mosqProbResting
    mean=double
    variance=double
  />

Documentation (element)

Probability of mosquito successfully resting after finding a resting site

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of a mosquito successfully laying eggs given that it has rested

→ scenario → entomology → vector → anopheles → mosq → mosqProbOvipositing

<mosqProbOvipositing
    value=double
  />

Documentation (element)

Probability of a mosquito successfully laying eggs given that it has rested

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human blood index

→ scenario → entomology → vector → anopheles → mosq → mosqHumanBloodIndex

<mosqHumanBloodIndex
    value=double
  />

Documentation (element)

Units: Proportion

The proportion of resting mosquitoes which fed on human blood during the last feed.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mosquito life cycle parameters

→ scenario → entomology → vector → anopheles → lifeCycle

<lifeCycle
  [ estimatedLarvalResources=double ] DEFAULT VALUE 1e8
  >
IN ANY ORDER:
|   <eggStage ... /> 
|   <larvalStage ... /> 
|   <pupalStage ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</lifeCycle>

Documentation (element)

Parameters describing the life-cycle of this species of mosquito

Attributes

Estimate of larval resources

estimatedLarvalResources=double

Units: X

Default value: 1e8

Egg stage

→ scenario → entomology → vector → anopheles → lifeCycle → eggStage

<eggStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the egg stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

larvalStage

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage

<larvalStage>
</larvalStage>

daily

Documentation (type)

Parameters for the larval stage of development

Documentation (base type)

Parameters associated with a mosquito development stage.

Daily development

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage → daily

<daily
    resourceUsage=double
    effectCompetition=double
  />

Documentation (element)

Attributes

Resource usage

resourceUsage=double

Units: X

Resource usage during larval stage of development. Units are arbitrary.

Effect of competition

effectCompetition=double

Units: none

Effect of competition over resources on development.

Pupal stage

→ scenario → entomology → vector → anopheles → lifeCycle → pupalStage

<pupalStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the pupal stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → lifeCycle → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Simple Mosq-Pop-Dynamics parameters

→ scenario → entomology → vector → anopheles → simpleMPD

<simpleMPD>
IN ANY ORDER:
|   <developmentDuration ... /> 
|   <developmentSurvival ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</simpleMPD>

Documentation (element)

Parameters describing the simple mosquito population dynamics model.

This is a simpler version of the life-cycle model, requiring less parameters and with much simpler initialisation.

Duration

→ scenario → entomology → vector → anopheles → simpleMPD → developmentDuration

<developmentDuration
    value=int
  />

Documentation (element)

Units: Days Min: 1

Duration from egg laying to emergence in days.

Attributes

Input parameter value

value=int

An integer value.

Probability of survival

→ scenario → entomology → vector → anopheles → simpleMPD → developmentSurvival

<developmentSurvival
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that mosquito survives from the egg being laid to emergence, given no resouce limitations (no density constraints).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → simpleMPD → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Alternative (non-human) host paramters

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN ANY ORDER:
|   <mosqRelativeEntoAvailability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
| [ <hostFecundityFactor ... /> ]
</nonHumanHosts>

Documentation (element)

Min: 0

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of non-human host (ξ_i)

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqRelativeEntoAvailability

<mosqRelativeEntoAvailability
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of the population of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative fecundity of biting mosquitoes

→ scenario → entomology → vector → anopheles → nonHumanHosts → hostFecundityFactor

<hostFecundityFactor
    value=double
  />

Documentation (element)

Units: Proportion

Multiplicative factor for the number of fertile eggs laid by a mosquito after biting this type of host, relative to an unprotected human.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Name of this species of non human hosts (must match up with those described per anopheles section).

Population size of non-human host species

number=double

Units: Animals

Parasite genetics

<parasiteGenetics
    samplingMode=("initial" or "tracking")
  >
IN THIS ORDER:
| ( <locus ... /> )+
</parasiteGenetics>

locus

Documentation (element)

A specification of genotypes of infection parasites.

May be omitted; in this case there is no modelling of genetic differences of infections (resistance, fitness).

Attributes

samplingMode

samplingMode=("initial" or "tracking")

Locus

→ scenario → parasiteGenetics → locus

<locus
    name=string
  >
IN THIS ORDER:
| ( <allele ... /> )+
</locus>

allele

Documentation (element)

Alleles at loci can affect fitness and resistance to any number of drugs.

Attributes

Name of locus

name=string

Name of the Locus

Allele

→ scenario → parasiteGenetics → locus → allele

<allele
    name=string
    initialFrequency=double
    fitness=double
  [ hrp2_deletion=boolean ] DEFAULT VALUE false
  />

Documentation (element)

Describes an allele, or one possible genetic option of multiple at one point of variance.

Attributes

Name

name=string

Name of the allele; used to refer to it elsewhere.

Initial frequency

initialFrequency=double

Fitness factor

fitness=double

HRP2 deletion

hrp2_deletion=boolean

Default value: false

Drug parameters (PK, PD and usage)

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
|   <treatments ... /> 
|   <drugs ... /> 
</pharmacology>

Documentation (element)

Drug model parameters and drug usage parameters

Documentation (type)

A library of drug related data for the PK/PD model.

Treatments library

→ scenario → pharmacology → treatments

<treatments>
IN THIS ORDER:
| ( <schedule ... /> )+
| ( <dosages ... /> )+
</treatments>

Documentation (element)

A library of drug deployment schedules and dosages.

schedule

→ scenario → pharmacology → treatments → schedule

<schedule
    name=string
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

A schedule for the administration of drugs in a course of treatment.

Note that dose sizes are multiplied by some multiplier (see dosages) and the times of all doses may be delayed.

Attributes

Name

name=string

Name for referring to this deployment schedule

medicate

→ scenario → pharmacology → treatments → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  />

Attributes

drug

drug=string

Abbreviated name of drug compound

Drug dose (mg with multiplier)

mg=double

Units: mg per something

Quantity of drug compound in mg per something. A separate dosage table must be used when medicating, which may specify multipliers of this number based on patient age or weight.

Time of administration

hour=double

Units: Hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

dosages

→ scenario → pharmacology → treatments → dosages

<dosages
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | ( <age ... /> )+
| | ( <bodymass ... /> )+
| |   <multiply ... /> 
</dosages>

Documentation (type)

A table for selecting a dose size. There are several ways this can work: using the patient's age or body mass in a look-up table to get a multplier, or directly using body mass as the multiplier.

The doses specified in "mg" in the treatment schedule are then multiplied by this multiplier.

Attributes

Name

name=string

Name for referring to this dosage table

Look-up table (age)

→ scenario → pharmacology → treatments → dosages → age

<age
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's age.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Look-up table (weight)

→ scenario → pharmacology → treatments → dosages → bodymass

<bodymass
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's body mass.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Multiply dose

→ scenario → pharmacology → treatments → dosages → multiply

<multiply
    by=("kg")
  />

Documentation (element)

Multiply the dose by some quantity, such as patient weight.

Attributes

By what?

by=("kg")

Quantity to multiply the dose by. Only option is "kg" (patient weight in kg).

Drug library

→ scenario → pharmacology → drugs

<drugs>
IN THIS ORDER:
| ( <drug ... /> )+
</drugs>

drug

Documentation (element)

A library of drug PK/PD data.

drug

→ scenario → pharmacology → drugs → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (type)

A drug description with PK/PD parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drugs → drug → PD

<PD
  [ locus=string ]
  >
IN THIS ORDER:
| ( <phenotype ... /> )+
</PD>

phenotype

Attributes

Locus

locus=string

PD parameters for some allele / resistance phenotype

→ scenario → pharmacology → drugs → drug → PD → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

Restrict phenotype applicability to certain alleles

→ scenario → pharmacology → drugs → drug → PD → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (element)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Maximal parasite killing rate

→ scenario → pharmacology → drugs → drug → PD → phenotype → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drugs → drug → PD → phenotype → IC50

<IC50
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

If CV > 0, the IC50 is sampled from a log-normal distribution.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Slope of effect curve

→ scenario → pharmacology → drugs → drug → PD → phenotype → slope

<slope>
    double
</slope>

Documentation (element)

Units: dimensionless

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drugs → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
| EXACTLY ONE OF:
| |   <half_life ... /> 
| | IN THIS ORDER:
| | |   <k ... /> 
| | |   <m_exponent ... /> 
| [ <k_a ... /> ]
| [ <conversion ... /> ]
|   <vol_dist ... /> 
| [ <compartment2 ... /> ]
| [ <compartment3 ... /> ]
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drugs → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drugs → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate λ, calculated as λ = ln(2) / half_life. The basic form of decay is C(t) = C0 * exp(-λ*t).

Alternatively, elimination rate can be specified via k and m_exponent.

Constant associated with elimination rate (k)

→ scenario → pharmacology → drugs → drug → PK → k

<k
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

If CV > 0, k is sampled per-human from the log-normal distribution: ln N( ln(mean) - σ^2 / 2, σ^2).

Alternatively, elimination rate can be specified via half_life.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Constant associated with elimination rate (m_exponent)

→ scenario → pharmacology → drugs → drug → PK → m_exponent

<m_exponent>
    double
</m_exponent>

Documentation (element)

Units: day^-1 Min: 0

Alternatively, elimination rate can be specified via half_life.

Note that in the case of a conversion model, this applies to both the elimination and the conversion rates.

Absorption rate constant (k_a)

→ scenario → pharmacology → drugs → drug → PK → k_a

<k_a
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Min: 0

Absorption rate parameter. Not allowed for one compartment models, but required for two and three compartment models and one compartment with conversion model (for the parent drug only).

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Conversion parameters (parent drug)

→ scenario → pharmacology → drugs → drug → PK → conversion

<conversion>
IN ANY ORDER:
|   <metabolite ... /> 
|   <rate ... /> 
|   <molRatio ... /> 
|   <IC50_log_correlation ... /> 
</conversion>

Documentation (element)

Configures the parent drug in a conversion model.

To use a conversion model, the parent drug should have this section defined as well as half-life or k (direct elimination; this may be zero) and k_a (absorption rate; this may be large).

Metabolite drug (abbreviation)

→ scenario → pharmacology → drugs → drug → PK → conversion → metabolite

<metabolite>
    string
</metabolite>

Documentation (element)

The abbreviation of the metabolite drug (e.g. "DHA" or "DHA_AR").

Rate of conversion

→ scenario → pharmacology → drugs → drug → PK → conversion → rate

<rate
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Rate of conversion of parent drug to metabolite.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Molecular weight ratio

→ scenario → pharmacology → drugs → drug → PK → conversion → molRatio

<molRatio>
    double
</molRatio>

Documentation (element)

Ratio of molecular weights: molecular weight of the metabolite divided by molecular weight of the parent.

IC50 log correlation

→ scenario → pharmacology → drugs → drug → PK → conversion → IC50_log_correlation

<IC50_log_correlation>
    double
</IC50_log_correlation>

Documentation (element)

Min: 0 Max: 1

If this value is 1, samples are fully correlated: a single z-score is used to calculate both samples. If this is 0, two independent samples are used.

Values between 0 and 1 (partial correlation) are supported; in this case IC50 values are sampled such that cor(log(x), log(y)) matches this value (where x, y are parent and metabolite IC50 values).

Volume of Distribution (Vd)

→ scenario → pharmacology → drugs → drug → PK → vol_dist

<vol_dist
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution.

If CV > 0 this is sampled from a log-normal distribution.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Second compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment2

<compartment2>
IN ANY ORDER:
|   <k12 ... /> 
|   <k21 ... /> 
</compartment2>

Documentation (element)

Optional element specifying conversion parameters to- and from- a second compartment.

Absorption rate to compartment 2 (k12)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → k12

<k12
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the first periphery compartment (2).

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Absorption rate from compartment 2 (k21)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → k21

<k21
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the first periphery compartment (2) to the central compartment.

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Third compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment3

<compartment3>
IN ANY ORDER:
|   <k13 ... /> 
|   <k31 ... /> 
</compartment3>

Documentation (element)

Optional element specifying conversion parameters to- and from- a third compartment.

Absorption rate to compartment 3 (k13)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → k13

<k13
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the second periphery compartment (3).

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Absorption rate from compartment 3 (k31)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → k31

<k31
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the second periphery compartment (3) to the central compartment.

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Diagnostic parameters

→ scenario → diagnostics

<diagnostics>
IN THIS ORDER:
| ( <diagnostic ... /> )*
</diagnostics>

diagnostic

Documentation (element)

Diagnostic model parameters

diagnostic

→ scenario → diagnostics → diagnostic

<diagnostic
    name=string
  [ units=("Other" or "Garki" or "Malariatherapy") ]
  [ mechanism=("Other" or "HRP2") ] DEFAULT VALUE Other
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterministic ... /> 
| |   <stochastic ... /> 
</diagnostic>

Attributes

Name of diagnostic

name=string

Name of this diagnostic (parameterisation). May be used elsewhere in the XML document to refer to this set of diagnostic parameters.

Parasite density units / methodology

units=("Other" or "Garki" or "Malariatherapy")

Mechanism

mechanism=("Other" or "HRP2")

Default value: Other

Deterministic detection

→ scenario → diagnostics → diagnostic → deterministic

<deterministic
    minDensity=double
  />

Documentation (element)

Specify that an artificial deterministic test is used: outcome is positive if parasite density is at least the minimum given.

Attributes

Minimum detectible density

minDensity=double

Units: parasites/microlitre Min: 0

The minimum density at which parasites can be detected. If 0, the test outcome is always positive.

Non-deterministic detection

→ scenario → diagnostics → diagnostic → stochastic

<stochastic
    dens_50=double
    specificity=double
  />

Documentation (element)

An improved model of detection which is non-deterministic, including false positive results as well as false negatives.

Some parameterisations:

Microscopy sensitivity/specificity data in Africa; Source: expert opinion — Allan Schapira dens_50 = 20.0 specificity = .75

RDT sensitivity/specificity for Plasmodium falciparum in Africa Source: Murray et al (Clinical Microbiological Reviews, Jan. 2008) dens_50 = 50.0; specificity = .942;

Attributes

Density 50

dens_50=double

Units: parasites/microlitre Min: 0

The density at which the test outcome has a 50% chance of being positive.

Specificity

specificity=double

Units: Dimensionless Min: 0 Max: 1

The probability of a positive test outcome in the absense of parasites.

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
| [ <vivax ... /> ]
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: model/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=string
  >
IN ANY ORDER:
| [ <NeonatalMortality ... /> ]
| [ <NonMalariaFevers ... /> ]
</clinical>

Documentation (type)

Attributes

Follow-up period during which recurrence is considered a treatment failure

healthSystemMemory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

Neonatal mortality parameters

→ scenario → model → clinical → NeonatalMortality

<NeonatalMortality
    diagnostic=string
  />

Attributes

Diagnostic used to parameterise model

diagnostic=string

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
| [ <prNeedTreatmentNMF ... /> ]
| [ <prNeedTreatmentMF ... /> ]
</NonMalariaFevers>

Documentation (type)

Description of the incidence of non-malaria fever. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a non-malarial fever requires treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

Availability of humans to mosquitoes relative to an adult, categorized by age group

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ]
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

Vivax model parameters

→ scenario → model → vivax

<vivax>
IN ANY ORDER:
|   <probBloodStageInfectiousToMosq ... /> 
|   <hypnozoiteRelease ... /> 
|   <bloodStageProtectionLatency ... /> 
|   <bloodStageLengthDays ... /> 
|   <clinicalEvents ... /> 
</vivax>

Documentation (element)

This describes Vivax model parameters, and is required when using the VIVAX_SIMPLE_MODEL model option.

Probability of mosquito infection

→ scenario → model → vivax → probBloodStageInfectiousToMosq

<probBloodStageInfectiousToMosq
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

The chance of a feeding mosquito becoming infected, given that the host is patent. (This may be adjusted by transmission-blocking vaccines.)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Hypnozoite releases

→ scenario → model → vivax → hypnozoiteRelease

<hypnozoiteRelease
  [ pSecondRelease=double ] DEFAULT VALUE 0
  >
IN ANY ORDER:
|   <numberHypnozoites ... /> 
|   <firstReleaseDays ... /> 
| [ <secondReleaseDays ... /> ]
</hypnozoiteRelease>

Documentation (element)

Describes the number and times of hypnozoite releases.

Documentation (type)

This element defines probabilites when and how many hypnozoites are released from the liverstage into the blood.

The gap between the start of a new brood of hypnozoites and its release are defined as follows:

latentP + latentRelapse + randomReleaseDelay

randomReleaseDelay is based on one or two lognormal distributions, which are defined in firstRelease and optionally secondRelease.

You can define 2 release distributions, which get added together and represent the probability of hypnozoites which get released before winter (first release) or after (second release).

You can omit the secondRelease element if no release to the blood happens after winter.

Attributes

latent relapse days

pSecondRelease=double

Default value: 0

Probability of a second release. If undefined it is zero.

Number of Hypnozoites

→ scenario → model → vivax → hypnozoiteRelease → numberHypnozoites

<numberHypnozoites
    max=int
    base=double
  />

Documentation (element)

numberHypnozoites calculates the number of hypnozoites in the liver stage based on a base which is between 0 and 1.

This number is random based on the following distribution and normalized:

max ∑ (base ^ n) n = 0

Attributes

max

max=int

base

base=double

firstReleaseDays

→ scenario → model → vivax → hypnozoiteRelease → firstReleaseDays

<firstReleaseDays
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
    latentRelapse=double
  />

Documentation (type)

Hypnozoites are released after a delay, calculated as: roundToTSFromDays(delay + latentRelapse)

Here, roundToTSFromDays rounds the input (in days) to the nearest timestep, delay is sampled from a log-normal, and latentRelapse is the parameter specified here.

The delay is sampled from a log-normal distribution, parameterised via the (linear) mean and CV (coefficient of variation) given here.

Documentation (base type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

latent relapse days

latentRelapse=double

Usually between 10 and 15 days.

secondReleaseDays

→ scenario → model → vivax → hypnozoiteRelease → secondReleaseDays

<secondReleaseDays
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
    latentRelapse=double
  />

Documentation (type)

Hypnozoites are released after a delay, calculated as: roundToTSFromDays(delay + latentRelapse)

Here, roundToTSFromDays rounds the input (in days) to the nearest timestep, delay is sampled from a log-normal, and latentRelapse is the parameter specified here.

The delay is sampled from a log-normal distribution, parameterised via the (linear) mean and CV (coefficient of variation) given here.

Documentation (base type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

latent relapse days

latentRelapse=double

Usually between 10 and 15 days.

Blood stage protection latency

→ scenario → model → vivax → bloodStageProtectionLatency

<bloodStageProtectionLatency
    value=double
  />

Documentation (element)

Min: 0

The length of time after expiry of a blood-stage infection during which relapses from the same brood are supressed by the immune system.

This is rounded to the nearest time-step.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Blood stage length

→ scenario → model → vivax → bloodStageLengthDays

<bloodStageLengthDays
    scale=double
    shape=double
    distr=("weibull")
  />

Documentation (element)

Units: Days

Parameters used to sample the length of blood-stage infections from a Weibull distribution (scale parameter lambda, shape parameter k).

Documentation (type)

Parameters of a Weibull distribution.

Attributes

Scale

scale=double

The Weibull scale parameter (λ).

shape

shape=double

The Weibull shape parameter (k).

Distribution

distr=("weibull")

To allow heterogeneity, a distribution must be specified. In this case, only "weibull" is allowed.

clinicalEvents

→ scenario → model → vivax → clinicalEvents

<clinicalEvents>
IN THIS ORDER:
|   <pPrimaryInfection ... /> 
|   <pRelapseOne ... /> 
|   <pRelapseTwoPlus ... /> 
|   <pEventIsSevere ... /> 
</clinicalEvents>

Documentation (type)

This elements holds all information about probabilites for clinical events from infections and relapses.

pPrimaryInfection

→ scenario → model → vivax → clinicalEvents → pPrimaryInfection

<pPrimaryInfection
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseOne

→ scenario → model → vivax → clinicalEvents → pRelapseOne

<pRelapseOne
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseTwoPlus

→ scenario → model → vivax → clinicalEvents → pRelapseTwoPlus

<pRelapseTwoPlus
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pEventIsSevere

→ scenario → model → vivax → clinicalEvents → pEventIsSevere

<pEventIsSevere
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=string
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=string

Units: User defined (default: steps) Min: 0 Max: 20

Pre-erythrocytic latent period Can be specified in steps (e.g. 3t) or days (e.g. 15d).

parameter

→ scenario → model → parameters → parameter

<parameter
  [ name=string ]
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 42 documentation

Generated from: scenario_42.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
  [ analysisNo=int ]
    name=string
  [ wuID=int ]
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:om="http://openmalaria.org/schema/scenario_42"
    xsi:schemaLocation="http://openmalaria.org/schema/scenario_42 scenario_42.xsd"
  >
IN ANY ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entomology ... /> 
| [ <parasiteGenetics ... /> ]
| [ <pharmacology ... /> ]
| [ <diagnostics ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Name of intervention

Work unit identifier

wuID=int

Units: Number

Work unit ID. Obselete and no longer required.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Description of demography

Attributes

Name of demography data

name=string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Years Min: 0 Max: 100

Maximum age of simulated humans in years

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

list of age groups included in demography

Documentation (type)

list of age groups included in demography or surveys

Attributes

Lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Units: Percentage Min: 0 Max: 100

Percentage of human population in age group

Upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ startDate=string ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
| [ <cohorts ... /> ]
</monitoring>

Documentation (element)

Description of surveys

Attributes

Name of monitoring settings

name=string

Name of monitoring settings

Start of monitoring

startDate=string

continuous

→ scenario → monitoring → continuous

<continuous
    period=string
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Delay between reports

period=string

Units: User defined (default: steps)

Delay between reports; typically one time step but can be greater. Can be specified in steps (e.g. 1t) or days (e.g. 5d).

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions
  [ onlyNewEpisode=boolean ] DEFAULT VALUE false
  >
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See model/mon/OutputMeasures.h for a list of supported outputs. Should also be on the wiki.

Attributes

Report only for new cases

onlyNewEpisode=boolean

Default value: false

option

→ scenario → monitoring → SurveyOptions → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  [ outputNumber=int ]
  [ byAge=boolean ]
  [ byCohort=boolean ]
  [ bySpecies=boolean ]
  [ byGenotype=boolean ]
  [ byDrugType=boolean ]
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Number identifying measure in output

outputNumber=int

Report by age category

byAge=boolean

Report by cohort

byCohort=boolean

Report by mosquito species

bySpecies=boolean

Report by parasite genotype

byGenotype=boolean

Report by drug type

byDrugType=boolean

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
  [ detectionLimit=double ]
  [ diagnostic=string ]
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/microlitre Min: 0

Deprecated: limit above which a human's infection is reported as patent. Alternative: do not specify this; instead specify "diagnostic".

Name of monitoring diagnostic

diagnostic=string

Name of a parameterised diagnostic to use in surveys (see scenario/diagnostics).

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime
  [ repeatStep=string ]
  [ repeatEnd=string ]
  [ reported=boolean ] DEFAULT VALUE true
  >
    string
</surveyTime>

Documentation (element)

Units: User defined (defaults to steps) Min: 0

The simulation ends immediately after the last survey is taken.

Attributes

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

reported

reported=boolean

Default value: true

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Cohorts

→ scenario → monitoring → cohorts

<cohorts>
IN THIS ORDER:
| ( <subPop ... /> )+
</cohorts>

subPop

Documentation (element)

Allows the configuration of multiple cohorts (output segregated according to membership within specific sub-populations).

If this element is omitted, monitoring surveys cover the entire simulated human population.

It does not affect the "continuous" outputs (these never take cohorts into account).

Sub-population

→ scenario → monitoring → cohorts → subPop

<subPop
    id=string
    number=integer
  />

Documentation (element)

In the output file, the output set is identified by multiplying this number by 1000 then adding it to the age group column.

Attributes

Sub-population identifier

id=string

Textual identifier for the sub-population (i.e. for an intervention component, since sub-populations are defined as the hosts an intervention component is deployed to).

Sub-population number

number=integer

Units: dimensionless Min: 1 Max: 2097152

Number identifying a sub-population; used to define identifiers of output sets. This number must be a power of 2 (i.e. 1, 2, 4, 8, ...). See documentation of subPop element.

Preventative interventions

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfections ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <vectorPop ... /> ]
| [ <vectorTrap ... /> ]
| [ <human ... /> ]
</interventions>

Documentation (element)

Attributes

Name of intervention set

name=string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeHS>

timedDeployment

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeHS → timedDeployment

<timedDeployment
    time=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timedDeployment>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</uncomplicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

multiple

→ scenario → interventions → human → component → decisionTree → multiple

<multiple
  [ name=string ]
  >
IN THIS ORDER:
| ( <caseType ... /> )*
| ( <diagnostic ... /> )*
| ( <random ... /> )*
| ( <age ... /> )*
| ( <treatPKPD ... /> )*
| [ <treatSimple ... /> ]
| ( <deploy ... /> )*
</multiple>

Documentation (type)

A special node allowing multiple sub-trees to be evaluated.

This is different from an ordinary decision tree node in that:

a) multiple types of child can occur simultaneously (e.g. multiple types of treatment or treatment plus a 'random' sub-tree)

b) the 'noTreatment' and 'treatFailure' nodes are not allowed

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → multiple → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

firstLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → firstLine

<firstLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</firstLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

secondLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → secondLine

<secondLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</secondLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

positive

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

outcome

→ scenario → interventions → human → component → decisionTree → multiple → random → outcome

<outcome
  [ name=string ]
    p=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</outcome>

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Probability

p=double

Units: None Min: 0 Max: 1

Probability of selecting this outcome. The sum of probabilities across all outcomes must be 1.

age

→ scenario → interventions → human → component → decisionTree → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Age range

→ scenario → interventions → human → component → decisionTree → multiple → age → age

<age
  [ name=string ]
    lb=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</age>

Documentation (element)

Describes a branch, selected for patients of a certain age.

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Lower bound (inclusive)

lb=double

Min: 0

noTreatment

→ scenario → interventions → human → component → decisionTree → noTreatment

<noTreatment
  [ name=string ]
  />

Documentation (type)

An end node doing nothing. This exists to explicitly state that no treatment happens and to prevent trees from accidentally being left incomplete.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatFailure

→ scenario → interventions → human → component → decisionTree → treatFailure

<treatFailure
  [ name=string ]
  />

Documentation (type)

An end node which reports treatment but does not change parasitalogical status. This allows correct labelling of second-line cases.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → multiple → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

age

→ scenario → interventions → human → component → decisionTree → multiple → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → multiple → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → multiple → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → multiple → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</complicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: Days Min: 0 Max: unbounded

Maximum number of timesteps (including first day of case) that an individual with an uncomplicated case of malaria will remember he/she was sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial or non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of a complicated or severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
  [ name=string ]
  [ useDiagnosticUC=boolean ] DEFAULT VALUE false
  >
IN ANY ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <treatmentActions ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
</ImmediateOutcomes>

Documentation (type)

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Name of case management parameterisation

name=string

Name of health system

useDiagnosticUC

useDiagnosticUC=boolean

Default value: false

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Description of drug regimen.

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Artemisinine based combination therapy

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Quinine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0 Max: 1name:P(self-treat)

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Effectiveness of treatment for non-compliant patients

treatmentActions

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions

<treatmentActions>
IN ANY ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
</treatmentActions>

CQ
SP
AQ
SPAQ
ACT
QN

CQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ

<CQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</CQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

deploy

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy

<deploy
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ p=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| ( <component ... /> )+
</deploy>

component

Attributes

Maximum age of eligible humans

maxAge=double

Units: Years Min: 0

Maximum age of eligible humans (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible humans

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible humans (defaults to 0). Input is rounded to the nearest time step.

Probability of delivery to eligible humans

p=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Probability of this list of components being deployed, given that other constraints are met.

component

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Prophylactic treatment

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere → clearInfections

<clearInfections
    timesteps=string
    stage=("liver" or "blood" or "both")
  />

Documentation (element)

Attributes

Length of effect

timesteps=string

Units: User defined (defaults to steps)

Target stage

stage=("liver" or "blood" or "both")

SP

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SP

<SP
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SP>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

AQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → AQ

<AQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</AQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

SPAQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SPAQ

<SPAQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SPAQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

ACT

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → ACT

<ACT
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</ACT>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

QN

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → QN

<QN
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</QN>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

Probability that human is incompatible with liver-stage drug treatment

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pHumanCannotReceive

<pHumanCannotReceive
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that a human is determined to be unable to receive liver-stage drug treatment. Treatment is neither reported or given for such humans.

This is sampled once per human at birth.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Ignore liver-stage drug treatment incompatibility

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → ignoreCannotReceive

<ignoreCannotReceive
    value=boolean
  />

Documentation (element)

If true, ignore pHumanCannotReceive and consider all humans eligible for treatment; if false (or not specified), do not treat those demed incompatible with liver-stage drug treatment.

The point of this is that pHumanCannotReceive cannot be altered by changeHS interventions, but this property can be.

Attributes

Input parameter value

value=boolean

A boolean value.

Prob use in UC case

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pUseUncomplicated

<pUseUncomplicated
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

This feature is deprecated; it is suggested to use the "simple treatment" feature configured to clear liver-stage parasites, leaving this option unset or zero.

Chance of liver-stage drug treatment being used for routine treatment of an uncomplicated case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Effectiveness

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → effectivenessOnUse

<effectivenessOnUse
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that liver-stage drug treatment is effective.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

DecisionTree5Day

<DecisionTree5Day
  [ name=string ]
  >
IN ANY ORDER:
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
|   <treeUCOfficial ... /> 
|   <treeUCSelfTreat ... /> 
|   <cureRateSevere ... /> 
|   <treatmentSevere ... /> 
</DecisionTree5Day>

Documentation (type)

Besides greater flexibility, this allows treatment via PK/PD models.

Attributes

Name of case management parameterisation

name=string

Name of health system

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → DecisionTree5Day → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → DecisionTree5Day → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

treeUCOfficial

→ scenario → healthSystem → DecisionTree5Day → treeUCOfficial

<treeUCOfficial
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCOfficial>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treeUCSelfTreat

→ scenario → healthSystem → DecisionTree5Day → treeUCSelfTreat

<treeUCSelfTreat
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCSelfTreat>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Cure rate (severe cases)

→ scenario → healthSystem → DecisionTree5Day → cureRateSevere

<cureRateSevere
    value=double
  />

Documentation (element)

Min: 0 Max: 1

The probability of clearing parasites given access to appropriate (hospital) care, for a severe case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

treatmentSevere

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere

<treatmentSevere
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</treatmentSevere>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Case fatality rate for inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: Dimensionless

List of age-specific probabilities of sequelae in inpatients, during a severe bout of malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeEIR>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeEIR → timedDeployment

<timedDeployment
    eipDuration=int
    time=string
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timedDeployment>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Time

time=string

Units: User defined (defauls to steps) Min: 0

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=string ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=string

Units: User defined (default: steps) Min: 0

Default value: 0

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=string
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time of start

time=string

Units: User defined (defauls to steps) Min: 0

Insert R_0 case

<insertR_0Case
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</insertR_0Case>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → insertR_0Case → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Uninfect vectors

<uninfectVectors
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</uninfectVectors>

timedDeployment

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → uninfectVectors → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Vector population intervention

→ scenario → interventions → vectorPop

<vectorPop>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorPop>

intervention

Documentation (element)

Units: List of elements

A list of parameterisations of generic vector host-inspecific interventions.

intervention

→ scenario → interventions → vectorPop → intervention

<intervention
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

Units: List of elements

An intervention which may have various effects on the vector populations as a whole. (Not host specific.)

Multiple instances of this intervention class are allowed (multiple parameterisations, not just deployments).

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → vectorPop → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → vectorPop → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <seekingDeathRateIncrease ... /> ]
| [ <probDeathOvipositing ... /> ]
| [ <emergenceReduction ... /> ]
</anopheles>

Documentation (type)

Units: dimensionless Min: 0 Max: 1

Descriptions of the effects of vector interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Proportional increase in deaths while host searching

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease

<seekingDeathRateIncrease
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</seekingDeathRateIncrease>

decay

Documentation (element)

Units: dimensionless

Describe an effect on the increase in the death rate while host seeking (mu_vA) due to this intervention.

Enter the rate increase (i.e. if rate increases to 120% of normal, give 0.2). New death rate while seeking is old × (1 + increase) where increase is this factor given. Must have increas ≥ -1.

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Proportion ovipositing mosquitoes killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing

<probDeathOvipositing
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probDeathOvipositing>

decay

Documentation (element)

Units: dimensionless

Describe an effect of increased mortality while ovipositing due to this intervention. Enter the probability of dying due to this intervention.

Attributes

Initial probability of killing

initial=double

Units: dimensionless Min: 0 Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Proportion of emerging pupa killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction

<emergenceReduction
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</emergenceReduction>

decay

Documentation (element)

Units: dimensionless

Describe an effect on emergence of pupa into adults: this value is the proportion of emerging pupa which are killed by this intervention.

Attributes

Initial proportion reduction

initial=double

Units: dimensionless Min: -inf Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Vector population intervention deployment

→ scenario → interventions → vectorPop → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

deploy

→ scenario → interventions → vectorPop → intervention → timed → deploy

<deploy
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Baited trap

→ scenario → interventions → vectorTrap

<vectorTrap>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorTrap>

intervention

Documentation (element)

intervention

→ scenario → interventions → vectorTrap → intervention

<intervention
  [ name=string ]
  >
IN THIS ORDER:
| ( <description ... /> )+
| [ <timed ... /> ]
</intervention>

Documentation (type)

Attributes

Descriptive name for type of trap

name=string

Optional name for this type of trap

Description

→ scenario → interventions → vectorTrap → intervention → description

<description
    mosquito=string
  >
IN THIS ORDER:
|   <relativeAvailability ... /> 
|   <decayOfAvailability ... /> 
</description>

Documentation (element)

Parameters associated with a vector trap intervention, per mosquito species.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Initial relative availability

→ scenario → interventions → vectorTrap → intervention → description → relativeAvailability

<relativeAvailability
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: inf

Describes the availiability of a trap to a host-seeking mosquito relative to an average unprotected adult.

I.e. if this parameter is 2, then each trap will on average attract twice as many mosquitoes as unprotected adults.

This is the initial availability; it may decay towards zero depending on the configured decay function.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay of availability

→ scenario → interventions → vectorTrap → intervention → description → decayOfAvailability

<decayOfAvailability
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Describes how availability decays to zero.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Vector trap intervention deployment

→ scenario → interventions → vectorTrap → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )*
</timed>

deploy

Documentation (element)

List of timed vector trap intervention deployment

deploy

→ scenario → interventions → vectorTrap → intervention → timed → deploy

<deploy
    time=string
    ratioToHumans=double
    lifespan=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Ratio to humans

ratioToHumans=double

Min: 0 Max: inf

The number of traps deployed, by this deployment, per adult human. E.g. if there are currently 100 traps and 1000 humans, then a ratio of 0.1 will increase the number of traps to 200.

Lifespan

lifespan=string

Units: Steps or Days or Years

Human-specific interventions

→ scenario → interventions → human

<human>
IN THIS ORDER:
| ( <component ... /> )+
| ( <deployment ... /> )*
</human>

Documentation (element)

Encapsulates all interventions whose effects are specific to the human host: any interventions where target humans may be selected via population-coverage, age limits and sub-population membership.

Component

→ scenario → interventions → human → component

<component
    id=string
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <screen ... /> 
| |   <treatSimple ... /> 
| |   <treatPKPD ... /> 
| |   <decisionTree ... /> 
| |   <PEV ... /> 
| |   <BSV ... /> 
| |   <TBV ... /> 
| |   <ITN ... /> 
| |   <IRS ... /> 
| |   <GVI ... /> 
| | [ <recruitmentOnly ... /> ]
| |   <clearImmunity ... /> 
| [ <subPopRemoval ... /> ]
</component>

Documentation (element)

Each element describes one component: its effects, decay of the(se) effect(s), and related stuff (e.g. description of indirect decay and of usage levels).

Attributes

Component identifier

id=string

Name of component

name=string

An informal name/description for the component

screen

→ scenario → interventions → human → component → screen

<screen
    diagnostic=string
  >
IN THIS ORDER:
| ( <positive ... /> )*
| ( <negative ... /> )*
</screen>

Documentation (type)

This can be combined with MDA to achieve mass screen and treat (MSAT) or other types of mass screening intervention.

The use of the screening itself is reported (if enabled), but not the outcome. Deployment of interventions triggered by the screening may be reported, however.

Attributes

Name of diagnostic

diagnostic=string

Name of a parameterised diagnostic (see scenario/diagnostics).

positive

→ scenario → interventions → human → component → screen → positive

<positive
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → screen → negative

<negative
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

treatSimple

→ scenario → interventions → human → component → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

treatPKPD

→ scenario → interventions → human → component → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

decisionTree

→ scenario → interventions → human → component → decisionTree

<decisionTree
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</decisionTree>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Vaccines

→ scenario → interventions → human → component → PEV

<PEV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</PEV>

Documentation (element)

Pre-erythrocytic vaccine (PEV): prevents a proportion of infections from commencing.

Documentation (type)

Description of a vaccine's effect

Decay of effect

→ scenario → interventions → human → component → PEV → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Specification of decay of efficacy. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Variance parameter for vaccine efficacy

→ scenario → interventions → human → component → PEV → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vaccines

→ scenario → interventions → human → component → BSV

<BSV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</BSV>

Documentation (element)

Blood-stage vaccine (BSV): acts as a killing factor on blood-stage parasites. Exact action depends on the within host model.

Documentation (type)

Description of a vaccine's effect

Vaccines

→ scenario → interventions → human → component → TBV

<TBV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</TBV>

Documentation (element)

Transmission-blocking vaccine (TBV): one minus this scales the probability of transmission to mosquitoes

Documentation (type)

Description of a vaccine's effect

Bed nets

→ scenario → interventions → human → component → ITN

<ITN>
IN THIS ORDER:
| [ <usage ... /> ]
|   <holeRate ... /> 
|   <ripRate ... /> 
|   <ripFactor ... /> 
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
|   <attritionOfNets ... /> 
| ( <anophelesParams ... /> )+
</ITN>

Documentation (element)

Description of bed-net interventions (ITNs, LLINs).

Proportion of time nets are used by humans

→ scenario → interventions → human → component → ITN → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of nets by humans, from 0 to 1.

At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing.

See also "propActing" (proportion of bits for which net acts).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Rate at which holes are made

→ scenario → interventions → human → component → ITN → holeRate

<holeRate
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: Holes per annum Min: 0

The rate at which new holes are made in nets.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Rate at which holes are enlarged

→ scenario → interventions → human → component → ITN → ripRate

<ripRate
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: Rips per existing hole per annum Min: 0

Each existing hole has a probability of being ripped bigger according to a Poisson process with this rate as (only) parameter.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Rip factor

→ scenario → interventions → human → component → ITN → ripFactor

<ripFactor
    value=double
  />

Documentation (element)

Units: none Min: 0

This factor expresses how important rips are in increasing the hole.

The hole index of a net is h + F×x where h and x are the total numbers of holes and rips respectively and F is the rip factor.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → ITN → initialInsecticide

<initialInsecticide
    mean=double
  [ SD=double ]
  [ distr=("const" or "normal") ] DEFAULT VALUE const
  />

Documentation (element)

Units: mg/m² Min: 0

Documentation (type)

A parameter with optional heterogeneity.

Optionally, a distribution ("distr") and standard of deviation ("SD") may be specified.

Attributes

mean

mean=double

The mean value.

standard deviation

SD=double

The standard deviation of variates.

Distribution

distr=("const" or "normal")

Default value: const

Decay of insecticide

→ scenario → interventions → human → component → ITN → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of nets. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Attrition of nets

→ scenario → interventions → human → component → ITN → attritionOfNets

<attritionOfNets
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: dimensionless

Specifies the rate at which nets are disposed of over time. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Humans are removed from the intervention component's sub-population on disposal (attrition) of their nets. Currently this event is not reported.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → human → component → ITN → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <holeIndexMax ... /> ]
| EXACTLY ONE OF:
| |   <deterrency ... /> 
| |   <twoStageDeterrency ... /> 
| EXACTLY ONE OF:
| |   <preprandialKillingEffect ... /> 
| |   <preprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| |   <postprandialKillingEffect ... /> 
| |   <postprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| | [ <fecundityReduction ... /> ]
| | [ <fecundityReductionLogit ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which net acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Deprecated: propActive is now always set to 1. This value will be ignored. The proportion of bites, when nets are in use, for which the net has any action whatsoever on the mosquito. At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing. See also "usage" (proportion of time nets are used by humans).

maximum of holed surface area that has an effect (comparable to no net)

→ scenario → interventions → human → component → ITN → anophelesParams → holeIndexMax

<holeIndexMax
    value=double
  />

Documentation (element)

Units: in same unit as holeIndex

Used by logit attacking and killing models only, holeIndexMax is a user defined maximum hole index (typically, the total surface area of a net).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency

<twoStageDeterrency>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <entering ... /> 
| |   <enteringLogit ... /> 
| EXACTLY ONE OF:
| |   <attacking ... /> 
| |   <attackingLogit ... /> 
</twoStageDeterrency>

Documentation (element)

Units: dimensionless

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

This deterrency model multiplies human attractiveness by pEnt×pAtt.

Deterrency: entering

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → entering

<entering
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless

pEnt represents the relative probability of entering due to ITNs: pEnt = exp(log(P)×p) where P is the insecticide factor and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Deterrency: entering (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → enteringLogit

<enteringLogit
    baseFactor=double
    insecticideFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: none

See parent element documentation

Insecticide factor

insecticideFactor=double

Units: none

See parent element documentation

Deterrency: attacking

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attacking

<attacking
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Deterrency: attacking (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attackingLogit

<attackingLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Pre-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Pre-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffectLogit

<preprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Post-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffectLogit

<postprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Fecundity reduction

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-B), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReductionLogit

<fecundityReductionLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-K0), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Indoor residual spraying

→ scenario → interventions → human → component → IRS

<IRS>
IN THIS ORDER:
| [ <usage ... /> ]
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
| ( <anophelesParams ... /> )+
</IRS>

Documentation (element)

Description of indoor residual spraying interventions.

Documentation (type)

Description of effect for the more complex and probably more realistic Briet model: IRS has three effects, whos strength is calculated as a function of surviving insecticide content.

Proportion of Indoor residual spraying (IRS) interventions

→ scenario → interventions → human → component → IRS → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Indoor residual spraying (IRS) interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → IRS → initialInsecticide

<initialInsecticide
    mean=double
  [ SD=double ]
  [ distr=("const" or "normal") ] DEFAULT VALUE const
  />

Documentation (element)

Units: μg/cm² Min: 0

Documentation (type)

A parameter with optional heterogeneity.

Optionally, a distribution ("distr") and standard of deviation ("SD") may be specified.

Attributes

mean

mean=double

The mean value.

standard deviation

SD=double

The standard deviation of variates.

Distribution

distr=("const" or "normal")

Default value: const

Decay of insecticide

→ scenario → interventions → human → component → IRS → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → IRS → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → IRS → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied by exp(P×log(p)) where P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction

→ scenario → interventions → human → component → IRS → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

First, we calculate K = B + P×p where B is the base (without protection) probability of death, and P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Fecundity is multiplied by (1−K) / (1−B). It is not allowed to be greater than 1. To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Generic vector intervention

→ scenario → interventions → human → component → GVI

<GVI>
IN THIS ORDER:
| [ <usage ... /> ]
|   <decay ... /> 
| ( <anophelesParams ... /> )+
</GVI>

Documentation (element)

Note that all actions of this intervention component will decay according to a single decay function. If independant decay is wanted, a separate component can be used for each action.

Proportion of generic vector interventions

→ scenario → interventions → human → component → GVI → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Generic vector interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay

→ scenario → interventions → human → component → GVI → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Description of decay of all intervention effects. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → GVI → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <deterrency ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → GVI → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of intervention on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied this factor times survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Fecundity reduction effect

→ scenario → interventions → human → component → GVI → anophelesParams → fecundityReduction

<fecundityReduction
    value=double
  />

Documentation (element)

Min: 0

Fertility is multiplied by 1 - (fecundityReduction * decay).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Recruitment only

→ scenario → interventions → human → component → recruitmentOnly

<recruitmentOnly/>

Documentation (element)

Recruitment of a host into a sub-population.

Clear Immunity

→ scenario → interventions → human → component → clearImmunity

<clearImmunity/>

Documentation (element)

Removes all exposure-related immunitsy gained over time by hosts without removing infections (or affecting the ability to gain immunity through exposure).

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

subPopRemoval

→ scenario → interventions → human → component → subPopRemoval

<subPopRemoval
  [ onFirstBout=boolean ] DEFAULT VALUE false
  [ onFirstTreatment=boolean ] DEFAULT VALUE false
  [ onFirstInfection=boolean ] DEFAULT VALUE false
  [ afterYears=double ]
  />

Documentation (type)

ITN attrition also removes humans from sub-populations.

Attributes

Time to first episode only

onFirstBout=boolean

Default value: false

Time to first treatment only

onFirstTreatment=boolean

Default value: false

Time to first infection only

onFirstInfection=boolean

Default value: false

Remove from sub-population after

afterYears=double

Units: Years Min: 0

Deployment

→ scenario → interventions → human → deployment

<deployment
  [ name=string ]
  >
IN THIS ORDER:
| ( <component ... /> )+
| ( <condition ... /> )*
| ( <continuous ... /> )*
| ( <timed ... /> )*
</deployment>

Documentation (element)

All components deployed by this intervention are deployed to the same people (each timed or continuous deployment selects recipients and then gives each recipient all components of the intervention).

Attributes

Intervention name

name=string

Name of intervention

component

→ scenario → interventions → human → deployment → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Condition

→ scenario → interventions → human → deployment → condition

<condition
    measure=string
  [ minValue=double ]
  [ maxValue=double ]
    initialState=boolean
  />

Documentation (element)

Conditions are evaluated for the whole population, not for individual age-groups or cohorts.

This affects all types of deployment.

Attributes

Measure

measure=string

The monitoring measure to test. Not all measures are available for use.

Minimum value

minValue=double

Minimum value. If specified, the measured variable must be greater than or equal to this value for the condition to be satisfied.

Maximum value

maxValue=double

Maximum value. If specified, the measured variable must be less than or equal to this value for the condition to be satisfied.

Initial state

initialState=boolean

Whether this condition is considered true or false before updated by a survey.

Age-based (continuous) deployment

→ scenario → interventions → human → deployment → continuous

<continuous>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| ( <deploy ... /> )+
</continuous>

Documentation (element)

List of ages at which deployment takes place (through EPI, post-natal and school-based programmes, etc.).

A sub-population restriction may be added as a property of the list of continuous deployments.

restrictToSubPop

→ scenario → interventions → human → deployment → continuous → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

deploy

→ scenario → interventions → human → deployment → continuous → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    targetAgeYrs=double
  [ begin=string ]
  [ end=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention. Input is rounded to the nearest time step.

First time active

begin=string

Units: User defined (defauls to steps)

End step

end=string

Units: User defined (defauls to steps)

Mass (timed) deployment

→ scenario → interventions → human → deployment → timed

<timed>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| [ <cumulativeCoverage ... /> ]
| ( <deploy ... /> )+
</timed>

Documentation (element)

List of timed deployments of the intervention (that is, of deployment campaigns).

Cumulative deployment mode can be specified for all deployments in a timed list. To allow multiple cumulative deployment descriptions, the entire timed list may be repeated.

restrictToSubPop

→ scenario → interventions → human → deployment → timed → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

Cumulative coverage

→ scenario → interventions → human → deployment → timed → cumulativeCoverage

<cumulativeCoverage
    component=string
  />

Documentation (element)

Attributes

Component identifier

component=string

The identifier (short name) of the component used when selecting people.

deploy

→ scenario → interventions → human → deployment → timed → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    time=string
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ repeatStep=string ]
  [ repeatEnd=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Time

time=string

Units: User defined (defauls to steps) Min: 0

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0

Maximum age of eligible individuals (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible individuals (defaults to 0). Input is rounded to the nearest time step.

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Description of health system.

Documentation (type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("forced" or "dynamic")
  [ scaledAnnualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Description of entomological data

Attributes

Entomology dataset name

name=string

Name of entomology data

Transmission model mode

mode=("forced" or "dynamic")

Override annual EIR

scaledAnnualEIR=double

Units: Infectious bites per adult per year

If set, the annual EIR (for all species of vector) is scaled to this level; can be omitted if not needed.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters of the transmission model

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <seasonality ... /> 
|   <mosq ... /> 
| [ <lifeCycle ... /> ]
| [ <simpleMPD ... /> ]
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial estimate of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial estimate of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial estimate of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Seasonality of transmission

→ scenario → entomology → vector → anopheles → seasonality

<seasonality
    input=("EIR")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <fourierSeries ... /> 
| |   <monthlyValues ... /> 
| |   <dailyValues ... /> 
</seasonality>

Documentation (element)

Specifies the seasonality of transmission and optionally the level of annual transmission.

Attributes

Seasonality input

input=("EIR")

Annual EIR

annualEIR=double

Units: Inoculations per adult per annum Min: 0

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries

<fourierSeries
    EIRRotateAngle=double
  >
IN THIS ORDER:
| ( <coeffic ... /> )*
</fourierSeries>

coeffic

Documentation (element)

Units: Infectious bites per adult per day

Attributes

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: Radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Pair of Fourier coefficients

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries → coeffic

<coeffic
    a=double
    b=double
  />

Documentation (element)

A pair of Fourier series coefficients. The first element specifies a1 and b1, the second a2 and b2, etc. Any number (from 0 up) of pairs may be given.

Attributes

a_n parameter of Fourier approximation to ln(EIR)

a=double

a_n parameter of Fourier approximation to ln(EIR) for some natural number n.

b_n parameter of Fourier approximation to ln(EIR)

b=double

b_n parameter of Fourier approximation to ln(EIR) for some natural number n.

List of monthly values

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues

<monthlyValues
    smoothing=("none" or "fourier")
  >
IN THIS ORDER:
| ( <value ... /> ){12,12}
</monthlyValues>

value

Documentation (element)

Description of seasonality from monthly values. Multiple smoothing methods are possible (see smoothing attribute).

List should contain twelve entries: January to December.

Attributes

Smoothing function

smoothing=("none" or "fourier")

How the monthly values are converted into a daily sequence of values:

none: no smoothing (step function)
Fourier: a Fourier series (with terms up to a2/b2) is fit to the sequence of monthly values and used to generate a smoothed list of daily values.

Monthly value

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Monthly value

List of daily values

→ scenario → entomology → vector → anopheles → seasonality → dailyValues

<dailyValues>
IN THIS ORDER:
| ( <value ... /> ){365,365}
</dailyValues>

value

Documentation (element)

Description of seasonality from daily values.

List should contain 365 entries: 1st January to 31st December.

Daily value

→ scenario → entomology → vector → anopheles → seasonality → dailyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Daily value

Mosquito feeding cycle parameters

→ scenario → entomology → vector → anopheles → mosq

<mosq
    minInfectedThreshold=double
  >
IN ANY ORDER:
|   <mosqRestDuration ... /> 
|   <extrinsicIncubationPeriod ... /> 
|   <mosqLaidEggsSameDayProportion ... /> 
|   <mosqSeekingDuration ... /> 
|   <mosqSurvivalFeedingCycleProbability ... /> 
|   <availability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <mosqProbOvipositing ... /> 
|   <mosqHumanBloodIndex ... /> 
</mosq>

Documentation (element)

Parameters describing the feeding cycle and human mosquito interaction of a single species of anopheles mosquito.

Attributes

Mininum infected threshold for mosquitos

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

Duration of the resting period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqRestDuration

<mosqRestDuration
    value=int
  />

Documentation (element)

Units: Days

name:Duration of the resting period of the vector (days);

Attributes

Input parameter value

value=int

An integer value.

Extrinsic incubation period

→ scenario → entomology → vector → anopheles → mosq → extrinsicIncubationPeriod

<extrinsicIncubationPeriod
    value=int
  />

Documentation (element)

Units: Days

name:Extrinsic incubation period (days)

Attributes

Input parameter value

value=int

An integer value.

Proportion of mosquitoes host seeking on same day as ovipositing

→ scenario → entomology → vector → anopheles → mosq → mosqLaidEggsSameDayProportion

<mosqLaidEggsSameDayProportion
    value=double
  />

Documentation (element)

Units: Proportion

Proportion of mosquitoes host seeking on same day as ovipositing

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Duration of the host-seeking period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqSeekingDuration

<mosqSeekingDuration
    value=double
  />

Documentation (element)

Units: Days

Duration of the host-seeking period of the vector (days)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito survives the feeding cycle

→ scenario → entomology → vector → anopheles → mosq → mosqSurvivalFeedingCycleProbability

<mosqSurvivalFeedingCycleProbability
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito survives the feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human availability rate heterogeneity

→ scenario → entomology → vector → anopheles → mosq → availability

<availability
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
  />

Documentation (element)

If no attributes are specified or distr="const" or CV="0" then there will be no heterogeneity.

Documentation (type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

Probability that the mosquito succesfully bites chosen host

→ scenario → entomology → vector → anopheles → mosq → mosqProbBiting

<mosqProbBiting
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito succesfully bites chosen host

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → mosq → mosqProbFindRestSite

<mosqProbFindRestSite
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito escapes host and finds a resting place after biting

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → mosq → mosqProbResting

<mosqProbResting
    mean=double
    variance=double
  />

Documentation (element)

Probability of mosquito successfully resting after finding a resting site

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of a mosquito successfully laying eggs given that it has rested

→ scenario → entomology → vector → anopheles → mosq → mosqProbOvipositing

<mosqProbOvipositing
    value=double
  />

Documentation (element)

Probability of a mosquito successfully laying eggs given that it has rested

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human blood index

→ scenario → entomology → vector → anopheles → mosq → mosqHumanBloodIndex

<mosqHumanBloodIndex
    value=double
  />

Documentation (element)

Units: Proportion

The proportion of resting mosquitoes which fed on human blood during the last feed.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mosquito life cycle parameters

→ scenario → entomology → vector → anopheles → lifeCycle

<lifeCycle
  [ estimatedLarvalResources=double ] DEFAULT VALUE 1e8
  >
IN ANY ORDER:
|   <eggStage ... /> 
|   <larvalStage ... /> 
|   <pupalStage ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</lifeCycle>

Documentation (element)

Parameters describing the life-cycle of this species of mosquito

Attributes

Estimate of larval resources

estimatedLarvalResources=double

Units: X

Default value: 1e8

Egg stage

→ scenario → entomology → vector → anopheles → lifeCycle → eggStage

<eggStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the egg stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

larvalStage

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage

<larvalStage>
</larvalStage>

daily

Documentation (type)

Parameters for the larval stage of development

Documentation (base type)

Parameters associated with a mosquito development stage.

Daily development

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage → daily

<daily
    resourceUsage=double
    effectCompetition=double
  />

Documentation (element)

Attributes

Resource usage

resourceUsage=double

Units: X

Resource usage during larval stage of development. Units are arbitrary.

Effect of competition

effectCompetition=double

Units: none

Effect of competition over resources on development.

Pupal stage

→ scenario → entomology → vector → anopheles → lifeCycle → pupalStage

<pupalStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the pupal stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → lifeCycle → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Simple Mosq-Pop-Dynamics parameters

→ scenario → entomology → vector → anopheles → simpleMPD

<simpleMPD>
IN ANY ORDER:
|   <developmentDuration ... /> 
|   <developmentSurvival ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</simpleMPD>

Documentation (element)

Parameters describing the simple mosquito population dynamics model.

This is a simpler version of the life-cycle model, requiring less parameters and with much simpler initialisation.

Duration

→ scenario → entomology → vector → anopheles → simpleMPD → developmentDuration

<developmentDuration
    value=int
  />

Documentation (element)

Units: Days Min: 1

Duration from egg laying to emergence in days.

Attributes

Input parameter value

value=int

An integer value.

Probability of survival

→ scenario → entomology → vector → anopheles → simpleMPD → developmentSurvival

<developmentSurvival
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that mosquito survives from the egg being laid to emergence, given no resouce limitations (no density constraints).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → simpleMPD → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Alternative (non-human) host paramters

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN ANY ORDER:
|   <mosqRelativeEntoAvailability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
| [ <hostFecundityFactor ... /> ]
</nonHumanHosts>

Documentation (element)

Min: 0

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of non-human host (ξ_i)

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqRelativeEntoAvailability

<mosqRelativeEntoAvailability
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of the population of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative fecundity of biting mosquitoes

→ scenario → entomology → vector → anopheles → nonHumanHosts → hostFecundityFactor

<hostFecundityFactor
    value=double
  />

Documentation (element)

Units: Proportion

Multiplicative factor for the number of fertile eggs laid by a mosquito after biting this type of host, relative to an unprotected human.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Name of this species of non human hosts (must match up with those described per anopheles section).

Population size of non-human host species

number=double

Units: Animals

Parasite genetics

<parasiteGenetics
    samplingMode=("initial" or "tracking")
  >
IN THIS ORDER:
| ( <locus ... /> )+
</parasiteGenetics>

locus

Documentation (element)

A specification of genotypes of infection parasites.

May be omitted; in this case there is no modelling of genetic differences of infections (resistance, fitness).

Attributes

samplingMode

samplingMode=("initial" or "tracking")

Locus

→ scenario → parasiteGenetics → locus

<locus
    name=string
  >
IN THIS ORDER:
| ( <allele ... /> )+
</locus>

allele

Documentation (element)

Alleles at loci can affect fitness and resistance to any number of drugs.

Attributes

Name of locus

name=string

Name of the Locus

Allele

→ scenario → parasiteGenetics → locus → allele

<allele
    name=string
    initialFrequency=double
    fitness=double
  [ hrp2_deletion=boolean ] DEFAULT VALUE false
  />

Documentation (element)

Describes an allele, or one possible genetic option of multiple at one point of variance.

Attributes

Name

name=string

Name of the allele; used to refer to it elsewhere.

Initial frequency

initialFrequency=double

Fitness factor

fitness=double

HRP2 deletion

hrp2_deletion=boolean

Default value: false

Drug parameters (PK, PD and usage)

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
|   <treatments ... /> 
|   <drugs ... /> 
</pharmacology>

Documentation (element)

Drug model parameters and drug usage parameters

Documentation (type)

A library of drug related data for the PK/PD model.

Treatments library

→ scenario → pharmacology → treatments

<treatments>
IN THIS ORDER:
| ( <schedule ... /> )+
| ( <dosages ... /> )+
</treatments>

Documentation (element)

A library of drug deployment schedules and dosages.

schedule

→ scenario → pharmacology → treatments → schedule

<schedule
    name=string
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

A schedule for the administration of drugs in a course of treatment.

Note that dose sizes are multiplied by some multiplier (see dosages) and the times of all doses may be delayed.

Attributes

Name

name=string

Name for referring to this deployment schedule

medicate

→ scenario → pharmacology → treatments → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  />

Attributes

drug

drug=string

Abbreviated name of drug compound

Drug dose (mg with multiplier)

mg=double

Units: mg per something

Quantity of drug compound in mg per something. A separate dosage table must be used when medicating, which may specify multipliers of this number based on patient age or weight.

Time of administration

hour=double

Units: Hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

dosages

→ scenario → pharmacology → treatments → dosages

<dosages
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | ( <age ... /> )+
| | ( <bodymass ... /> )+
| |   <multiply ... /> 
</dosages>

Documentation (type)

A table for selecting a dose size. There are several ways this can work: using the patient's age or body mass in a look-up table to get a multplier, or directly using body mass as the multiplier.

The doses specified in "mg" in the treatment schedule are then multiplied by this multiplier.

Attributes

Name

name=string

Name for referring to this dosage table

Look-up table (age)

→ scenario → pharmacology → treatments → dosages → age

<age
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's age.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Look-up table (weight)

→ scenario → pharmacology → treatments → dosages → bodymass

<bodymass
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's body mass.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Multiply dose

→ scenario → pharmacology → treatments → dosages → multiply

<multiply
    by=("kg")
  />

Documentation (element)

Multiply the dose by some quantity, such as patient weight.

Attributes

By what?

by=("kg")

Quantity to multiply the dose by. Only option is "kg" (patient weight in kg).

Drug library

→ scenario → pharmacology → drugs

<drugs>
IN THIS ORDER:
| ( <drug ... /> )+
</drugs>

drug

Documentation (element)

A library of drug PK/PD data.

drug

→ scenario → pharmacology → drugs → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (type)

A drug description with PK/PD parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drugs → drug → PD

<PD
  [ locus=string ]
  >
IN THIS ORDER:
| ( <phenotype ... /> )+
</PD>

phenotype

Attributes

Locus

locus=string

PD parameters for some allele / resistance phenotype

→ scenario → pharmacology → drugs → drug → PD → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

Restrict phenotype applicability to certain alleles

→ scenario → pharmacology → drugs → drug → PD → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (element)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Maximal parasite killing rate

→ scenario → pharmacology → drugs → drug → PD → phenotype → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drugs → drug → PD → phenotype → IC50

<IC50
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

If CV > 0, the IC50 is sampled from a log-normal distribution.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Slope of effect curve

→ scenario → pharmacology → drugs → drug → PD → phenotype → slope

<slope>
    double
</slope>

Documentation (element)

Units: dimensionless

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drugs → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
| EXACTLY ONE OF:
| |   <half_life ... /> 
| | IN THIS ORDER:
| | |   <k ... /> 
| | |   <m_exponent ... /> 
| [ <k_a ... /> ]
| [ <conversion ... /> ]
|   <vol_dist ... /> 
| [ <compartment2 ... /> ]
| [ <compartment3 ... /> ]
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drugs → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drugs → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate λ, calculated as λ = ln(2) / half_life. The basic form of decay is C(t) = C0 * exp(-λ*t).

Alternatively, elimination rate can be specified via k and m_exponent.

Constant associated with elimination rate (k)

→ scenario → pharmacology → drugs → drug → PK → k

<k
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

If CV > 0, k is sampled per-human from the log-normal distribution: ln N( ln(mean) - σ^2 / 2, σ^2).

Alternatively, elimination rate can be specified via half_life.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Constant associated with elimination rate (m_exponent)

→ scenario → pharmacology → drugs → drug → PK → m_exponent

<m_exponent>
    double
</m_exponent>

Documentation (element)

Units: day^-1 Min: 0

Alternatively, elimination rate can be specified via half_life.

Note that in the case of a conversion model, this applies to both the elimination and the conversion rates.

Absorption rate constant (k_a)

→ scenario → pharmacology → drugs → drug → PK → k_a

<k_a
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Min: 0

Absorption rate parameter. Not allowed for one compartment models, but required for two and three compartment models and one compartment with conversion model (for the parent drug only).

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Conversion parameters (parent drug)

→ scenario → pharmacology → drugs → drug → PK → conversion

<conversion>
IN ANY ORDER:
|   <metabolite ... /> 
|   <rate ... /> 
|   <molRatio ... /> 
|   <IC50_log_correlation ... /> 
</conversion>

Documentation (element)

Configures the parent drug in a conversion model.

To use a conversion model, the parent drug should have this section defined as well as half-life or k (direct elimination; this may be zero) and k_a (absorption rate; this may be large).

Metabolite drug (abbreviation)

→ scenario → pharmacology → drugs → drug → PK → conversion → metabolite

<metabolite>
    string
</metabolite>

Documentation (element)

The abbreviation of the metabolite drug (e.g. "DHA" or "DHA_AR").

Rate of conversion

→ scenario → pharmacology → drugs → drug → PK → conversion → rate

<rate
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Rate of conversion of parent drug to metabolite.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Molecular weight ratio

→ scenario → pharmacology → drugs → drug → PK → conversion → molRatio

<molRatio>
    double
</molRatio>

Documentation (element)

Ratio of molecular weights: molecular weight of the metabolite divided by molecular weight of the parent.

IC50 log correlation

→ scenario → pharmacology → drugs → drug → PK → conversion → IC50_log_correlation

<IC50_log_correlation>
    double
</IC50_log_correlation>

Documentation (element)

Min: 0 Max: 1

If this value is 1, samples are fully correlated: a single z-score is used to calculate both samples. If this is 0, two independent samples are used.

Values between 0 and 1 (partial correlation) are supported; in this case IC50 values are sampled such that cor(log(x), log(y)) matches this value (where x, y are parent and metabolite IC50 values).

Volume of Distribution (Vd)

→ scenario → pharmacology → drugs → drug → PK → vol_dist

<vol_dist
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution.

If CV > 0 this is sampled from a log-normal distribution.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Second compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment2

<compartment2>
IN ANY ORDER:
|   <k12 ... /> 
|   <k21 ... /> 
</compartment2>

Documentation (element)

Optional element specifying conversion parameters to- and from- a second compartment.

Absorption rate to compartment 2 (k12)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → k12

<k12
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the first periphery compartment (2).

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Absorption rate from compartment 2 (k21)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → k21

<k21
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the first periphery compartment (2) to the central compartment.

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Third compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment3

<compartment3>
IN ANY ORDER:
|   <k13 ... /> 
|   <k31 ... /> 
</compartment3>

Documentation (element)

Optional element specifying conversion parameters to- and from- a third compartment.

Absorption rate to compartment 3 (k13)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → k13

<k13
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the second periphery compartment (3).

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Absorption rate from compartment 3 (k31)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → k31

<k31
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the second periphery compartment (3) to the central compartment.

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Diagnostic parameters

→ scenario → diagnostics

<diagnostics>
IN THIS ORDER:
| ( <diagnostic ... /> )*
</diagnostics>

diagnostic

Documentation (element)

Diagnostic model parameters

diagnostic

→ scenario → diagnostics → diagnostic

<diagnostic
    name=string
  [ units=("Other" or "Garki" or "Malariatherapy") ]
  [ mechanism=("Other" or "HRP2") ] DEFAULT VALUE Other
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterministic ... /> 
| |   <stochastic ... /> 
</diagnostic>

Attributes

Name of diagnostic

name=string

Name of this diagnostic (parameterisation). May be used elsewhere in the XML document to refer to this set of diagnostic parameters.

Parasite density units / methodology

units=("Other" or "Garki" or "Malariatherapy")

Mechanism

mechanism=("Other" or "HRP2")

Default value: Other

Deterministic detection

→ scenario → diagnostics → diagnostic → deterministic

<deterministic
    minDensity=double
  />

Documentation (element)

Specify that an artificial deterministic test is used: outcome is positive if parasite density is at least the minimum given.

Attributes

Minimum detectible density

minDensity=double

Units: parasites/microlitre Min: 0

The minimum density at which parasites can be detected. If 0, the test outcome is always positive.

Non-deterministic detection

→ scenario → diagnostics → diagnostic → stochastic

<stochastic
    dens_50=double
    specificity=double
  />

Documentation (element)

An improved model of detection which is non-deterministic, including false positive results as well as false negatives.

Some parameterisations:

Microscopy sensitivity/specificity data in Africa; Source: expert opinion — Allan Schapira dens_50 = 20.0 specificity = .75

RDT sensitivity/specificity for Plasmodium falciparum in Africa Source: Murray et al (Clinical Microbiological Reviews, Jan. 2008) dens_50 = 50.0; specificity = .942;

Attributes

Density 50

dens_50=double

Units: parasites/microlitre Min: 0

The density at which the test outcome has a 50% chance of being positive.

Specificity

specificity=double

Units: Dimensionless Min: 0 Max: 1

The probability of a positive test outcome in the absense of parasites.

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
| [ <vivax ... /> ]
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: model/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=string
  >
IN ANY ORDER:
| [ <NeonatalMortality ... /> ]
| [ <NonMalariaFevers ... /> ]
</clinical>

Documentation (type)

Attributes

Follow-up period during which recurrence is considered a treatment failure

healthSystemMemory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

Neonatal mortality parameters

→ scenario → model → clinical → NeonatalMortality

<NeonatalMortality
    diagnostic=string
  />

Attributes

Diagnostic used to parameterise model

diagnostic=string

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
| [ <prNeedTreatmentNMF ... /> ]
| [ <prNeedTreatmentMF ... /> ]
</NonMalariaFevers>

Documentation (type)

Description of the incidence of non-malaria fever. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a non-malarial fever requires treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

Availability of humans to mosquitoes relative to an adult, categorized by age group

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ]
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

Vivax model parameters

→ scenario → model → vivax

<vivax>
IN ANY ORDER:
|   <probBloodStageInfectiousToMosq ... /> 
|   <hypnozoiteRelease ... /> 
|   <bloodStageProtectionLatency ... /> 
|   <bloodStageLengthDays ... /> 
|   <clinicalEvents ... /> 
</vivax>

Documentation (element)

This describes Vivax model parameters, and is required when using the VIVAX_SIMPLE_MODEL model option.

Probability of mosquito infection

→ scenario → model → vivax → probBloodStageInfectiousToMosq

<probBloodStageInfectiousToMosq
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

The chance of a feeding mosquito becoming infected, given that the host is patent. (This may be adjusted by transmission-blocking vaccines.)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Hypnozoite releases

→ scenario → model → vivax → hypnozoiteRelease

<hypnozoiteRelease
  [ pSecondRelease=double ] DEFAULT VALUE 0
  >
IN ANY ORDER:
|   <numberHypnozoites ... /> 
|   <firstReleaseDays ... /> 
| [ <secondReleaseDays ... /> ]
</hypnozoiteRelease>

Documentation (element)

Describes the number and times of hypnozoite releases.

Documentation (type)

This element defines probabilites when and how many hypnozoites are released from the liverstage into the blood.

The gap between the start of a new brood of hypnozoites and its release are defined as follows:

latentP + latentRelapse + randomReleaseDelay

randomReleaseDelay is based on one or two lognormal distributions, which are defined in firstRelease and optionally secondRelease.

You can define 2 release distributions, which get added together and represent the probability of hypnozoites which get released before winter (first release) or after (second release).

You can omit the secondRelease element if no release to the blood happens after winter.

Attributes

latent relapse days

pSecondRelease=double

Default value: 0

Probability of a second release. If undefined it is zero.

Number of Hypnozoites

→ scenario → model → vivax → hypnozoiteRelease → numberHypnozoites

<numberHypnozoites
    max=int
    base=double
  />

Documentation (element)

numberHypnozoites calculates the number of hypnozoites in the liver stage based on a base which is between 0 and 1.

This number is random based on the following distribution and normalized:

max ∑ (base ^ n) n = 0

Attributes

max

max=int

base

base=double

firstReleaseDays

→ scenario → model → vivax → hypnozoiteRelease → firstReleaseDays

<firstReleaseDays
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
    latentRelapse=double
  />

Documentation (type)

Hypnozoites are released after a delay, calculated as: roundToTSFromDays(delay + latentRelapse)

Here, roundToTSFromDays rounds the input (in days) to the nearest timestep, delay is sampled from a log-normal, and latentRelapse is the parameter specified here.

The delay is sampled from a log-normal distribution, parameterised via the (linear) mean and CV (coefficient of variation) given here.

Documentation (base type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

latent relapse days

latentRelapse=double

Usually between 10 and 15 days.

secondReleaseDays

→ scenario → model → vivax → hypnozoiteRelease → secondReleaseDays

<secondReleaseDays
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
    latentRelapse=double
  />

Documentation (type)

Hypnozoites are released after a delay, calculated as: roundToTSFromDays(delay + latentRelapse)

Here, roundToTSFromDays rounds the input (in days) to the nearest timestep, delay is sampled from a log-normal, and latentRelapse is the parameter specified here.

The delay is sampled from a log-normal distribution, parameterised via the (linear) mean and CV (coefficient of variation) given here.

Documentation (base type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

latent relapse days

latentRelapse=double

Usually between 10 and 15 days.

Blood stage protection latency

→ scenario → model → vivax → bloodStageProtectionLatency

<bloodStageProtectionLatency
    value=double
  />

Documentation (element)

Min: 0

The length of time after expiry of a blood-stage infection during which relapses from the same brood are supressed by the immune system.

This is rounded to the nearest time-step.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Blood stage length

→ scenario → model → vivax → bloodStageLengthDays

<bloodStageLengthDays
    scale=double
    shape=double
    distr=("weibull")
  />

Documentation (element)

Units: Days

Parameters used to sample the length of blood-stage infections from a Weibull distribution (scale parameter lambda, shape parameter k).

Documentation (type)

Parameters of a Weibull distribution.

Attributes

Scale

scale=double

The Weibull scale parameter (λ).

shape

shape=double

The Weibull shape parameter (k).

Distribution

distr=("weibull")

To allow heterogeneity, a distribution must be specified. In this case, only "weibull" is allowed.

clinicalEvents

→ scenario → model → vivax → clinicalEvents

<clinicalEvents>
IN THIS ORDER:
|   <pPrimaryInfection ... /> 
|   <pRelapseOne ... /> 
|   <pRelapseTwoPlus ... /> 
|   <pEventIsSevere ... /> 
</clinicalEvents>

Documentation (type)

This elements holds all information about probabilites for clinical events from infections and relapses.

pPrimaryInfection

→ scenario → model → vivax → clinicalEvents → pPrimaryInfection

<pPrimaryInfection
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseOne

→ scenario → model → vivax → clinicalEvents → pRelapseOne

<pRelapseOne
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseTwoPlus

→ scenario → model → vivax → clinicalEvents → pRelapseTwoPlus

<pRelapseTwoPlus
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pEventIsSevere

→ scenario → model → vivax → clinicalEvents → pEventIsSevere

<pEventIsSevere
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=string
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=string

Units: User defined (default: steps) Min: 0 Max: 20

Pre-erythrocytic latent period Can be specified in steps (e.g. 3t) or days (e.g. 15d).

parameter

→ scenario → model → parameters → parameter

<parameter
  [ name=string ]
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 41 documentation

Generated from: scenario_41.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
  [ analysisNo=int ]
    name=string
  [ wuID=int ]
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:om="http://openmalaria.org/schema/scenario_41"
    xsi:schemaLocation="http://openmalaria.org/schema/scenario_41 scenario_41.xsd"
  >
IN ANY ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entomology ... /> 
| [ <parasiteGenetics ... /> ]
| [ <pharmacology ... /> ]
| [ <diagnostics ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Name of intervention

Work unit identifier

wuID=int

Units: Number

Work unit ID. Obselete and no longer required.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Description of demography

Attributes

Name of demography data

name=string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Years Min: 0 Max: 100

Maximum age of simulated humans in years

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

list of age groups included in demography

Documentation (type)

list of age groups included in demography or surveys

Attributes

Lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Units: Percentage Min: 0 Max: 100

Percentage of human population in age group

Upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ startDate=string ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
| [ <cohorts ... /> ]
</monitoring>

Documentation (element)

Description of surveys

Attributes

Name of monitoring settings

name=string

Name of monitoring settings

Start of monitoring

startDate=string

continuous

→ scenario → monitoring → continuous

<continuous
    period=string
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Delay between reports

period=string

Units: User defined (default: steps)

Delay between reports; typically one time step but can be greater. Can be specified in steps (e.g. 1t) or days (e.g. 5d).

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions
  [ onlyNewEpisode=boolean ] DEFAULT VALUE false
  >
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See model/mon/OutputMeasures.h for a list of supported outputs. Should also be on the wiki.

Attributes

Report only for new cases

onlyNewEpisode=boolean

Default value: false

option

→ scenario → monitoring → SurveyOptions → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  [ outputNumber=int ]
  [ byAge=boolean ]
  [ byCohort=boolean ]
  [ bySpecies=boolean ]
  [ byGenotype=boolean ]
  [ byDrugType=boolean ]
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Number identifying measure in output

outputNumber=int

Report by age category

byAge=boolean

Report by cohort

byCohort=boolean

Report by mosquito species

bySpecies=boolean

Report by parasite genotype

byGenotype=boolean

Report by drug type

byDrugType=boolean

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
  [ detectionLimit=double ]
  [ diagnostic=string ]
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/microlitre Min: 0

Deprecated: limit above which a human's infection is reported as patent. Alternative: do not specify this; instead specify "diagnostic".

Name of monitoring diagnostic

diagnostic=string

Name of a parameterised diagnostic to use in surveys (see scenario/diagnostics).

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime
  [ repeatStep=string ]
  [ repeatEnd=string ]
  [ reported=boolean ] DEFAULT VALUE true
  >
    string
</surveyTime>

Documentation (element)

Units: User defined (defaults to steps) Min: 0

The simulation ends immediately after the last survey is taken.

Attributes

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

reported

reported=boolean

Default value: true

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Cohorts

→ scenario → monitoring → cohorts

<cohorts>
IN THIS ORDER:
| ( <subPop ... /> )+
</cohorts>

subPop

Documentation (element)

Allows the configuration of multiple cohorts (output segregated according to membership within specific sub-populations).

If this element is omitted, monitoring surveys cover the entire simulated human population.

It does not affect the "continuous" outputs (these never take cohorts into account).

Sub-population

→ scenario → monitoring → cohorts → subPop

<subPop
    id=string
    number=integer
  />

Documentation (element)

In the output file, the output set is identified by multiplying this number by 1000 then adding it to the age group column.

Attributes

Sub-population identifier

id=string

Textual identifier for the sub-population (i.e. for an intervention component, since sub-populations are defined as the hosts an intervention component is deployed to).

Sub-population number

number=integer

Units: dimensionless Min: 1 Max: 2097152

Number identifying a sub-population; used to define identifiers of output sets. This number must be a power of 2 (i.e. 1, 2, 4, 8, ...). See documentation of subPop element.

Preventative interventions

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfections ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <vectorPop ... /> ]
| [ <vectorTrap ... /> ]
| [ <human ... /> ]
</interventions>

Documentation (element)

Attributes

Name of intervention set

name=string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeHS>

timedDeployment

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeHS → timedDeployment

<timedDeployment
    time=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timedDeployment>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</uncomplicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

multiple

→ scenario → interventions → human → component → decisionTree → multiple

<multiple
  [ name=string ]
  >
IN THIS ORDER:
| ( <caseType ... /> )*
| ( <diagnostic ... /> )*
| ( <random ... /> )*
| ( <age ... /> )*
| ( <treatPKPD ... /> )*
| [ <treatSimple ... /> ]
| ( <deploy ... /> )*
</multiple>

Documentation (type)

A special node allowing multiple sub-trees to be evaluated.

This is different from an ordinary decision tree node in that:

a) multiple types of child can occur simultaneously (e.g. multiple types of treatment or treatment plus a 'random' sub-tree)

b) the 'noTreatment' and 'treatFailure' nodes are not allowed

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → multiple → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

firstLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → firstLine

<firstLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</firstLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

secondLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → secondLine

<secondLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</secondLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

positive

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

outcome

→ scenario → interventions → human → component → decisionTree → multiple → random → outcome

<outcome
  [ name=string ]
    p=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</outcome>

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Probability

p=double

Units: None Min: 0 Max: 1

Probability of selecting this outcome. The sum of probabilities across all outcomes must be 1.

age

→ scenario → interventions → human → component → decisionTree → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Age range

→ scenario → interventions → human → component → decisionTree → multiple → age → age

<age
  [ name=string ]
    lb=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</age>

Documentation (element)

Describes a branch, selected for patients of a certain age.

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Lower bound (inclusive)

lb=double

Min: 0

noTreatment

→ scenario → interventions → human → component → decisionTree → noTreatment

<noTreatment
  [ name=string ]
  />

Documentation (type)

An end node doing nothing. This exists to explicitly state that no treatment happens and to prevent trees from accidentally being left incomplete.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatFailure

→ scenario → interventions → human → component → decisionTree → treatFailure

<treatFailure
  [ name=string ]
  />

Documentation (type)

An end node which reports treatment but does not change parasitalogical status. This allows correct labelling of second-line cases.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → multiple → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

age

→ scenario → interventions → human → component → decisionTree → multiple → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → multiple → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → multiple → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → multiple → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</complicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: Days Min: 0 Max: unbounded

Maximum number of timesteps (including first day of case) that an individual with an uncomplicated case of malaria will remember he/she was sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial or non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of a complicated or severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
  [ name=string ]
  [ useDiagnosticUC=boolean ] DEFAULT VALUE false
  >
IN ANY ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <treatmentActions ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
</ImmediateOutcomes>

Documentation (type)

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Name of case management parameterisation

name=string

Name of health system

useDiagnosticUC

useDiagnosticUC=boolean

Default value: false

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Description of drug regimen.

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Artemisinine based combination therapy

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Quinine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0 Max: 1name:P(self-treat)

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Effectiveness of treatment for non-compliant patients

treatmentActions

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions

<treatmentActions>
IN ANY ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
</treatmentActions>

CQ
SP
AQ
SPAQ
ACT
QN

CQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ

<CQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</CQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

deploy

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy

<deploy
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ p=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| ( <component ... /> )+
</deploy>

component

Attributes

Maximum age of eligible humans

maxAge=double

Units: Years Min: 0

Maximum age of eligible humans (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible humans

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible humans (defaults to 0). Input is rounded to the nearest time step.

Probability of delivery to eligible humans

p=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Probability of this list of components being deployed, given that other constraints are met.

component

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Prophylactic treatment

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere → clearInfections

<clearInfections
    timesteps=string
    stage=("liver" or "blood" or "both")
  />

Documentation (element)

Attributes

Length of effect

timesteps=string

Units: User defined (defaults to steps)

Target stage

stage=("liver" or "blood" or "both")

SP

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SP

<SP
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SP>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

AQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → AQ

<AQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</AQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

SPAQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SPAQ

<SPAQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SPAQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

ACT

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → ACT

<ACT
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</ACT>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

QN

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → QN

<QN
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</QN>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

Probability that human is incompatible with liver-stage drug treatment

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pHumanCannotReceive

<pHumanCannotReceive
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that a human is determined to be unable to receive liver-stage drug treatment. Treatment is neither reported or given for such humans.

This is sampled once per human at birth.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Ignore liver-stage drug treatment incompatibility

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → ignoreCannotReceive

<ignoreCannotReceive
    value=boolean
  />

Documentation (element)

If true, ignore pHumanCannotReceive and consider all humans eligible for treatment; if false (or not specified), do not treat those demed incompatible with liver-stage drug treatment.

The point of this is that pHumanCannotReceive cannot be altered by changeHS interventions, but this property can be.

Attributes

Input parameter value

value=boolean

A boolean value.

Prob use in UC case

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pUseUncomplicated

<pUseUncomplicated
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

This feature is deprecated; it is suggested to use the "simple treatment" feature configured to clear liver-stage parasites, leaving this option unset or zero.

Chance of liver-stage drug treatment being used for routine treatment of an uncomplicated case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Effectiveness

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → effectivenessOnUse

<effectivenessOnUse
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that liver-stage drug treatment is effective.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

DecisionTree5Day

<DecisionTree5Day
  [ name=string ]
  >
IN ANY ORDER:
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
|   <treeUCOfficial ... /> 
|   <treeUCSelfTreat ... /> 
|   <cureRateSevere ... /> 
|   <treatmentSevere ... /> 
</DecisionTree5Day>

Documentation (type)

Besides greater flexibility, this allows treatment via PK/PD models.

Attributes

Name of case management parameterisation

name=string

Name of health system

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → DecisionTree5Day → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → DecisionTree5Day → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

treeUCOfficial

→ scenario → healthSystem → DecisionTree5Day → treeUCOfficial

<treeUCOfficial
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCOfficial>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treeUCSelfTreat

→ scenario → healthSystem → DecisionTree5Day → treeUCSelfTreat

<treeUCSelfTreat
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCSelfTreat>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Cure rate (severe cases)

→ scenario → healthSystem → DecisionTree5Day → cureRateSevere

<cureRateSevere
    value=double
  />

Documentation (element)

Min: 0 Max: 1

The probability of clearing parasites given access to appropriate (hospital) care, for a severe case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

treatmentSevere

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere

<treatmentSevere
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</treatmentSevere>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Case fatality rate for inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: Dimensionless

List of age-specific probabilities of sequelae in inpatients, during a severe bout of malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeEIR>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeEIR → timedDeployment

<timedDeployment
    eipDuration=int
    time=string
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timedDeployment>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Time

time=string

Units: User defined (defauls to steps) Min: 0

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=string ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=string

Units: User defined (default: steps) Min: 0

Default value: 0

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=string
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time of start

time=string

Units: User defined (defauls to steps) Min: 0

Insert R_0 case

<insertR_0Case
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</insertR_0Case>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → insertR_0Case → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Uninfect vectors

<uninfectVectors
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</uninfectVectors>

timedDeployment

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → uninfectVectors → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Vector population intervention

→ scenario → interventions → vectorPop

<vectorPop>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorPop>

intervention

Documentation (element)

Units: List of elements

A list of parameterisations of generic vector host-inspecific interventions.

intervention

→ scenario → interventions → vectorPop → intervention

<intervention
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

Units: List of elements

An intervention which may have various effects on the vector populations as a whole. (Not host specific.)

Multiple instances of this intervention class are allowed (multiple parameterisations, not just deployments).

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → vectorPop → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → vectorPop → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <seekingDeathRateIncrease ... /> ]
| [ <probDeathOvipositing ... /> ]
| [ <emergenceReduction ... /> ]
</anopheles>

Documentation (type)

Units: dimensionless Min: 0 Max: 1

Descriptions of the effects of vector interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Proportional increase in deaths while host searching

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease

<seekingDeathRateIncrease
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</seekingDeathRateIncrease>

decay

Documentation (element)

Units: dimensionless

Describe an effect on the increase in the death rate while host seeking (mu_vA) due to this intervention.

Enter the rate increase (i.e. if rate increases to 120% of normal, give 0.2). New death rate while seeking is old × (1 + increase) where increase is this factor given. Must have increas ≥ -1.

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Proportion ovipositing mosquitoes killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing

<probDeathOvipositing
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probDeathOvipositing>

decay

Documentation (element)

Units: dimensionless

Describe an effect of increased mortality while ovipositing due to this intervention. Enter the probability of dying due to this intervention.

Attributes

Initial probability of killing

initial=double

Units: dimensionless Min: 0 Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Proportion of emerging pupa killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction

<emergenceReduction
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</emergenceReduction>

decay

Documentation (element)

Units: dimensionless

Describe an effect on emergence of pupa into adults: this value is the proportion of emerging pupa which are killed by this intervention.

Attributes

Initial proportion reduction

initial=double

Units: dimensionless Min: -inf Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Vector population intervention deployment

→ scenario → interventions → vectorPop → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

deploy

→ scenario → interventions → vectorPop → intervention → timed → deploy

<deploy
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Baited trap

→ scenario → interventions → vectorTrap

<vectorTrap>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorTrap>

intervention

Documentation (element)

intervention

→ scenario → interventions → vectorTrap → intervention

<intervention
  [ name=string ]
  >
IN THIS ORDER:
| ( <description ... /> )+
| [ <timed ... /> ]
</intervention>

Documentation (type)

Attributes

Descriptive name for type of trap

name=string

Optional name for this type of trap

Description

→ scenario → interventions → vectorTrap → intervention → description

<description
    mosquito=string
  >
IN THIS ORDER:
|   <relativeAvailability ... /> 
|   <decayOfAvailability ... /> 
</description>

Documentation (element)

Parameters associated with a vector trap intervention, per mosquito species.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Initial relative availability

→ scenario → interventions → vectorTrap → intervention → description → relativeAvailability

<relativeAvailability
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: inf

Describes the availiability of a trap to a host-seeking mosquito relative to an average unprotected adult.

I.e. if this parameter is 2, then each trap will on average attract twice as many mosquitoes as unprotected adults.

This is the initial availability; it may decay towards zero depending on the configured decay function.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay of availability

→ scenario → interventions → vectorTrap → intervention → description → decayOfAvailability

<decayOfAvailability
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Describes how availability decays to zero.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Vector trap intervention deployment

→ scenario → interventions → vectorTrap → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )*
</timed>

deploy

Documentation (element)

List of timed vector trap intervention deployment

deploy

→ scenario → interventions → vectorTrap → intervention → timed → deploy

<deploy
    time=string
    ratioToHumans=double
    lifespan=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Ratio to humans

ratioToHumans=double

Min: 0 Max: inf

The number of traps deployed, by this deployment, per adult human. E.g. if there are currently 100 traps and 1000 humans, then a ratio of 0.1 will increase the number of traps to 200.

Lifespan

lifespan=string

Units: Steps or Days or Years

Human-specific interventions

→ scenario → interventions → human

<human>
IN THIS ORDER:
| ( <component ... /> )+
| ( <deployment ... /> )*
</human>

Documentation (element)

Encapsulates all interventions whose effects are specific to the human host: any interventions where target humans may be selected via population-coverage, age limits and sub-population membership.

Component

→ scenario → interventions → human → component

<component
    id=string
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <screen ... /> 
| |   <treatSimple ... /> 
| |   <treatPKPD ... /> 
| |   <decisionTree ... /> 
| |   <PEV ... /> 
| |   <BSV ... /> 
| |   <TBV ... /> 
| |   <ITN ... /> 
| |   <IRS ... /> 
| |   <GVI ... /> 
| | [ <recruitmentOnly ... /> ]
| |   <clearImmunity ... /> 
| [ <subPopRemoval ... /> ]
</component>

Documentation (element)

Each element describes one component: its effects, decay of the(se) effect(s), and related stuff (e.g. description of indirect decay and of usage levels).

Attributes

Component identifier

id=string

Name of component

name=string

An informal name/description for the component

screen

→ scenario → interventions → human → component → screen

<screen
    diagnostic=string
  >
IN THIS ORDER:
| ( <positive ... /> )*
| ( <negative ... /> )*
</screen>

Documentation (type)

This can be combined with MDA to achieve mass screen and treat (MSAT) or other types of mass screening intervention.

The use of the screening itself is reported (if enabled), but not the outcome. Deployment of interventions triggered by the screening may be reported, however.

Attributes

Name of diagnostic

diagnostic=string

Name of a parameterised diagnostic (see scenario/diagnostics).

positive

→ scenario → interventions → human → component → screen → positive

<positive
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → screen → negative

<negative
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

treatSimple

→ scenario → interventions → human → component → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

treatPKPD

→ scenario → interventions → human → component → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

decisionTree

→ scenario → interventions → human → component → decisionTree

<decisionTree
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</decisionTree>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Vaccines

→ scenario → interventions → human → component → PEV

<PEV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</PEV>

Documentation (element)

Pre-erythrocytic vaccine (PEV): prevents a proportion of infections from commencing.

Documentation (type)

Description of a vaccine's effect

Decay of effect

→ scenario → interventions → human → component → PEV → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Specification of decay of efficacy. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Variance parameter for vaccine efficacy

→ scenario → interventions → human → component → PEV → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vaccines

→ scenario → interventions → human → component → BSV

<BSV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</BSV>

Documentation (element)

Blood-stage vaccine (BSV): acts as a killing factor on blood-stage parasites. Exact action depends on the within host model.

Documentation (type)

Description of a vaccine's effect

Vaccines

→ scenario → interventions → human → component → TBV

<TBV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</TBV>

Documentation (element)

Transmission-blocking vaccine (TBV): one minus this scales the probability of transmission to mosquitoes

Documentation (type)

Description of a vaccine's effect

Bed nets

→ scenario → interventions → human → component → ITN

<ITN>
IN THIS ORDER:
| [ <usage ... /> ]
|   <holeRate ... /> 
|   <ripRate ... /> 
|   <ripFactor ... /> 
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
|   <attritionOfNets ... /> 
| ( <anophelesParams ... /> )+
</ITN>

Documentation (element)

Description of bed-net interventions (ITNs, LLINs).

Proportion of time nets are used by humans

→ scenario → interventions → human → component → ITN → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of nets by humans, from 0 to 1.

At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing.

See also "propActing" (proportion of bits for which net acts).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Rate at which holes are made

→ scenario → interventions → human → component → ITN → holeRate

<holeRate
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: Holes per annum Min: 0

The rate at which new holes are made in nets.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Rate at which holes are enlarged

→ scenario → interventions → human → component → ITN → ripRate

<ripRate
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: Rips per existing hole per annum Min: 0

Each existing hole has a probability of being ripped bigger according to a Poisson process with this rate as (only) parameter.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Rip factor

→ scenario → interventions → human → component → ITN → ripFactor

<ripFactor
    value=double
  />

Documentation (element)

Units: none Min: 0

This factor expresses how important rips are in increasing the hole.

The hole index of a net is h + F×x where h and x are the total numbers of holes and rips respectively and F is the rip factor.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → ITN → initialInsecticide

<initialInsecticide
    mean=double
  [ SD=double ]
  [ distr=("const" or "normal") ] DEFAULT VALUE const
  />

Documentation (element)

Units: mg/m² Min: 0

Documentation (type)

A parameter with optional heterogeneity.

Optionally, a distribution ("distr") and standard of deviation ("SD") may be specified.

Attributes

mean

mean=double

The mean value.

standard deviation

SD=double

The standard deviation of variates.

Distribution

distr=("const" or "normal")

Default value: const

Decay of insecticide

→ scenario → interventions → human → component → ITN → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of nets. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Attrition of nets

→ scenario → interventions → human → component → ITN → attritionOfNets

<attritionOfNets
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: dimensionless

Specifies the rate at which nets are disposed of over time. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Humans are removed from the intervention component's sub-population on disposal (attrition) of their nets. Currently this event is not reported.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → human → component → ITN → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <holeIndexMax ... /> ]
| EXACTLY ONE OF:
| |   <deterrency ... /> 
| |   <twoStageDeterrency ... /> 
| EXACTLY ONE OF:
| |   <preprandialKillingEffect ... /> 
| |   <preprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| |   <postprandialKillingEffect ... /> 
| |   <postprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| | [ <fecundityReduction ... /> ]
| | [ <fecundityReductionLogit ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which net acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

The proportion of bites, when nets are in use, for which the net has any action whatsoever on the mosquito. At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing. See also "usage" (proportion of time nets are used by humans).

maximum of holed surface area that has an effect (comparable to no net)

→ scenario → interventions → human → component → ITN → anophelesParams → holeIndexMax

<holeIndexMax
    value=double
  />

Documentation (element)

Units: in same unit as holeIndex

Used by logit attacking and killing models only, holeIndexMax is a user defined maximum hole index (typically, the total surface area of a net).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency

<twoStageDeterrency>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <entering ... /> 
| |   <enteringLogit ... /> 
| EXACTLY ONE OF:
| |   <attacking ... /> 
| |   <attackingLogit ... /> 
</twoStageDeterrency>

Documentation (element)

Units: dimensionless

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

This deterrency model multiplies human attractiveness by pEnt×pAtt.

Deterrency: entering

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → entering

<entering
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless

pEnt represents the relative probability of entering due to ITNs: pEnt = exp(log(P)×p) where P is the insecticide factor and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Deterrency: entering (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → enteringLogit

<enteringLogit
    baseFactor=double
    insecticideFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: none

See parent element documentation

Insecticide factor

insecticideFactor=double

Units: none

See parent element documentation

Deterrency: attacking

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attacking

<attacking
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Deterrency: attacking (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attackingLogit

<attackingLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Pre-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Pre-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffectLogit

<preprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Post-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffectLogit

<postprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Fecundity reduction

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-B), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReductionLogit

<fecundityReductionLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-K0), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Indoor residual spraying

→ scenario → interventions → human → component → IRS

<IRS>
IN THIS ORDER:
| [ <usage ... /> ]
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
| ( <anophelesParams ... /> )+
</IRS>

Documentation (element)

Description of indoor residual spraying interventions.

Documentation (type)

Description of effect for the more complex and probably more realistic Briet model: IRS has three effects, whos strength is calculated as a function of surviving insecticide content.

Proportion of Indoor residual spraying (IRS) interventions

→ scenario → interventions → human → component → IRS → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Indoor residual spraying (IRS) interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → IRS → initialInsecticide

<initialInsecticide
    mean=double
  [ SD=double ]
  [ distr=("const" or "normal") ] DEFAULT VALUE const
  />

Documentation (element)

Units: μg/cm² Min: 0

Documentation (type)

A parameter with optional heterogeneity.

Optionally, a distribution ("distr") and standard of deviation ("SD") may be specified.

Attributes

mean

mean=double

The mean value.

standard deviation

SD=double

The standard deviation of variates.

Distribution

distr=("const" or "normal")

Default value: const

Decay of insecticide

→ scenario → interventions → human → component → IRS → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → IRS → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → IRS → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied by exp(P×log(p)) where P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction

→ scenario → interventions → human → component → IRS → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

First, we calculate K = B + P×p where B is the base (without protection) probability of death, and P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Fecundity is multiplied by (1−K) / (1−B). It is not allowed to be greater than 1. To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Generic vector intervention

→ scenario → interventions → human → component → GVI

<GVI>
IN THIS ORDER:
| [ <usage ... /> ]
|   <decay ... /> 
| ( <anophelesParams ... /> )+
</GVI>

Documentation (element)

Note that all actions of this intervention component will decay according to a single decay function. If independant decay is wanted, a separate component can be used for each action.

Proportion of generic vector interventions

→ scenario → interventions → human → component → GVI → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Generic vector interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay

→ scenario → interventions → human → component → GVI → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Description of decay of all intervention effects. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → GVI → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <deterrency ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → GVI → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of intervention on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied this factor times survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Fecundity reduction effect

→ scenario → interventions → human → component → GVI → anophelesParams → fecundityReduction

<fecundityReduction
    value=double
  />

Documentation (element)

Min: 0

Fertility is multiplied by 1 - (fecundityReduction * decay).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Recruitment only

→ scenario → interventions → human → component → recruitmentOnly

<recruitmentOnly/>

Documentation (element)

Recruitment of a host into a sub-population.

Clear Immunity

→ scenario → interventions → human → component → clearImmunity

<clearImmunity/>

Documentation (element)

Removes all exposure-related immunitsy gained over time by hosts without removing infections (or affecting the ability to gain immunity through exposure).

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

subPopRemoval

→ scenario → interventions → human → component → subPopRemoval

<subPopRemoval
  [ onFirstBout=boolean ] DEFAULT VALUE false
  [ onFirstTreatment=boolean ] DEFAULT VALUE false
  [ onFirstInfection=boolean ] DEFAULT VALUE false
  [ afterYears=double ]
  />

Documentation (type)

ITN attrition also removes humans from sub-populations.

Attributes

Time to first episode only

onFirstBout=boolean

Default value: false

Time to first treatment only

onFirstTreatment=boolean

Default value: false

Time to first infection only

onFirstInfection=boolean

Default value: false

Remove from sub-population after

afterYears=double

Units: Years Min: 0

Deployment

→ scenario → interventions → human → deployment

<deployment
  [ name=string ]
  >
IN THIS ORDER:
| ( <component ... /> )+
| ( <condition ... /> )*
| ( <continuous ... /> )*
| ( <timed ... /> )*
</deployment>

Documentation (element)

All components deployed by this intervention are deployed to the same people (each timed or continuous deployment selects recipients and then gives each recipient all components of the intervention).

Attributes

Intervention name

name=string

Name of intervention

component

→ scenario → interventions → human → deployment → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Condition

→ scenario → interventions → human → deployment → condition

<condition
    measure=string
  [ minValue=double ]
  [ maxValue=double ]
    initialState=boolean
  />

Documentation (element)

Conditions are evaluated for the whole population, not for individual age-groups or cohorts.

This affects all types of deployment.

Attributes

Measure

measure=string

The monitoring measure to test. Not all measures are available for use.

Minimum value

minValue=double

Minimum value. If specified, the measured variable must be greater than or equal to this value for the condition to be satisfied.

Maximum value

maxValue=double

Maximum value. If specified, the measured variable must be less than or equal to this value for the condition to be satisfied.

Initial state

initialState=boolean

Whether this condition is considered true or false before updated by a survey.

Age-based (continuous) deployment

→ scenario → interventions → human → deployment → continuous

<continuous>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| ( <deploy ... /> )+
</continuous>

Documentation (element)

List of ages at which deployment takes place (through EPI, post-natal and school-based programmes, etc.).

A sub-population restriction may be added as a property of the list of continuous deployments.

restrictToSubPop

→ scenario → interventions → human → deployment → continuous → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

deploy

→ scenario → interventions → human → deployment → continuous → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    targetAgeYrs=double
  [ begin=string ]
  [ end=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention. Input is rounded to the nearest time step.

First time active

begin=string

Units: User defined (defauls to steps)

End step

end=string

Units: User defined (defauls to steps)

Mass (timed) deployment

→ scenario → interventions → human → deployment → timed

<timed>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| [ <cumulativeCoverage ... /> ]
| ( <deploy ... /> )+
</timed>

Documentation (element)

List of timed deployments of the intervention (that is, of deployment campaigns).

Cumulative deployment mode can be specified for all deployments in a timed list. To allow multiple cumulative deployment descriptions, the entire timed list may be repeated.

restrictToSubPop

→ scenario → interventions → human → deployment → timed → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

Cumulative coverage

→ scenario → interventions → human → deployment → timed → cumulativeCoverage

<cumulativeCoverage
    component=string
  />

Documentation (element)

Attributes

Component identifier

component=string

The identifier (short name) of the component used when selecting people.

deploy

→ scenario → interventions → human → deployment → timed → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    time=string
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ repeatStep=string ]
  [ repeatEnd=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Time

time=string

Units: User defined (defauls to steps) Min: 0

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0

Maximum age of eligible individuals (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible individuals (defaults to 0). Input is rounded to the nearest time step.

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Description of health system.

Documentation (type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("forced" or "dynamic")
  [ scaledAnnualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Description of entomological data

Attributes

Entomology dataset name

name=string

Name of entomology data

Transmission model mode

mode=("forced" or "dynamic")

Override annual EIR

scaledAnnualEIR=double

Units: Infectious bites per adult per year

If set, the annual EIR (for all species of vector) is scaled to this level; can be omitted if not needed.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters of the transmission model

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <seasonality ... /> 
|   <mosq ... /> 
| [ <lifeCycle ... /> ]
| [ <simpleMPD ... /> ]
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial estimate of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial estimate of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial estimate of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Seasonality of transmission

→ scenario → entomology → vector → anopheles → seasonality

<seasonality
    input=("EIR")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <fourierSeries ... /> 
| |   <monthlyValues ... /> 
| |   <dailyValues ... /> 
</seasonality>

Documentation (element)

Specifies the seasonality of transmission and optionally the level of annual transmission.

Attributes

Seasonality input

input=("EIR")

Annual EIR

annualEIR=double

Units: Inoculations per adult per annum Min: 0

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries

<fourierSeries
    EIRRotateAngle=double
  >
IN THIS ORDER:
| ( <coeffic ... /> )*
</fourierSeries>

coeffic

Documentation (element)

Units: Infectious bites per adult per day

Attributes

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: Radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Pair of Fourier coefficients

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries → coeffic

<coeffic
    a=double
    b=double
  />

Documentation (element)

A pair of Fourier series coefficients. The first element specifies a1 and b1, the second a2 and b2, etc. Any number (from 0 up) of pairs may be given.

Attributes

a_n parameter of Fourier approximation to ln(EIR)

a=double

a_n parameter of Fourier approximation to ln(EIR) for some natural number n.

b_n parameter of Fourier approximation to ln(EIR)

b=double

b_n parameter of Fourier approximation to ln(EIR) for some natural number n.

List of monthly values

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues

<monthlyValues
    smoothing=("none" or "fourier")
  >
IN THIS ORDER:
| ( <value ... /> ){12,12}
</monthlyValues>

value

Documentation (element)

Description of seasonality from monthly values. Multiple smoothing methods are possible (see smoothing attribute).

List should contain twelve entries: January to December.

Attributes

Smoothing function

smoothing=("none" or "fourier")

How the monthly values are converted into a daily sequence of values:

none: no smoothing (step function)
Fourier: a Fourier series (with terms up to a2/b2) is fit to the sequence of monthly values and used to generate a smoothed list of daily values.

Monthly value

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Monthly value

List of daily values

→ scenario → entomology → vector → anopheles → seasonality → dailyValues

<dailyValues>
IN THIS ORDER:
| ( <value ... /> ){365,365}
</dailyValues>

value

Documentation (element)

Description of seasonality from daily values.

List should contain 365 entries: 1st January to 31st December.

Daily value

→ scenario → entomology → vector → anopheles → seasonality → dailyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Daily value

Mosquito feeding cycle parameters

→ scenario → entomology → vector → anopheles → mosq

<mosq
    minInfectedThreshold=double
  >
IN ANY ORDER:
|   <mosqRestDuration ... /> 
|   <extrinsicIncubationPeriod ... /> 
|   <mosqLaidEggsSameDayProportion ... /> 
|   <mosqSeekingDuration ... /> 
|   <mosqSurvivalFeedingCycleProbability ... /> 
|   <availability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <mosqProbOvipositing ... /> 
|   <mosqHumanBloodIndex ... /> 
</mosq>

Documentation (element)

Parameters describing the feeding cycle and human mosquito interaction of a single species of anopheles mosquito.

Attributes

Mininum infected threshold for mosquitos

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

Duration of the resting period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqRestDuration

<mosqRestDuration
    value=int
  />

Documentation (element)

Units: Days

name:Duration of the resting period of the vector (days);

Attributes

Input parameter value

value=int

An integer value.

Extrinsic incubation period

→ scenario → entomology → vector → anopheles → mosq → extrinsicIncubationPeriod

<extrinsicIncubationPeriod
    value=int
  />

Documentation (element)

Units: Days

name:Extrinsic incubation period (days)

Attributes

Input parameter value

value=int

An integer value.

Proportion of mosquitoes host seeking on same day as ovipositing

→ scenario → entomology → vector → anopheles → mosq → mosqLaidEggsSameDayProportion

<mosqLaidEggsSameDayProportion
    value=double
  />

Documentation (element)

Units: Proportion

Proportion of mosquitoes host seeking on same day as ovipositing

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Duration of the host-seeking period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqSeekingDuration

<mosqSeekingDuration
    value=double
  />

Documentation (element)

Units: Days

Duration of the host-seeking period of the vector (days)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito survives the feeding cycle

→ scenario → entomology → vector → anopheles → mosq → mosqSurvivalFeedingCycleProbability

<mosqSurvivalFeedingCycleProbability
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito survives the feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human availability rate heterogeneity

→ scenario → entomology → vector → anopheles → mosq → availability

<availability
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
  />

Documentation (element)

If no attributes are specified or distr="const" or CV="0" then there will be no heterogeneity.

Documentation (type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

Probability that the mosquito succesfully bites chosen host

→ scenario → entomology → vector → anopheles → mosq → mosqProbBiting

<mosqProbBiting
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito succesfully bites chosen host

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → mosq → mosqProbFindRestSite

<mosqProbFindRestSite
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito escapes host and finds a resting place after biting

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → mosq → mosqProbResting

<mosqProbResting
    mean=double
    variance=double
  />

Documentation (element)

Probability of mosquito successfully resting after finding a resting site

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of a mosquito successfully laying eggs given that it has rested

→ scenario → entomology → vector → anopheles → mosq → mosqProbOvipositing

<mosqProbOvipositing
    value=double
  />

Documentation (element)

Probability of a mosquito successfully laying eggs given that it has rested

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human blood index

→ scenario → entomology → vector → anopheles → mosq → mosqHumanBloodIndex

<mosqHumanBloodIndex
    value=double
  />

Documentation (element)

Units: Proportion

The proportion of resting mosquitoes which fed on human blood during the last feed.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mosquito life cycle parameters

→ scenario → entomology → vector → anopheles → lifeCycle

<lifeCycle
  [ estimatedLarvalResources=double ] DEFAULT VALUE 1e8
  >
IN ANY ORDER:
|   <eggStage ... /> 
|   <larvalStage ... /> 
|   <pupalStage ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</lifeCycle>

Documentation (element)

Parameters describing the life-cycle of this species of mosquito

Attributes

Estimate of larval resources

estimatedLarvalResources=double

Units: X

Default value: 1e8

Egg stage

→ scenario → entomology → vector → anopheles → lifeCycle → eggStage

<eggStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the egg stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

larvalStage

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage

<larvalStage>
</larvalStage>

daily

Documentation (type)

Parameters for the larval stage of development

Documentation (base type)

Parameters associated with a mosquito development stage.

Daily development

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage → daily

<daily
    resourceUsage=double
    effectCompetition=double
  />

Documentation (element)

Attributes

Resource usage

resourceUsage=double

Units: X

Resource usage during larval stage of development. Units are arbitrary.

Effect of competition

effectCompetition=double

Units: none

Effect of competition over resources on development.

Pupal stage

→ scenario → entomology → vector → anopheles → lifeCycle → pupalStage

<pupalStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the pupal stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → lifeCycle → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Simple Mosq-Pop-Dynamics parameters

→ scenario → entomology → vector → anopheles → simpleMPD

<simpleMPD>
IN ANY ORDER:
|   <developmentDuration ... /> 
|   <developmentSurvival ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</simpleMPD>

Documentation (element)

Parameters describing the simple mosquito population dynamics model.

This is a simpler version of the life-cycle model, requiring less parameters and with much simpler initialisation.

Duration

→ scenario → entomology → vector → anopheles → simpleMPD → developmentDuration

<developmentDuration
    value=int
  />

Documentation (element)

Units: Days Min: 1

Duration from egg laying to emergence in days.

Attributes

Input parameter value

value=int

An integer value.

Probability of survival

→ scenario → entomology → vector → anopheles → simpleMPD → developmentSurvival

<developmentSurvival
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that mosquito survives from the egg being laid to emergence, given no resouce limitations (no density constraints).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → simpleMPD → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Alternative (non-human) host paramters

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN ANY ORDER:
|   <mosqRelativeEntoAvailability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
| [ <hostFecundityFactor ... /> ]
</nonHumanHosts>

Documentation (element)

Min: 0

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of non-human host (ξ_i)

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqRelativeEntoAvailability

<mosqRelativeEntoAvailability
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of the population of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative fecundity of biting mosquitoes

→ scenario → entomology → vector → anopheles → nonHumanHosts → hostFecundityFactor

<hostFecundityFactor
    value=double
  />

Documentation (element)

Units: Proportion

Multiplicative factor for the number of fertile eggs laid by a mosquito after biting this type of host, relative to an unprotected human.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Name of this species of non human hosts (must match up with those described per anopheles section).

Population size of non-human host species

number=double

Units: Animals

Parasite genetics

<parasiteGenetics
    samplingMode=("initial" or "tracking")
  >
IN THIS ORDER:
| ( <locus ... /> )+
</parasiteGenetics>

locus

Documentation (element)

A specification of genotypes of infection parasites.

May be omitted; in this case there is no modelling of genetic differences of infections (resistance, fitness).

Attributes

samplingMode

samplingMode=("initial" or "tracking")

Locus

→ scenario → parasiteGenetics → locus

<locus
    name=string
  >
IN THIS ORDER:
| ( <allele ... /> )+
</locus>

allele

Documentation (element)

Alleles at loci can affect fitness and resistance to any number of drugs.

Attributes

Name of locus

name=string

Name of the Locus

Allele

→ scenario → parasiteGenetics → locus → allele

<allele
    name=string
    initialFrequency=double
    fitness=double
  [ hrp2_deletion=boolean ] DEFAULT VALUE false
  />

Documentation (element)

Describes an allele, or one possible genetic option of multiple at one point of variance.

Attributes

Name

name=string

Name of the allele; used to refer to it elsewhere.

Initial frequency

initialFrequency=double

Fitness factor

fitness=double

HRP2 deletion

hrp2_deletion=boolean

Default value: false

Drug parameters (PK, PD and usage)

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
|   <treatments ... /> 
|   <drugs ... /> 
</pharmacology>

Documentation (element)

Drug model parameters and drug usage parameters

Documentation (type)

A library of drug related data for the PK/PD model.

Treatments library

→ scenario → pharmacology → treatments

<treatments>
IN THIS ORDER:
| ( <schedule ... /> )+
| ( <dosages ... /> )+
</treatments>

Documentation (element)

A library of drug deployment schedules and dosages.

schedule

→ scenario → pharmacology → treatments → schedule

<schedule
    name=string
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

A schedule for the administration of drugs in a course of treatment.

Note that dose sizes are multiplied by some multiplier (see dosages) and the times of all doses may be delayed.

Attributes

Name

name=string

Name for referring to this deployment schedule

medicate

→ scenario → pharmacology → treatments → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  />

Attributes

drug

drug=string

Abbreviated name of drug compound

Drug dose (mg with multiplier)

mg=double

Units: mg per something

Quantity of drug compound in mg per something. A separate dosage table must be used when medicating, which may specify multipliers of this number based on patient age or weight.

Time of administration

hour=double

Units: Hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

dosages

→ scenario → pharmacology → treatments → dosages

<dosages
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | ( <age ... /> )+
| | ( <bodymass ... /> )+
| |   <multiply ... /> 
</dosages>

Documentation (type)

A table for selecting a dose size. There are several ways this can work: using the patient's age or body mass in a look-up table to get a multplier, or directly using body mass as the multiplier.

The doses specified in "mg" in the treatment schedule are then multiplied by this multiplier.

Attributes

Name

name=string

Name for referring to this dosage table

Look-up table (age)

→ scenario → pharmacology → treatments → dosages → age

<age
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's age.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Look-up table (weight)

→ scenario → pharmacology → treatments → dosages → bodymass

<bodymass
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's body mass.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Multiply dose

→ scenario → pharmacology → treatments → dosages → multiply

<multiply
    by=("kg")
  />

Documentation (element)

Multiply the dose by some quantity, such as patient weight.

Attributes

By what?

by=("kg")

Quantity to multiply the dose by. Only option is "kg" (patient weight in kg).

Drug library

→ scenario → pharmacology → drugs

<drugs>
IN THIS ORDER:
| ( <drug ... /> )+
</drugs>

drug

Documentation (element)

A library of drug PK/PD data.

drug

→ scenario → pharmacology → drugs → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (type)

A drug description with PK/PD parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drugs → drug → PD

<PD
  [ locus=string ]
  >
IN THIS ORDER:
| ( <phenotype ... /> )+
</PD>

phenotype

Attributes

Locus

locus=string

PD parameters for some allele / resistance phenotype

→ scenario → pharmacology → drugs → drug → PD → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

Restrict phenotype applicability to certain alleles

→ scenario → pharmacology → drugs → drug → PD → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (element)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Maximal parasite killing rate

→ scenario → pharmacology → drugs → drug → PD → phenotype → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drugs → drug → PD → phenotype → IC50

<IC50
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

If CV > 0, the IC50 is sampled from a log-normal distribution.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Slope of effect curve

→ scenario → pharmacology → drugs → drug → PD → phenotype → slope

<slope>
    double
</slope>

Documentation (element)

Units: dimensionless

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drugs → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
| EXACTLY ONE OF:
| |   <half_life ... /> 
| | IN THIS ORDER:
| | |   <k ... /> 
| | |   <m_exponent ... /> 
| [ <k_a ... /> ]
| [ <conversion ... /> ]
|   <vol_dist ... /> 
| [ <compartment2 ... /> ]
| [ <compartment3 ... /> ]
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drugs → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drugs → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate λ, calculated as λ = ln(2) / half_life. The basic form of decay is C(t) = C0 * exp(-λ*t).

Alternatively, elimination rate can be specified via k and m_exponent.

Constant associated with elimination rate (k)

→ scenario → pharmacology → drugs → drug → PK → k

<k
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

If CV > 0, k is sampled per-human from the log-normal distribution: ln N( ln(mean) - σ^2 / 2, σ^2).

Alternatively, elimination rate can be specified via half_life.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Constant associated with elimination rate (m_exponent)

→ scenario → pharmacology → drugs → drug → PK → m_exponent

<m_exponent>
    double
</m_exponent>

Documentation (element)

Units: day^-1 Min: 0

Alternatively, elimination rate can be specified via half_life.

Note that in the case of a conversion model, this applies to both the elimination and the conversion rates.

Absorption rate constant (k_a)

→ scenario → pharmacology → drugs → drug → PK → k_a

<k_a
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Min: 0

Absorption rate parameter. Not allowed for one compartment models, but required for two and three compartment models and one compartment with conversion model (for the parent drug only).

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Conversion parameters (parent drug)

→ scenario → pharmacology → drugs → drug → PK → conversion

<conversion>
IN ANY ORDER:
|   <metabolite ... /> 
|   <rate ... /> 
|   <molRatio ... /> 
|   <IC50_log_correlation ... /> 
</conversion>

Documentation (element)

Configures the parent drug in a conversion model.

To use a conversion model, the parent drug should have this section defined as well as half-life or k (direct elimination; this may be zero) and k_a (absorption rate; this may be large).

Metabolite drug (abbreviation)

→ scenario → pharmacology → drugs → drug → PK → conversion → metabolite

<metabolite>
    string
</metabolite>

Documentation (element)

The abbreviation of the metabolite drug (e.g. "DHA" or "DHA_AR").

Rate of conversion

→ scenario → pharmacology → drugs → drug → PK → conversion → rate

<rate
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Rate of conversion of parent drug to metabolite.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Molecular weight ratio

→ scenario → pharmacology → drugs → drug → PK → conversion → molRatio

<molRatio>
    double
</molRatio>

Documentation (element)

Ratio of molecular weights: molecular weight of the metabolite divided by molecular weight of the parent.

IC50 log correlation

→ scenario → pharmacology → drugs → drug → PK → conversion → IC50_log_correlation

<IC50_log_correlation>
    double
</IC50_log_correlation>

Documentation (element)

Min: 0 Max: 1

If this value is 1, samples are fully correlated: a single z-score is used to calculate both samples. If this is 0, two independent samples are used.

Values between 0 and 1 (partial correlation) are supported; in this case IC50 values are sampled such that cor(log(x), log(y)) matches this value (where x, y are parent and metabolite IC50 values).

Volume of Distribution (Vd)

→ scenario → pharmacology → drugs → drug → PK → vol_dist

<vol_dist
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution.

If CV > 0 this is sampled from a log-normal distribution.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Second compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment2

<compartment2>
IN ANY ORDER:
|   <k12 ... /> 
|   <k21 ... /> 
</compartment2>

Documentation (element)

Optional element specifying conversion parameters to- and from- a second compartment.

Absorption rate to compartment 2 (k12)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → k12

<k12
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the first periphery compartment (2).

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Absorption rate from compartment 2 (k21)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → k21

<k21
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the first periphery compartment (2) to the central compartment.

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Third compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment3

<compartment3>
IN ANY ORDER:
|   <k13 ... /> 
|   <k31 ... /> 
</compartment3>

Documentation (element)

Optional element specifying conversion parameters to- and from- a third compartment.

Absorption rate to compartment 3 (k13)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → k13

<k13
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the second periphery compartment (3).

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Absorption rate from compartment 3 (k31)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → k31

<k31
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the second periphery compartment (3) to the central compartment.

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Diagnostic parameters

→ scenario → diagnostics

<diagnostics>
IN THIS ORDER:
| ( <diagnostic ... /> )*
</diagnostics>

diagnostic

Documentation (element)

Diagnostic model parameters

diagnostic

→ scenario → diagnostics → diagnostic

<diagnostic
    name=string
  [ units=("Other" or "Garki" or "Malariatherapy") ]
  [ mechanism=("Other" or "HRP2") ] DEFAULT VALUE Other
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterministic ... /> 
| |   <stochastic ... /> 
</diagnostic>

Attributes

Name of diagnostic

name=string

Name of this diagnostic (parameterisation). May be used elsewhere in the XML document to refer to this set of diagnostic parameters.

Parasite density units / methodology

units=("Other" or "Garki" or "Malariatherapy")

Mechanism

mechanism=("Other" or "HRP2")

Default value: Other

Deterministic detection

→ scenario → diagnostics → diagnostic → deterministic

<deterministic
    minDensity=double
  />

Documentation (element)

Specify that an artificial deterministic test is used: outcome is positive if parasite density is at least the minimum given.

Attributes

Minimum detectible density

minDensity=double

Units: parasites/microlitre Min: 0

The minimum density at which parasites can be detected. If 0, the test outcome is always positive.

Non-deterministic detection

→ scenario → diagnostics → diagnostic → stochastic

<stochastic
    dens_50=double
    specificity=double
  />

Documentation (element)

An improved model of detection which is non-deterministic, including false positive results as well as false negatives.

Some parameterisations:

Microscopy sensitivity/specificity data in Africa; Source: expert opinion — Allan Schapira dens_50 = 20.0 specificity = .75

RDT sensitivity/specificity for Plasmodium falciparum in Africa Source: Murray et al (Clinical Microbiological Reviews, Jan. 2008) dens_50 = 50.0; specificity = .942;

Attributes

Density 50

dens_50=double

Units: parasites/microlitre Min: 0

The density at which the test outcome has a 50% chance of being positive.

Specificity

specificity=double

Units: Dimensionless Min: 0 Max: 1

The probability of a positive test outcome in the absense of parasites.

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
| [ <vivax ... /> ]
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: model/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=string
  >
IN ANY ORDER:
| [ <NeonatalMortality ... /> ]
| [ <NonMalariaFevers ... /> ]
</clinical>

Documentation (type)

Attributes

Follow-up period during which recurrence is considered a treatment failure

healthSystemMemory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

Neonatal mortality parameters

→ scenario → model → clinical → NeonatalMortality

<NeonatalMortality
    diagnostic=string
  />

Attributes

Diagnostic used to parameterise model

diagnostic=string

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
| [ <prNeedTreatmentNMF ... /> ]
| [ <prNeedTreatmentMF ... /> ]
</NonMalariaFevers>

Documentation (type)

Description of the incidence of non-malaria fever. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a non-malarial fever requires treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

Availability of humans to mosquitoes relative to an adult, categorized by age group

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ]
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

Vivax model parameters

→ scenario → model → vivax

<vivax>
IN ANY ORDER:
|   <probBloodStageInfectiousToMosq ... /> 
|   <hypnozoiteRelease ... /> 
|   <bloodStageProtectionLatency ... /> 
|   <bloodStageLengthDays ... /> 
|   <clinicalEvents ... /> 
</vivax>

Documentation (element)

This describes Vivax model parameters, and is required when using the VIVAX_SIMPLE_MODEL model option.

Probability of mosquito infection

→ scenario → model → vivax → probBloodStageInfectiousToMosq

<probBloodStageInfectiousToMosq
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

The chance of a feeding mosquito becoming infected, given that the host is patent. (This may be adjusted by transmission-blocking vaccines.)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Hypnozoite releases

→ scenario → model → vivax → hypnozoiteRelease

<hypnozoiteRelease
  [ pSecondRelease=double ] DEFAULT VALUE 0
  >
IN ANY ORDER:
|   <numberHypnozoites ... /> 
|   <firstReleaseDays ... /> 
| [ <secondReleaseDays ... /> ]
</hypnozoiteRelease>

Documentation (element)

Describes the number and times of hypnozoite releases.

Documentation (type)

This element defines probabilites when and how many hypnozoites are released from the liverstage into the blood.

The gap between the start of a new brood of hypnozoites and its release are defined as follows:

latentP + latentRelapse + randomReleaseDelay

randomReleaseDelay is based on one or two lognormal distributions, which are defined in firstRelease and optionally secondRelease.

You can define 2 release distributions, which get added together and represent the probability of hypnozoites which get released before winter (first release) or after (second release).

You can omit the secondRelease element if no release to the blood happens after winter.

Attributes

latent relapse days

pSecondRelease=double

Default value: 0

Probability of a second release. If undefined it is zero.

Number of Hypnozoites

→ scenario → model → vivax → hypnozoiteRelease → numberHypnozoites

<numberHypnozoites
    max=int
    base=double
  />

Documentation (element)

numberHypnozoites calculates the number of hypnozoites in the liver stage based on a base which is between 0 and 1.

This number is random based on the following distribution and normalized:

max ∑ (base ^ n) n = 0

Attributes

max

max=int

base

base=double

firstReleaseDays

→ scenario → model → vivax → hypnozoiteRelease → firstReleaseDays

<firstReleaseDays
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
    latentRelapse=double
  />

Documentation (type)

Hypnozoites are released after a delay, calculated as: roundToTSFromDays(delay + latentRelapse)

Here, roundToTSFromDays rounds the input (in days) to the nearest timestep, delay is sampled from a log-normal, and latentRelapse is the parameter specified here.

The delay is sampled from a log-normal distribution, parameterised via the (linear) mean and CV (coefficient of variation) given here.

Documentation (base type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

latent relapse days

latentRelapse=double

Usually between 10 and 15 days.

secondReleaseDays

→ scenario → model → vivax → hypnozoiteRelease → secondReleaseDays

<secondReleaseDays
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
    latentRelapse=double
  />

Documentation (type)

Hypnozoites are released after a delay, calculated as: roundToTSFromDays(delay + latentRelapse)

Here, roundToTSFromDays rounds the input (in days) to the nearest timestep, delay is sampled from a log-normal, and latentRelapse is the parameter specified here.

The delay is sampled from a log-normal distribution, parameterised via the (linear) mean and CV (coefficient of variation) given here.

Documentation (base type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

latent relapse days

latentRelapse=double

Usually between 10 and 15 days.

Blood stage protection latency

→ scenario → model → vivax → bloodStageProtectionLatency

<bloodStageProtectionLatency
    value=double
  />

Documentation (element)

Min: 0

The length of time after expiry of a blood-stage infection during which relapses from the same brood are supressed by the immune system.

This is rounded to the nearest time-step.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Blood stage length

→ scenario → model → vivax → bloodStageLengthDays

<bloodStageLengthDays
    scale=double
    shape=double
    distr=("weibull")
  />

Documentation (element)

Units: Days

Parameters used to sample the length of blood-stage infections from a Weibull distribution (scale parameter lambda, shape parameter k).

Documentation (type)

Parameters of a Weibull distribution.

Attributes

Scale

scale=double

The Weibull scale parameter (λ).

shape

shape=double

The Weibull shape parameter (k).

Distribution

distr=("weibull")

To allow heterogeneity, a distribution must be specified. In this case, only "weibull" is allowed.

clinicalEvents

→ scenario → model → vivax → clinicalEvents

<clinicalEvents>
IN THIS ORDER:
|   <pPrimaryInfection ... /> 
|   <pRelapseOne ... /> 
|   <pRelapseTwoPlus ... /> 
|   <pEventIsSevere ... /> 
</clinicalEvents>

Documentation (type)

This elements holds all information about probabilites for clinical events from infections and relapses.

pPrimaryInfection

→ scenario → model → vivax → clinicalEvents → pPrimaryInfection

<pPrimaryInfection
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseOne

→ scenario → model → vivax → clinicalEvents → pRelapseOne

<pRelapseOne
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseTwoPlus

→ scenario → model → vivax → clinicalEvents → pRelapseTwoPlus

<pRelapseTwoPlus
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pEventIsSevere

→ scenario → model → vivax → clinicalEvents → pEventIsSevere

<pEventIsSevere
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=string
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=string

Units: User defined (default: steps) Min: 0 Max: 20

Pre-erythrocytic latent period Can be specified in steps (e.g. 3t) or days (e.g. 15d).

parameter

→ scenario → model → parameters → parameter

<parameter
  [ name=string ]
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 40 documentation

Generated from: scenario_40.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
  [ analysisNo=int ]
    name=string
  [ wuID=int ]
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:om="http://openmalaria.org/schema/scenario_40"
    xsi:schemaLocation="http://openmalaria.org/schema/scenario_40 scenario_40.xsd"
  >
IN ANY ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entomology ... /> 
| [ <parasiteGenetics ... /> ]
| [ <pharmacology ... /> ]
| [ <diagnostics ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Name of intervention

Work unit identifier

wuID=int

Units: Number

Work unit ID. Obselete and no longer required.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Description of demography

Attributes

Name of demography data

name=string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Years Min: 0 Max: 100

Maximum age of simulated humans in years

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

list of age groups included in demography

Documentation (type)

list of age groups included in demography or surveys

Attributes

Lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Units: Percentage Min: 0 Max: 100

Percentage of human population in age group

Upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ startDate=string ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
| [ <cohorts ... /> ]
</monitoring>

Documentation (element)

Description of surveys

Attributes

Name of monitoring settings

name=string

Name of monitoring settings

Start of monitoring

startDate=string

continuous

→ scenario → monitoring → continuous

<continuous
    period=string
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Delay between reports

period=string

Units: User defined (default: steps)

Delay between reports; typically one time step but can be greater. Can be specified in steps (e.g. 1t) or days (e.g. 5d).

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions
  [ onlyNewEpisode=boolean ] DEFAULT VALUE false
  >
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See model/mon/OutputMeasures.h for a list of supported outputs. Should also be on the wiki.

Attributes

Report only for new cases

onlyNewEpisode=boolean

Default value: false

option

→ scenario → monitoring → SurveyOptions → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  [ outputNumber=int ]
  [ byAge=boolean ]
  [ byCohort=boolean ]
  [ bySpecies=boolean ]
  [ byGenotype=boolean ]
  [ byDrugType=boolean ]
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Number identifying measure in output

outputNumber=int

Report by age category

byAge=boolean

Report by cohort

byCohort=boolean

Report by mosquito species

bySpecies=boolean

Report by parasite genotype

byGenotype=boolean

Report by drug type

byDrugType=boolean

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
  [ detectionLimit=double ]
  [ diagnostic=string ]
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/microlitre Min: 0

Deprecated: limit above which a human's infection is reported as patent. Alternative: do not specify this; instead specify "diagnostic".

Name of monitoring diagnostic

diagnostic=string

Name of a parameterised diagnostic to use in surveys (see scenario/diagnostics).

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime
  [ repeatStep=string ]
  [ repeatEnd=string ]
  [ reported=boolean ] DEFAULT VALUE true
  >
    string
</surveyTime>

Documentation (element)

Units: User defined (defaults to steps) Min: 0

The simulation ends immediately after the last survey is taken.

Attributes

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

reported

reported=boolean

Default value: true

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Cohorts

→ scenario → monitoring → cohorts

<cohorts>
IN THIS ORDER:
| ( <subPop ... /> )+
</cohorts>

subPop

Documentation (element)

Allows the configuration of multiple cohorts (output segregated according to membership within specific sub-populations).

If this element is omitted, monitoring surveys cover the entire simulated human population.

It does not affect the "continuous" outputs (these never take cohorts into account).

Sub-population

→ scenario → monitoring → cohorts → subPop

<subPop
    id=string
    number=integer
  />

Documentation (element)

In the output file, the output set is identified by multiplying this number by 1000 then adding it to the age group column.

Attributes

Sub-population identifier

id=string

Textual identifier for the sub-population (i.e. for an intervention component, since sub-populations are defined as the hosts an intervention component is deployed to).

Sub-population number

number=integer

Units: dimensionless Min: 1 Max: 2097152

Number identifying a sub-population; used to define identifiers of output sets. This number must be a power of 2 (i.e. 1, 2, 4, 8, ...). See documentation of subPop element.

Preventative interventions

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfections ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <vectorPop ... /> ]
| [ <vectorTrap ... /> ]
| [ <human ... /> ]
</interventions>

Documentation (element)

Attributes

Name of intervention set

name=string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeHS>

timedDeployment

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeHS → timedDeployment

<timedDeployment
    time=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timedDeployment>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</uncomplicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

multiple

→ scenario → interventions → human → component → decisionTree → multiple

<multiple
  [ name=string ]
  >
IN THIS ORDER:
| ( <caseType ... /> )*
| ( <diagnostic ... /> )*
| ( <random ... /> )*
| ( <age ... /> )*
| ( <treatPKPD ... /> )*
| [ <treatSimple ... /> ]
| ( <deploy ... /> )*
</multiple>

Documentation (type)

A special node allowing multiple sub-trees to be evaluated.

This is different from an ordinary decision tree node in that:

a) multiple types of child can occur simultaneously (e.g. multiple types of treatment or treatment plus a 'random' sub-tree)

b) the 'noTreatment' and 'treatFailure' nodes are not allowed

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → multiple → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

firstLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → firstLine

<firstLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</firstLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

secondLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → secondLine

<secondLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</secondLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

positive

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

outcome

→ scenario → interventions → human → component → decisionTree → multiple → random → outcome

<outcome
  [ name=string ]
    p=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</outcome>

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Probability

p=double

Units: None Min: 0 Max: 1

Probability of selecting this outcome. The sum of probabilities across all outcomes must be 1.

age

→ scenario → interventions → human → component → decisionTree → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Age range

→ scenario → interventions → human → component → decisionTree → multiple → age → age

<age
  [ name=string ]
    lb=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</age>

Documentation (element)

Describes a branch, selected for patients of a certain age.

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Lower bound (inclusive)

lb=double

Min: 0

noTreatment

→ scenario → interventions → human → component → decisionTree → noTreatment

<noTreatment
  [ name=string ]
  />

Documentation (type)

An end node doing nothing. This exists to explicitly state that no treatment happens and to prevent trees from accidentally being left incomplete.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatFailure

→ scenario → interventions → human → component → decisionTree → treatFailure

<treatFailure
  [ name=string ]
  />

Documentation (type)

An end node which reports treatment but does not change parasitalogical status. This allows correct labelling of second-line cases.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → multiple → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

age

→ scenario → interventions → human → component → decisionTree → multiple → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → multiple → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → multiple → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → multiple → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</complicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: Days Min: 0 Max: unbounded

Maximum number of timesteps (including first day of case) that an individual with an uncomplicated case of malaria will remember he/she was sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial or non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of a complicated or severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
  [ name=string ]
  [ useDiagnosticUC=boolean ] DEFAULT VALUE false
  >
IN ANY ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <treatmentActions ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
</ImmediateOutcomes>

Documentation (type)

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Name of case management parameterisation

name=string

Name of health system

useDiagnosticUC

useDiagnosticUC=boolean

Default value: false

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Description of drug regimen.

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Artemisinine based combination therapy

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Quinine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0 Max: 1name:P(self-treat)

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Effectiveness of treatment for non-compliant patients

treatmentActions

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions

<treatmentActions>
IN ANY ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
</treatmentActions>

CQ
SP
AQ
SPAQ
ACT
QN

CQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ

<CQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</CQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

deploy

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy

<deploy
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ p=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| ( <component ... /> )+
</deploy>

component

Attributes

Maximum age of eligible humans

maxAge=double

Units: Years Min: 0

Maximum age of eligible humans (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible humans

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible humans (defaults to 0). Input is rounded to the nearest time step.

Probability of delivery to eligible humans

p=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Probability of this list of components being deployed, given that other constraints are met.

component

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Prophylactic treatment

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere → clearInfections

<clearInfections
    timesteps=string
    stage=("liver" or "blood" or "both")
  />

Documentation (element)

Attributes

Length of effect

timesteps=string

Units: User defined (defaults to steps)

Target stage

stage=("liver" or "blood" or "both")

SP

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SP

<SP
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SP>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

AQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → AQ

<AQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</AQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

SPAQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SPAQ

<SPAQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SPAQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

ACT

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → ACT

<ACT
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</ACT>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

QN

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → QN

<QN
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</QN>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

Probability that human is incompatible with liver-stage drug treatment

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pHumanCannotReceive

<pHumanCannotReceive
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that a human is determined to be unable to receive liver-stage drug treatment. Treatment is neither reported or given for such humans.

This is sampled once per human at birth.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Ignore liver-stage drug treatment incompatibility

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → ignoreCannotReceive

<ignoreCannotReceive
    value=boolean
  />

Documentation (element)

If true, ignore pHumanCannotReceive and consider all humans eligible for treatment; if false (or not specified), do not treat those demed incompatible with liver-stage drug treatment.

The point of this is that pHumanCannotReceive cannot be altered by changeHS interventions, but this property can be.

Attributes

Input parameter value

value=boolean

A boolean value.

Prob use in UC case

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pUseUncomplicated

<pUseUncomplicated
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

This feature is deprecated; it is suggested to use the "simple treatment" feature configured to clear liver-stage parasites, leaving this option unset or zero.

Chance of liver-stage drug treatment being used for routine treatment of an uncomplicated case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Effectiveness

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → effectivenessOnUse

<effectivenessOnUse
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that liver-stage drug treatment is effective.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

DecisionTree5Day

<DecisionTree5Day
  [ name=string ]
  >
IN ANY ORDER:
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
|   <treeUCOfficial ... /> 
|   <treeUCSelfTreat ... /> 
|   <cureRateSevere ... /> 
|   <treatmentSevere ... /> 
</DecisionTree5Day>

Documentation (type)

Besides greater flexibility, this allows treatment via PK/PD models.

Attributes

Name of case management parameterisation

name=string

Name of health system

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → DecisionTree5Day → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → DecisionTree5Day → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

treeUCOfficial

→ scenario → healthSystem → DecisionTree5Day → treeUCOfficial

<treeUCOfficial
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCOfficial>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treeUCSelfTreat

→ scenario → healthSystem → DecisionTree5Day → treeUCSelfTreat

<treeUCSelfTreat
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCSelfTreat>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Cure rate (severe cases)

→ scenario → healthSystem → DecisionTree5Day → cureRateSevere

<cureRateSevere
    value=double
  />

Documentation (element)

Min: 0 Max: 1

The probability of clearing parasites given access to appropriate (hospital) care, for a severe case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

treatmentSevere

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere

<treatmentSevere
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</treatmentSevere>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Case fatality rate for inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: Dimensionless

List of age-specific probabilities of sequelae in inpatients, during a severe bout of malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeEIR>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeEIR → timedDeployment

<timedDeployment
    eipDuration=int
    time=string
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timedDeployment>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Time

time=string

Units: User defined (defauls to steps) Min: 0

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=string ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=string

Units: User defined (default: steps) Min: 0

Default value: 0

If period is 0 (or effectively infinite), the last specified value remains indefinitely in effect, otherwise the times of all values specified must be less than the period, and values are repeated modulo period (the step at time 'period+2t' has same value as the step at '2t', etc.). Can be specified in steps (e.g. 1t) or days (e.g. 365d).

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=string
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time of start

time=string

Units: User defined (defauls to steps) Min: 0

Insert R_0 case

<insertR_0Case
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</insertR_0Case>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → insertR_0Case → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Uninfect vectors

<uninfectVectors
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</uninfectVectors>

timedDeployment

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → uninfectVectors → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Vector population intervention

→ scenario → interventions → vectorPop

<vectorPop>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorPop>

intervention

Documentation (element)

Units: List of elements

A list of parameterisations of generic vector host-inspecific interventions.

intervention

→ scenario → interventions → vectorPop → intervention

<intervention
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

Units: List of elements

An intervention which may have various effects on the vector populations as a whole. (Not host specific.)

Multiple instances of this intervention class are allowed (multiple parameterisations, not just deployments).

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → vectorPop → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → vectorPop → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <seekingDeathRateIncrease ... /> ]
| [ <probDeathOvipositing ... /> ]
| [ <emergenceReduction ... /> ]
</anopheles>

Documentation (type)

Units: dimensionless Min: 0 Max: 1

Descriptions of the effects of vector interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Proportional increase in deaths while host searching

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease

<seekingDeathRateIncrease
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</seekingDeathRateIncrease>

decay

Documentation (element)

Units: dimensionless

Describe an effect on the increase in the death rate while host seeking (mu_vA) due to this intervention.

Enter the rate increase (i.e. if rate increases to 120% of normal, give 0.2). New death rate while seeking is old × (1 + increase) where increase is this factor given. Must have increas ≥ -1.

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Proportion ovipositing mosquitoes killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing

<probDeathOvipositing
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probDeathOvipositing>

decay

Documentation (element)

Units: dimensionless

Describe an effect of increased mortality while ovipositing due to this intervention. Enter the probability of dying due to this intervention.

Attributes

Initial probability of killing

initial=double

Units: dimensionless Min: 0 Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Proportion of emerging pupa killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction

<emergenceReduction
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</emergenceReduction>

decay

Documentation (element)

Units: dimensionless

Describe an effect on emergence of pupa into adults: this value is the proportion of emerging pupa which are killed by this intervention.

Attributes

Initial proportion reduction

initial=double

Units: dimensionless Min: -inf Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Vector population intervention deployment

→ scenario → interventions → vectorPop → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

deploy

→ scenario → interventions → vectorPop → intervention → timed → deploy

<deploy
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Baited trap

→ scenario → interventions → vectorTrap

<vectorTrap>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorTrap>

intervention

Documentation (element)

intervention

→ scenario → interventions → vectorTrap → intervention

<intervention
  [ name=string ]
  >
IN THIS ORDER:
| ( <description ... /> )+
| [ <timed ... /> ]
</intervention>

Documentation (type)

Attributes

Descriptive name for type of trap

name=string

Optional name for this type of trap

Description

→ scenario → interventions → vectorTrap → intervention → description

<description
    mosquito=string
  >
IN THIS ORDER:
|   <relativeAvailability ... /> 
|   <decayOfAvailability ... /> 
</description>

Documentation (element)

Parameters associated with a vector trap intervention, per mosquito species.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Initial relative availability

→ scenario → interventions → vectorTrap → intervention → description → relativeAvailability

<relativeAvailability
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: inf

Describes the availiability of a trap to a host-seeking mosquito relative to an average unprotected adult.

I.e. if this parameter is 2, then each trap will on average attract twice as many mosquitoes as unprotected adults.

This is the initial availability; it may decay towards zero depending on the configured decay function.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay of availability

→ scenario → interventions → vectorTrap → intervention → description → decayOfAvailability

<decayOfAvailability
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Describes how availability decays to zero.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Vector trap intervention deployment

→ scenario → interventions → vectorTrap → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )*
</timed>

deploy

Documentation (element)

List of timed vector trap intervention deployment

deploy

→ scenario → interventions → vectorTrap → intervention → timed → deploy

<deploy
    time=string
    ratioToHumans=double
    lifespan=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Ratio to humans

ratioToHumans=double

Min: 0 Max: inf

The number of traps deployed, by this deployment, per adult human. E.g. if there are currently 100 traps and 1000 humans, then a ratio of 0.1 will increase the number of traps to 200.

Lifespan

lifespan=string

Units: Steps or Days or Years

Human-specific interventions

→ scenario → interventions → human

<human>
IN THIS ORDER:
| ( <component ... /> )+
| ( <deployment ... /> )*
</human>

Documentation (element)

Encapsulates all interventions whose effects are specific to the human host: any interventions where target humans may be selected via population-coverage, age limits and sub-population membership.

Component

→ scenario → interventions → human → component

<component
    id=string
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <screen ... /> 
| |   <treatSimple ... /> 
| |   <treatPKPD ... /> 
| |   <decisionTree ... /> 
| |   <PEV ... /> 
| |   <BSV ... /> 
| |   <TBV ... /> 
| |   <ITN ... /> 
| |   <IRS ... /> 
| |   <GVI ... /> 
| | [ <recruitmentOnly ... /> ]
| |   <clearImmunity ... /> 
| [ <subPopRemoval ... /> ]
</component>

Documentation (element)

Each element describes one component: its effects, decay of the(se) effect(s), and related stuff (e.g. description of indirect decay and of usage levels).

Attributes

Component identifier

id=string

Name of component

name=string

An informal name/description for the component

screen

→ scenario → interventions → human → component → screen

<screen
    diagnostic=string
  >
IN THIS ORDER:
| ( <positive ... /> )*
| ( <negative ... /> )*
</screen>

Documentation (type)

This can be combined with MDA to achieve mass screen and treat (MSAT) or other types of mass screening intervention.

The use of the screening itself is reported (if enabled), but not the outcome. Deployment of interventions triggered by the screening may be reported, however.

Attributes

Name of diagnostic

diagnostic=string

Name of a parameterised diagnostic (see scenario/diagnostics).

positive

→ scenario → interventions → human → component → screen → positive

<positive
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → screen → negative

<negative
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

treatSimple

→ scenario → interventions → human → component → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

treatPKPD

→ scenario → interventions → human → component → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

decisionTree

→ scenario → interventions → human → component → decisionTree

<decisionTree
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</decisionTree>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Vaccines

→ scenario → interventions → human → component → PEV

<PEV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</PEV>

Documentation (element)

Pre-erythrocytic vaccine (PEV): prevents a proportion of infections from commencing.

Documentation (type)

Description of a vaccine's effect

Decay of effect

→ scenario → interventions → human → component → PEV → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Specification of decay of efficacy. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Variance parameter for vaccine efficacy

→ scenario → interventions → human → component → PEV → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vaccines

→ scenario → interventions → human → component → BSV

<BSV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</BSV>

Documentation (element)

Blood-stage vaccine (BSV): acts as a killing factor on blood-stage parasites. Exact action depends on the within host model.

Documentation (type)

Description of a vaccine's effect

Vaccines

→ scenario → interventions → human → component → TBV

<TBV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</TBV>

Documentation (element)

Transmission-blocking vaccine (TBV): one minus this scales the probability of transmission to mosquitoes

Documentation (type)

Description of a vaccine's effect

Bed nets

→ scenario → interventions → human → component → ITN

<ITN>
IN THIS ORDER:
| [ <usage ... /> ]
|   <holeRate ... /> 
|   <ripRate ... /> 
|   <ripFactor ... /> 
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
|   <attritionOfNets ... /> 
| ( <anophelesParams ... /> )+
</ITN>

Documentation (element)

Description of bed-net interventions (ITNs, LLINs).

Proportion of time nets are used by humans

→ scenario → interventions → human → component → ITN → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of nets by humans, from 0 to 1.

At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing.

See also "propActing" (proportion of bits for which net acts).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Rate at which holes are made

→ scenario → interventions → human → component → ITN → holeRate

<holeRate
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: Holes per annum Min: 0

The rate at which new holes are made in nets.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Rate at which holes are enlarged

→ scenario → interventions → human → component → ITN → ripRate

<ripRate
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: Rips per existing hole per annum Min: 0

Each existing hole has a probability of being ripped bigger according to a Poisson process with this rate as (only) parameter.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Rip factor

→ scenario → interventions → human → component → ITN → ripFactor

<ripFactor
    value=double
  />

Documentation (element)

Units: none Min: 0

This factor expresses how important rips are in increasing the hole.

The hole index of a net is h + F×x where h and x are the total numbers of holes and rips respectively and F is the rip factor.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → ITN → initialInsecticide

<initialInsecticide
    mean=double
  [ SD=double ]
  [ distr=("const" or "normal") ] DEFAULT VALUE const
  />

Documentation (element)

Units: mg/m² Min: 0

Documentation (type)

A parameter with optional heterogeneity.

Optionally, a distribution ("distr") and standard of deviation ("SD") may be specified.

Attributes

mean

mean=double

The mean value.

standard deviation

SD=double

The standard deviation of variates.

Distribution

distr=("const" or "normal")

Default value: const

Decay of insecticide

→ scenario → interventions → human → component → ITN → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of nets. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Attrition of nets

→ scenario → interventions → human → component → ITN → attritionOfNets

<attritionOfNets
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: dimensionless

Specifies the rate at which nets are disposed of over time. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Humans are removed from the intervention component's sub-population on disposal (attrition) of their nets. Currently this event is not reported.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → human → component → ITN → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <holeIndexMax ... /> ]
| EXACTLY ONE OF:
| |   <deterrency ... /> 
| |   <twoStageDeterrency ... /> 
| EXACTLY ONE OF:
| |   <preprandialKillingEffect ... /> 
| |   <preprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| |   <postprandialKillingEffect ... /> 
| |   <postprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| | [ <fecundityReduction ... /> ]
| | [ <fecundityReductionLogit ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which net acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

maximum of holed surface area that has an effect (comparable to no net)

→ scenario → interventions → human → component → ITN → anophelesParams → holeIndexMax

<holeIndexMax
    value=double
  />

Documentation (element)

Units: in same unit as holeIndex

Used by logit attacking and killing models only, holeIndexMax is a user defined maximum hole index (typically, the total surface area of a net).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency

<twoStageDeterrency>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <entering ... /> 
| |   <enteringLogit ... /> 
| EXACTLY ONE OF:
| |   <attacking ... /> 
| |   <attackingLogit ... /> 
</twoStageDeterrency>

Documentation (element)

Units: dimensionless

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

This deterrency model multiplies human attractiveness by pEnt×pAtt.

Deterrency: entering

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → entering

<entering
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless

pEnt represents the relative probability of entering due to ITNs: pEnt = exp(log(P)×p) where P is the insecticide factor and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Deterrency: entering (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → enteringLogit

<enteringLogit
    baseFactor=double
    insecticideFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: none

See parent element documentation

Insecticide factor

insecticideFactor=double

Units: none

See parent element documentation

Deterrency: attacking

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attacking

<attacking
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Deterrency: attacking (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attackingLogit

<attackingLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Pre-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Pre-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffectLogit

<preprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Post-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffectLogit

<postprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Fecundity reduction

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-B), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReductionLogit

<fecundityReductionLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-K0), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Indoor residual spraying

→ scenario → interventions → human → component → IRS

<IRS>
IN THIS ORDER:
| [ <usage ... /> ]
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
| ( <anophelesParams ... /> )+
</IRS>

Documentation (element)

Description of indoor residual spraying interventions.

Documentation (type)

Description of effect for the more complex and probably more realistic Briet model: IRS has three effects, whos strength is calculated as a function of surviving insecticide content.

Proportion of Indoor residual spraying (IRS) interventions

→ scenario → interventions → human → component → IRS → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Indoor residual spraying (IRS) interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → IRS → initialInsecticide

<initialInsecticide
    mean=double
  [ SD=double ]
  [ distr=("const" or "normal") ] DEFAULT VALUE const
  />

Documentation (element)

Units: μg/cm² Min: 0

Documentation (type)

A parameter with optional heterogeneity.

Optionally, a distribution ("distr") and standard of deviation ("SD") may be specified.

Attributes

mean

mean=double

The mean value.

standard deviation

SD=double

The standard deviation of variates.

Distribution

distr=("const" or "normal")

Default value: const

Decay of insecticide

→ scenario → interventions → human → component → IRS → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → IRS → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → IRS → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied by exp(P×log(p)) where P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction

→ scenario → interventions → human → component → IRS → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

First, we calculate K = B + P×p where B is the base (without protection) probability of death, and P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Fecundity is multiplied by (1−K) / (1−B). It is not allowed to be greater than 1. To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Generic vector intervention

→ scenario → interventions → human → component → GVI

<GVI>
IN THIS ORDER:
| [ <usage ... /> ]
|   <decay ... /> 
| ( <anophelesParams ... /> )+
</GVI>

Documentation (element)

Note that all actions of this intervention component will decay according to a single decay function. If independant decay is wanted, a separate component can be used for each action.

Proportion of generic vector interventions

→ scenario → interventions → human → component → GVI → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Generic vector interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay

→ scenario → interventions → human → component → GVI → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ CV=double ] DEFAULT VALUE 0
  />

Documentation (element)

Description of decay of all intervention effects. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Coefficient of Variation

CV=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → GVI → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <deterrency ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → GVI → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of intervention on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied this factor times survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Fecundity reduction effect

→ scenario → interventions → human → component → GVI → anophelesParams → fecundityReduction

<fecundityReduction
    value=double
  />

Documentation (element)

Min: 0

Fertility is multiplied by 1 - (fecundityReduction * decay).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Recruitment only

→ scenario → interventions → human → component → recruitmentOnly

<recruitmentOnly/>

Documentation (element)

Recruitment of a host into a sub-population.

Clear Immunity

→ scenario → interventions → human → component → clearImmunity

<clearImmunity/>

Documentation (element)

Removes all exposure-related immunitsy gained over time by hosts without removing infections (or affecting the ability to gain immunity through exposure).

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

subPopRemoval

→ scenario → interventions → human → component → subPopRemoval

<subPopRemoval
  [ onFirstBout=boolean ] DEFAULT VALUE false
  [ onFirstTreatment=boolean ] DEFAULT VALUE false
  [ onFirstInfection=boolean ] DEFAULT VALUE false
  [ afterYears=double ]
  />

Documentation (type)

ITN attrition also removes humans from sub-populations.

Attributes

Time to first episode only

onFirstBout=boolean

Default value: false

Time to first treatment only

onFirstTreatment=boolean

Default value: false

Time to first infection only

onFirstInfection=boolean

Default value: false

Remove from sub-population after

afterYears=double

Units: Years Min: 0

Deployment

→ scenario → interventions → human → deployment

<deployment
  [ name=string ]
  >
IN THIS ORDER:
| ( <component ... /> )+
| ( <condition ... /> )*
| ( <continuous ... /> )*
| ( <timed ... /> )*
</deployment>

Documentation (element)

All components deployed by this intervention are deployed to the same people (each timed or continuous deployment selects recipients and then gives each recipient all components of the intervention).

Attributes

Intervention name

name=string

Name of intervention

component

→ scenario → interventions → human → deployment → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Condition

→ scenario → interventions → human → deployment → condition

<condition
    measure=string
  [ minValue=double ]
  [ maxValue=double ]
    initialState=boolean
  />

Documentation (element)

Conditions are evaluated for the whole population, not for individual age-groups or cohorts.

This affects all types of deployment.

Attributes

Measure

measure=string

The monitoring measure to test. Not all measures are available for use.

Minimum value

minValue=double

Minimum value. If specified, the measured variable must be greater than or equal to this value for the condition to be satisfied.

Maximum value

maxValue=double

Maximum value. If specified, the measured variable must be less than or equal to this value for the condition to be satisfied.

Initial state

initialState=boolean

Whether this condition is considered true or false before updated by a survey.

Age-based (continuous) deployment

→ scenario → interventions → human → deployment → continuous

<continuous>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| ( <deploy ... /> )+
</continuous>

Documentation (element)

List of ages at which deployment takes place (through EPI, post-natal and school-based programmes, etc.).

A sub-population restriction may be added as a property of the list of continuous deployments.

restrictToSubPop

→ scenario → interventions → human → deployment → continuous → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

deploy

→ scenario → interventions → human → deployment → continuous → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    targetAgeYrs=double
  [ begin=string ]
  [ end=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention. Input is rounded to the nearest time step.

First time active

begin=string

Units: User defined (defauls to steps)

End step

end=string

Units: User defined (defauls to steps)

Mass (timed) deployment

→ scenario → interventions → human → deployment → timed

<timed>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| [ <cumulativeCoverage ... /> ]
| ( <deploy ... /> )+
</timed>

Documentation (element)

List of timed deployments of the intervention (that is, of deployment campaigns).

Cumulative deployment mode can be specified for all deployments in a timed list. To allow multiple cumulative deployment descriptions, the entire timed list may be repeated.

restrictToSubPop

→ scenario → interventions → human → deployment → timed → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

Cumulative coverage

→ scenario → interventions → human → deployment → timed → cumulativeCoverage

<cumulativeCoverage
    component=string
  />

Documentation (element)

Attributes

Component identifier

component=string

The identifier (short name) of the component used when selecting people.

deploy

→ scenario → interventions → human → deployment → timed → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    time=string
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ repeatStep=string ]
  [ repeatEnd=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Time

time=string

Units: User defined (defauls to steps) Min: 0

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0

Maximum age of eligible individuals (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible individuals (defaults to 0). Input is rounded to the nearest time step.

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Description of health system.

Documentation (type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("forced" or "dynamic")
  [ scaledAnnualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Description of entomological data

Attributes

Entomology dataset name

name=string

Name of entomology data

Transmission model mode

mode=("forced" or "dynamic")

Override annual EIR

scaledAnnualEIR=double

Units: Infectious bites per adult per year

If set, the annual EIR (for all species of vector) is scaled to this level; can be omitted if not needed.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters of the transmission model

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <seasonality ... /> 
|   <mosq ... /> 
| [ <lifeCycle ... /> ]
| [ <simpleMPD ... /> ]
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial estimate of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial estimate of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial estimate of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Seasonality of transmission

→ scenario → entomology → vector → anopheles → seasonality

<seasonality
    input=("EIR")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <fourierSeries ... /> 
| |   <monthlyValues ... /> 
| |   <dailyValues ... /> 
</seasonality>

Documentation (element)

Specifies the seasonality of transmission and optionally the level of annual transmission.

Attributes

Seasonality input

input=("EIR")

Annual EIR

annualEIR=double

Units: Inoculations per adult per annum Min: 0

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries

<fourierSeries
    EIRRotateAngle=double
  >
IN THIS ORDER:
| ( <coeffic ... /> )*
</fourierSeries>

coeffic

Documentation (element)

Units: Infectious bites per adult per day

Attributes

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: Radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Pair of Fourier coefficients

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries → coeffic

<coeffic
    a=double
    b=double
  />

Documentation (element)

A pair of Fourier series coefficients. The first element specifies a1 and b1, the second a2 and b2, etc. Any number (from 0 up) of pairs may be given.

Attributes

a_n parameter of Fourier approximation to ln(EIR)

a=double

a_n parameter of Fourier approximation to ln(EIR) for some natural number n.

b_n parameter of Fourier approximation to ln(EIR)

b=double

b_n parameter of Fourier approximation to ln(EIR) for some natural number n.

List of monthly values

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues

<monthlyValues
    smoothing=("none" or "fourier")
  >
IN THIS ORDER:
| ( <value ... /> ){12,12}
</monthlyValues>

value

Documentation (element)

Description of seasonality from monthly values. Multiple smoothing methods are possible (see smoothing attribute).

List should contain twelve entries: January to December.

Attributes

Smoothing function

smoothing=("none" or "fourier")

How the monthly values are converted into a daily sequence of values:

none: no smoothing (step function)
Fourier: a Fourier series (with terms up to a2/b2) is fit to the sequence of monthly values and used to generate a smoothed list of daily values.

Monthly value

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Monthly value

List of daily values

→ scenario → entomology → vector → anopheles → seasonality → dailyValues

<dailyValues>
IN THIS ORDER:
| ( <value ... /> ){365,365}
</dailyValues>

value

Documentation (element)

Description of seasonality from daily values.

List should contain 365 entries: 1st January to 31st December.

Daily value

→ scenario → entomology → vector → anopheles → seasonality → dailyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Daily value

Mosquito feeding cycle parameters

→ scenario → entomology → vector → anopheles → mosq

<mosq
    minInfectedThreshold=double
  >
IN ANY ORDER:
|   <mosqRestDuration ... /> 
|   <extrinsicIncubationPeriod ... /> 
|   <mosqLaidEggsSameDayProportion ... /> 
|   <mosqSeekingDuration ... /> 
|   <mosqSurvivalFeedingCycleProbability ... /> 
|   <availability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <mosqProbOvipositing ... /> 
|   <mosqHumanBloodIndex ... /> 
</mosq>

Documentation (element)

Parameters describing the feeding cycle and human mosquito interaction of a single species of anopheles mosquito.

Attributes

Mininum infected threshold for mosquitos

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

Duration of the resting period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqRestDuration

<mosqRestDuration
    value=int
  />

Documentation (element)

Units: Days

name:Duration of the resting period of the vector (days);

Attributes

Input parameter value

value=int

An integer value.

Extrinsic incubation period

→ scenario → entomology → vector → anopheles → mosq → extrinsicIncubationPeriod

<extrinsicIncubationPeriod
    value=int
  />

Documentation (element)

Units: Days

name:Extrinsic incubation period (days)

Attributes

Input parameter value

value=int

An integer value.

Proportion of mosquitoes host seeking on same day as ovipositing

→ scenario → entomology → vector → anopheles → mosq → mosqLaidEggsSameDayProportion

<mosqLaidEggsSameDayProportion
    value=double
  />

Documentation (element)

Units: Proportion

Proportion of mosquitoes host seeking on same day as ovipositing

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Duration of the host-seeking period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqSeekingDuration

<mosqSeekingDuration
    value=double
  />

Documentation (element)

Units: Days

Duration of the host-seeking period of the vector (days)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito survives the feeding cycle

→ scenario → entomology → vector → anopheles → mosq → mosqSurvivalFeedingCycleProbability

<mosqSurvivalFeedingCycleProbability
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito survives the feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human availability rate heterogeneity

→ scenario → entomology → vector → anopheles → mosq → availability

<availability
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
  />

Documentation (element)

If no attributes are specified or distr="const" or CV="0" then there will be no heterogeneity.

Documentation (type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

Probability that the mosquito succesfully bites chosen host

→ scenario → entomology → vector → anopheles → mosq → mosqProbBiting

<mosqProbBiting
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito succesfully bites chosen host

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → mosq → mosqProbFindRestSite

<mosqProbFindRestSite
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito escapes host and finds a resting place after biting

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → mosq → mosqProbResting

<mosqProbResting
    mean=double
    variance=double
  />

Documentation (element)

Probability of mosquito successfully resting after finding a resting site

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of a mosquito successfully laying eggs given that it has rested

→ scenario → entomology → vector → anopheles → mosq → mosqProbOvipositing

<mosqProbOvipositing
    value=double
  />

Documentation (element)

Probability of a mosquito successfully laying eggs given that it has rested

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human blood index

→ scenario → entomology → vector → anopheles → mosq → mosqHumanBloodIndex

<mosqHumanBloodIndex
    value=double
  />

Documentation (element)

Units: Proportion

The proportion of resting mosquitoes which fed on human blood during the last feed.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mosquito life cycle parameters

→ scenario → entomology → vector → anopheles → lifeCycle

<lifeCycle
  [ estimatedLarvalResources=double ] DEFAULT VALUE 1e8
  >
IN ANY ORDER:
|   <eggStage ... /> 
|   <larvalStage ... /> 
|   <pupalStage ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</lifeCycle>

Documentation (element)

Parameters describing the life-cycle of this species of mosquito

Attributes

Estimate of larval resources

estimatedLarvalResources=double

Units: X

Default value: 1e8

Egg stage

→ scenario → entomology → vector → anopheles → lifeCycle → eggStage

<eggStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the egg stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

larvalStage

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage

<larvalStage>
</larvalStage>

daily

Documentation (type)

Parameters for the larval stage of development

Documentation (base type)

Parameters associated with a mosquito development stage.

Daily development

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage → daily

<daily
    resourceUsage=double
    effectCompetition=double
  />

Documentation (element)

Attributes

Resource usage

resourceUsage=double

Units: X

Resource usage during larval stage of development. Units are arbitrary.

Effect of competition

effectCompetition=double

Units: none

Effect of competition over resources on development.

Pupal stage

→ scenario → entomology → vector → anopheles → lifeCycle → pupalStage

<pupalStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the pupal stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → lifeCycle → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Simple Mosq-Pop-Dynamics parameters

→ scenario → entomology → vector → anopheles → simpleMPD

<simpleMPD>
IN ANY ORDER:
|   <developmentDuration ... /> 
|   <developmentSurvival ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</simpleMPD>

Documentation (element)

Parameters describing the simple mosquito population dynamics model.

This is a simpler version of the life-cycle model, requiring less parameters and with much simpler initialisation.

Duration

→ scenario → entomology → vector → anopheles → simpleMPD → developmentDuration

<developmentDuration
    value=int
  />

Documentation (element)

Units: Days Min: 1

Duration from egg laying to emergence in days.

Attributes

Input parameter value

value=int

An integer value.

Probability of survival

→ scenario → entomology → vector → anopheles → simpleMPD → developmentSurvival

<developmentSurvival
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that mosquito survives from the egg being laid to emergence, given no resouce limitations (no density constraints).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → simpleMPD → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Alternative (non-human) host paramters

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN ANY ORDER:
|   <mosqRelativeEntoAvailability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
| [ <hostFecundityFactor ... /> ]
</nonHumanHosts>

Documentation (element)

Min: 0

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of non-human host (ξ_i)

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqRelativeEntoAvailability

<mosqRelativeEntoAvailability
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of the population of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative fecundity of biting mosquitoes

→ scenario → entomology → vector → anopheles → nonHumanHosts → hostFecundityFactor

<hostFecundityFactor
    value=double
  />

Documentation (element)

Units: Proportion

Multiplicative factor for the number of fertile eggs laid by a mosquito after biting this type of host, relative to an unprotected human.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Name of this species of non human hosts (must match up with those described per anopheles section).

Population size of non-human host species

number=double

Units: Animals

Parasite genetics

<parasiteGenetics
    samplingMode=("initial" or "tracking")
  >
IN THIS ORDER:
| ( <locus ... /> )+
</parasiteGenetics>

locus

Documentation (element)

A specification of genotypes of infection parasites.

May be omitted; in this case there is no modelling of genetic differences of infections (resistance, fitness).

Attributes

samplingMode

samplingMode=("initial" or "tracking")

Locus

→ scenario → parasiteGenetics → locus

<locus
    name=string
  >
IN THIS ORDER:
| ( <allele ... /> )+
</locus>

allele

Documentation (element)

Alleles at loci can affect fitness and resistance to any number of drugs.

Attributes

Name of locus

name=string

Name of the Locus

Allele

→ scenario → parasiteGenetics → locus → allele

<allele
    name=string
    initialFrequency=double
    fitness=double
  />

Documentation (element)

Describes an allele, or one possible genetic option of multiple at one point of variance.

Attributes

Name

name=string

Name of the allele; used to refer to it elsewhere.

Initial frequency

initialFrequency=double

Fitness factor

fitness=double

Drug parameters (PK, PD and usage)

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
|   <treatments ... /> 
|   <drugs ... /> 
</pharmacology>

Documentation (element)

Drug model parameters and drug usage parameters

Documentation (type)

A library of drug related data for the PK/PD model.

Treatments library

→ scenario → pharmacology → treatments

<treatments>
IN THIS ORDER:
| ( <schedule ... /> )+
| ( <dosages ... /> )+
</treatments>

Documentation (element)

A library of drug deployment schedules and dosages.

schedule

→ scenario → pharmacology → treatments → schedule

<schedule
    name=string
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

A schedule for the administration of drugs in a course of treatment.

Note that dose sizes are multiplied by some multiplier (see dosages) and the times of all doses may be delayed.

Attributes

Name

name=string

Name for referring to this deployment schedule

medicate

→ scenario → pharmacology → treatments → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  />

Attributes

drug

drug=string

Abbreviated name of drug compound

Drug dose (mg with multiplier)

mg=double

Units: mg per something

Quantity of drug compound in mg per something. A separate dosage table must be used when medicating, which may specify multipliers of this number based on patient age or weight.

Time of administration

hour=double

Units: Hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

dosages

→ scenario → pharmacology → treatments → dosages

<dosages
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | ( <age ... /> )+
| | ( <bodymass ... /> )+
| |   <multiply ... /> 
</dosages>

Documentation (type)

A table for selecting a dose size. There are several ways this can work: using the patient's age or body mass in a look-up table to get a multplier, or directly using body mass as the multiplier.

The doses specified in "mg" in the treatment schedule are then multiplied by this multiplier.

Attributes

Name

name=string

Name for referring to this dosage table

Look-up table (age)

→ scenario → pharmacology → treatments → dosages → age

<age
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's age.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Look-up table (weight)

→ scenario → pharmacology → treatments → dosages → bodymass

<bodymass
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's body mass.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Multiply dose

→ scenario → pharmacology → treatments → dosages → multiply

<multiply
    by=("kg")
  />

Documentation (element)

Multiply the dose by some quantity, such as patient weight.

Attributes

By what?

by=("kg")

Quantity to multiply the dose by. Only option is "kg" (patient weight in kg).

Drug library

→ scenario → pharmacology → drugs

<drugs>
IN THIS ORDER:
| ( <drug ... /> )+
</drugs>

drug

Documentation (element)

A library of drug PK/PD data.

drug

→ scenario → pharmacology → drugs → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (type)

A drug description with PK/PD parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drugs → drug → PD

<PD
  [ locus=string ]
  >
IN THIS ORDER:
| ( <phenotype ... /> )+
</PD>

phenotype

Attributes

Locus

locus=string

PD parameters for some allele / resistance phenotype

→ scenario → pharmacology → drugs → drug → PD → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

Restrict phenotype applicability to certain alleles

→ scenario → pharmacology → drugs → drug → PD → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (element)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Maximal parasite killing rate

→ scenario → pharmacology → drugs → drug → PD → phenotype → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drugs → drug → PD → phenotype → IC50

<IC50
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

If CV > 0, the IC50 is sampled from a log-normal distribution.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Slope of effect curve

→ scenario → pharmacology → drugs → drug → PD → phenotype → slope

<slope>
    double
</slope>

Documentation (element)

Units: dimensionless

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drugs → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
| EXACTLY ONE OF:
| |   <half_life ... /> 
| | IN THIS ORDER:
| | |   <k ... /> 
| | |   <m_exponent ... /> 
| [ <k_a ... /> ]
| [ <conversion ... /> ]
|   <vol_dist ... /> 
| [ <compartment2 ... /> ]
| [ <compartment3 ... /> ]
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drugs → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drugs → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate λ, calculated as λ = ln(2) / half_life. The basic form of decay is C(t) = C0 * exp(-λ*t).

Alternatively, elimination rate can be specified via k and m_exponent.

Constant associated with elimination rate (k)

→ scenario → pharmacology → drugs → drug → PK → k

<k
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

If CV > 0, k is sampled per-human from the log-normal distribution: ln N( ln(mean) - σ^2 / 2, σ^2).

Alternatively, elimination rate can be specified via half_life.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Constant associated with elimination rate (m_exponent)

→ scenario → pharmacology → drugs → drug → PK → m_exponent

<m_exponent>
    double
</m_exponent>

Documentation (element)

Units: day^-1 Min: 0

Alternatively, elimination rate can be specified via half_life.

Note that in the case of a conversion model, this applies to both the elimination and the conversion rates.

Absorption rate constant (k_a)

→ scenario → pharmacology → drugs → drug → PK → k_a

<k_a
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Min: 0

Absorption rate parameter. Not allowed for one compartment models, but required for two and three compartment models and one compartment with conversion model (for the parent drug only).

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Conversion parameters (parent drug)

→ scenario → pharmacology → drugs → drug → PK → conversion

<conversion>
IN ANY ORDER:
|   <metabolite ... /> 
|   <rate ... /> 
|   <molRatio ... /> 
|   <IC50_log_correlation ... /> 
</conversion>

Documentation (element)

Configures the parent drug in a conversion model.

To use a conversion model, the parent drug should have this section defined as well as half-life or k (direct elimination; this may be zero) and k_a (absorption rate; this may be large).

Metabolite drug (abbreviation)

→ scenario → pharmacology → drugs → drug → PK → conversion → metabolite

<metabolite>
    string
</metabolite>

Documentation (element)

The abbreviation of the metabolite drug (e.g. "DHA" or "DHA_AR").

Rate of conversion

→ scenario → pharmacology → drugs → drug → PK → conversion → rate

<rate
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Rate of conversion of parent drug to metabolite.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Molecular weight ratio

→ scenario → pharmacology → drugs → drug → PK → conversion → molRatio

<molRatio>
    double
</molRatio>

Documentation (element)

Ratio of molecular weights: molecular weight of the metabolite divided by molecular weight of the parent.

IC50 log correlation

→ scenario → pharmacology → drugs → drug → PK → conversion → IC50_log_correlation

<IC50_log_correlation>
    double
</IC50_log_correlation>

Documentation (element)

Min: 0 Max: 1

If this value is 1, samples are fully correlated: a single z-score is used to calculate both samples. If this is 0, two independent samples are used.

Values between 0 and 1 (partial correlation) are supported; in this case IC50 values are sampled such that cor(log(x), log(y)) matches this value (where x, y are parent and metabolite IC50 values).

Volume of Distribution (Vd)

→ scenario → pharmacology → drugs → drug → PK → vol_dist

<vol_dist
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution.

If CV > 0 this is sampled from a log-normal distribution.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Second compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment2

<compartment2>
IN ANY ORDER:
|   <k12 ... /> 
|   <k21 ... /> 
</compartment2>

Documentation (element)

Optional element specifying conversion parameters to- and from- a second compartment.

Absorption rate to compartment 2 (k12)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → k12

<k12
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the first periphery compartment (2).

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Absorption rate from compartment 2 (k21)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → k21

<k21
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the first periphery compartment (2) to the central compartment.

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Third compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment3

<compartment3>
IN ANY ORDER:
|   <k13 ... /> 
|   <k31 ... /> 
</compartment3>

Documentation (element)

Optional element specifying conversion parameters to- and from- a third compartment.

Absorption rate to compartment 3 (k13)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → k13

<k13
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the second periphery compartment (3).

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Absorption rate from compartment 3 (k31)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → k31

<k31
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the second periphery compartment (3) to the central compartment.

It is sampled per-patient when CV > 0.

Documentation (type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

Diagnostic parameters

→ scenario → diagnostics

<diagnostics>
IN THIS ORDER:
| ( <diagnostic ... /> )*
</diagnostics>

diagnostic

Documentation (element)

Diagnostic model parameters

diagnostic

→ scenario → diagnostics → diagnostic

<diagnostic
    name=string
  [ units=("Other" or "Garki" or "Malariatherapy") ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterministic ... /> 
| |   <stochastic ... /> 
</diagnostic>

Attributes

Name of diagnostic

name=string

Name of this diagnostic (parameterisation). May be used elsewhere in the XML document to refer to this set of diagnostic parameters.

Parasite density units / methodology

units=("Other" or "Garki" or "Malariatherapy")

Deterministic detection

→ scenario → diagnostics → diagnostic → deterministic

<deterministic
    minDensity=double
  />

Documentation (element)

Specify that an artificial deterministic test is used: outcome is positive if parasite density is at least the minimum given.

Attributes

Minimum detectible density

minDensity=double

Units: parasites/microlitre Min: 0

The minimum density at which parasites can be detected. If 0, the test outcome is always positive.

Non-deterministic detection

→ scenario → diagnostics → diagnostic → stochastic

<stochastic
    dens_50=double
    specificity=double
  />

Documentation (element)

An improved model of detection which is non-deterministic, including false positive results as well as false negatives.

Some parameterisations:

Microscopy sensitivity/specificity data in Africa; Source: expert opinion — Allan Schapira dens_50 = 20.0 specificity = .75

RDT sensitivity/specificity for Plasmodium falciparum in Africa Source: Murray et al (Clinical Microbiological Reviews, Jan. 2008) dens_50 = 50.0; specificity = .942;

Attributes

Density 50

dens_50=double

Units: parasites/microlitre Min: 0

The density at which the test outcome has a 50% chance of being positive.

Specificity

specificity=double

Units: Dimensionless Min: 0 Max: 1

The probability of a positive test outcome in the absense of parasites.

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
| [ <vivax ... /> ]
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: model/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=string
  >
IN ANY ORDER:
| [ <NeonatalMortality ... /> ]
| [ <NonMalariaFevers ... /> ]
</clinical>

Documentation (type)

Attributes

Follow-up period during which recurrence is considered a treatment failure

healthSystemMemory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

Neonatal mortality parameters

→ scenario → model → clinical → NeonatalMortality

<NeonatalMortality
    diagnostic=string
  />

Attributes

Diagnostic used to parameterise model

diagnostic=string

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
| [ <prNeedTreatmentNMF ... /> ]
| [ <prNeedTreatmentMF ... /> ]
</NonMalariaFevers>

Documentation (type)

Description of the incidence of non-malaria fever. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a non-malarial fever requires treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

Availability of humans to mosquitoes relative to an adult, categorized by age group

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ]
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

Vivax model parameters

→ scenario → model → vivax

<vivax>
IN ANY ORDER:
|   <probBloodStageInfectiousToMosq ... /> 
|   <hypnozoiteRelease ... /> 
|   <bloodStageProtectionLatency ... /> 
|   <bloodStageLengthDays ... /> 
|   <clinicalEvents ... /> 
</vivax>

Documentation (element)

This describes Vivax model parameters, and is required when using the VIVAX_SIMPLE_MODEL model option.

Probability of mosquito infection

→ scenario → model → vivax → probBloodStageInfectiousToMosq

<probBloodStageInfectiousToMosq
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

The chance of a feeding mosquito becoming infected, given that the host is patent. (This may be adjusted by transmission-blocking vaccines.)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Hypnozoite releases

→ scenario → model → vivax → hypnozoiteRelease

<hypnozoiteRelease
  [ pSecondRelease=double ] DEFAULT VALUE 0
  >
IN ANY ORDER:
|   <numberHypnozoites ... /> 
|   <firstReleaseDays ... /> 
| [ <secondReleaseDays ... /> ]
</hypnozoiteRelease>

Documentation (element)

Describes the number and times of hypnozoite releases.

Documentation (type)

This element defines probabilites when and how many hypnozoites are released from the liverstage into the blood.

The gap between the start of a new brood of hypnozoites and its release are defined as follows:

latentP + latentRelapse + randomReleaseDelay

randomReleaseDelay is based on one or two lognormal distributions, which are defined in firstRelease and optionally secondRelease.

You can define 2 release distributions, which get added together and represent the probability of hypnozoites which get released before winter (first release) or after (second release).

You can omit the secondRelease element if no release to the blood happens after winter.

Attributes

latent relapse days

pSecondRelease=double

Default value: 0

Probability of a second release. If undefined it is zero.

Number of Hypnozoites

→ scenario → model → vivax → hypnozoiteRelease → numberHypnozoites

<numberHypnozoites
    max=int
    base=double
  />

Documentation (element)

numberHypnozoites calculates the number of hypnozoites in the liver stage based on a base which is between 0 and 1.

This number is random based on the following distribution and normalized:

max ∑ (base ^ n) n = 0

Attributes

max

max=int

base

base=double

firstReleaseDays

→ scenario → model → vivax → hypnozoiteRelease → firstReleaseDays

<firstReleaseDays
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
    latentRelapse=double
  />

Documentation (type)

Hypnozoites are released after a delay, calculated as: roundToTSFromDays(delay + latentRelapse)

Here, roundToTSFromDays rounds the input (in days) to the nearest timestep, delay is sampled from a log-normal, and latentRelapse is the parameter specified here.

The delay is sampled from a log-normal distribution, parameterised via the (linear) mean and CV (coefficient of variation) given here.

Documentation (base type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

latent relapse days

latentRelapse=double

Usually between 10 and 15 days.

secondReleaseDays

→ scenario → model → vivax → hypnozoiteRelease → secondReleaseDays

<secondReleaseDays
  [ CV=double ]
  [ distr=("const" or "lognormal") ] DEFAULT VALUE const
    mean=double
    latentRelapse=double
  />

Documentation (type)

Hypnozoites are released after a delay, calculated as: roundToTSFromDays(delay + latentRelapse)

Here, roundToTSFromDays rounds the input (in days) to the nearest timestep, delay is sampled from a log-normal, and latentRelapse is the parameter specified here.

The delay is sampled from a log-normal distribution, parameterised via the (linear) mean and CV (coefficient of variation) given here.

Documentation (base type)

A parameter with optional log-normal heterogeneity.

The mean value must be specified. Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Documentation (base type)

A parameter with optional heterogeneity.

The mean cannot be specified (unless this type is extended). Optionally, a distribution ("distr") and coefficient of variation ("CV") may be specified.

Attributes

Coefficient of variation

CV=double

Units: unitless

Distribution

distr=("const" or "lognormal")

Default value: const

mean

mean=double

The (linear) mean value.

latent relapse days

latentRelapse=double

Usually between 10 and 15 days.

Blood stage protection latency

→ scenario → model → vivax → bloodStageProtectionLatency

<bloodStageProtectionLatency
    value=double
  />

Documentation (element)

Min: 0

The length of time after expiry of a blood-stage infection during which relapses from the same brood are supressed by the immune system.

This is rounded to the nearest time-step.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Blood stage length

→ scenario → model → vivax → bloodStageLengthDays

<bloodStageLengthDays
    scale=double
    shape=double
    distr=("weibull")
  />

Documentation (element)

Units: Days

Parameters used to sample the length of blood-stage infections from a Weibull distribution (scale parameter lambda, shape parameter k).

Documentation (type)

Parameters of a Weibull distribution.

Attributes

Scale

scale=double

The Weibull scale parameter (λ).

shape

shape=double

The Weibull shape parameter (k).

Distribution

distr=("weibull")

To allow heterogeneity, a distribution must be specified. In this case, only "weibull" is allowed.

clinicalEvents

→ scenario → model → vivax → clinicalEvents

<clinicalEvents>
IN THIS ORDER:
|   <pPrimaryInfection ... /> 
|   <pRelapseOne ... /> 
|   <pRelapseTwoPlus ... /> 
|   <pEventIsSevere ... /> 
</clinicalEvents>

Documentation (type)

This elements holds all information about probabilites for clinical events from infections and relapses.

pPrimaryInfection

→ scenario → model → vivax → clinicalEvents → pPrimaryInfection

<pPrimaryInfection
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseOne

→ scenario → model → vivax → clinicalEvents → pRelapseOne

<pRelapseOne
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseTwoPlus

→ scenario → model → vivax → clinicalEvents → pRelapseTwoPlus

<pRelapseTwoPlus
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pEventIsSevere

→ scenario → model → vivax → clinicalEvents → pEventIsSevere

<pEventIsSevere
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=string
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=string

Units: User defined (default: steps) Min: 0 Max: 20

Pre-erythrocytic latent period Can be specified in steps (e.g. 3t) or days (e.g. 15d).

parameter

→ scenario → model → parameters → parameter

<parameter
  [ name=string ]
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 39 documentation

Generated from: scenario_39.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
  [ analysisNo=int ]
    name=string
  [ wuID=int ]
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:om="http://openmalaria.org/schema/scenario_39"
    xsi:schemaLocation="http://openmalaria.org/schema/scenario_39 scenario_39.xsd"
  >
IN ANY ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entomology ... /> 
| [ <parasiteGenetics ... /> ]
| [ <pharmacology ... /> ]
| [ <diagnostics ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Name of intervention

Work unit identifier

wuID=int

Units: Number

Work unit ID. Obselete and no longer required.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Description of demography

Attributes

Name of demography data

name=string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Years Min: 0 Max: 100

Maximum age of simulated humans in years

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

list of age groups included in demography

Documentation (type)

list of age groups included in demography or surveys

Attributes

Lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Units: Percentage Min: 0 Max: 100

Percentage of human population in age group

Upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ startDate=string ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
| [ <cohorts ... /> ]
</monitoring>

Documentation (element)

Description of surveys

Attributes

Name of monitoring settings

name=string

Name of monitoring settings

Start of monitoring

startDate=string

continuous

→ scenario → monitoring → continuous

<continuous
    period=string
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Delay between reports

period=string

Units: User defined (default: steps)

Delay between reports; typically one time step but can be greater. Can be specified in steps (e.g. 1t) or days (e.g. 5d).

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions
  [ onlyNewEpisode=boolean ] DEFAULT VALUE false
  >
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See model/mon/OutputMeasures.h for a list of supported outputs. Should also be on the wiki.

Attributes

Report only for new cases

onlyNewEpisode=boolean

Default value: false

option

→ scenario → monitoring → SurveyOptions → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  [ outputNumber=int ]
  [ byAge=boolean ]
  [ byCohort=boolean ]
  [ bySpecies=boolean ]
  [ byGenotype=boolean ]
  [ byDrugType=boolean ]
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Number identifying measure in output

outputNumber=int

Report by age category

byAge=boolean

Report by cohort

byCohort=boolean

Report by mosquito species

bySpecies=boolean

Report by parasite genotype

byGenotype=boolean

Report by drug type

byDrugType=boolean

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
  [ detectionLimit=double ]
  [ diagnostic=string ]
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/microlitre Min: 0

Deprecated: limit above which a human's infection is reported as patent. Alternative: do not specify this; instead specify "diagnostic".

Name of monitoring diagnostic

diagnostic=string

Name of a parameterised diagnostic to use in surveys (see scenario/diagnostics).

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime
  [ repeatStep=string ]
  [ repeatEnd=string ]
  [ reported=boolean ] DEFAULT VALUE true
  >
    string
</surveyTime>

Documentation (element)

Units: User defined (defaults to steps) Min: 0

The simulation ends immediately after the last survey is taken.

Attributes

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

reported

reported=boolean

Default value: true

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Cohorts

→ scenario → monitoring → cohorts

<cohorts>
IN THIS ORDER:
| ( <subPop ... /> )+
</cohorts>

subPop

Documentation (element)

Allows the configuration of multiple cohorts (output segregated according to membership within specific sub-populations).

If this element is omitted, monitoring surveys cover the entire simulated human population.

It does not affect the "continuous" outputs (these never take cohorts into account).

Sub-population

→ scenario → monitoring → cohorts → subPop

<subPop
    id=string
    number=integer
  />

Documentation (element)

In the output file, the output set is identified by multiplying this number by 1000 then adding it to the age group column.

Attributes

Sub-population identifier

id=string

Textual identifier for the sub-population (i.e. for an intervention component, since sub-populations are defined as the hosts an intervention component is deployed to).

Sub-population number

number=integer

Units: dimensionless Min: 1 Max: 2097152

Number identifying a sub-population; used to define identifiers of output sets. This number must be a power of 2 (i.e. 1, 2, 4, 8, ...). See documentation of subPop element.

Preventative interventions

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfections ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <vectorPop ... /> ]
| [ <vectorTrap ... /> ]
| [ <human ... /> ]
</interventions>

Documentation (element)

Attributes

Name of intervention set

name=string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeHS>

timedDeployment

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeHS → timedDeployment

<timedDeployment
    time=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timedDeployment>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</uncomplicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

multiple

→ scenario → interventions → human → component → decisionTree → multiple

<multiple
  [ name=string ]
  >
IN THIS ORDER:
| ( <caseType ... /> )*
| ( <diagnostic ... /> )*
| ( <random ... /> )*
| ( <age ... /> )*
| ( <treatPKPD ... /> )*
| [ <treatSimple ... /> ]
| ( <deploy ... /> )*
</multiple>

Documentation (type)

A special node allowing multiple sub-trees to be evaluated.

This is different from an ordinary decision tree node in that:

a) multiple types of child can occur simultaneously (e.g. multiple types of treatment or treatment plus a 'random' sub-tree)

b) the 'noTreatment' and 'treatFailure' nodes are not allowed

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → multiple → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

firstLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → firstLine

<firstLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</firstLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

secondLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → secondLine

<secondLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</secondLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

positive

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

outcome

→ scenario → interventions → human → component → decisionTree → multiple → random → outcome

<outcome
  [ name=string ]
    p=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</outcome>

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Probability

p=double

Units: None Min: 0 Max: 1

Probability of selecting this outcome. The sum of probabilities across all outcomes must be 1.

age

→ scenario → interventions → human → component → decisionTree → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Age range

→ scenario → interventions → human → component → decisionTree → multiple → age → age

<age
  [ name=string ]
    lb=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</age>

Documentation (element)

Describes a branch, selected for patients of a certain age.

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Lower bound (inclusive)

lb=double

Min: 0

noTreatment

→ scenario → interventions → human → component → decisionTree → noTreatment

<noTreatment
  [ name=string ]
  />

Documentation (type)

An end node doing nothing. This exists to explicitly state that no treatment happens and to prevent trees from accidentally being left incomplete.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatFailure

→ scenario → interventions → human → component → decisionTree → treatFailure

<treatFailure
  [ name=string ]
  />

Documentation (type)

An end node which reports treatment but does not change parasitalogical status. This allows correct labelling of second-line cases.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → multiple → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

age

→ scenario → interventions → human → component → decisionTree → multiple → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → multiple → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → multiple → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → multiple → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</complicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: Days Min: 0 Max: unbounded

Maximum number of timesteps (including first day of case) that an individual with an uncomplicated case of malaria will remember he/she was sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial or non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of a complicated or severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
  [ name=string ]
  [ useDiagnosticUC=boolean ] DEFAULT VALUE false
  >
IN ANY ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <treatmentActions ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
</ImmediateOutcomes>

Documentation (type)

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Name of case management parameterisation

name=string

Name of health system

useDiagnosticUC

useDiagnosticUC=boolean

Default value: false

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Description of drug regimen.

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Artemisinine based combination therapy

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Quinine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0 Max: 1name:P(self-treat)

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Effectiveness of treatment for non-compliant patients

treatmentActions

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions

<treatmentActions>
IN ANY ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
</treatmentActions>

CQ
SP
AQ
SPAQ
ACT
QN

CQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ

<CQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</CQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

deploy

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy

<deploy
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ p=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| ( <component ... /> )+
</deploy>

component

Attributes

Maximum age of eligible humans

maxAge=double

Units: Years Min: 0

Maximum age of eligible humans (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible humans

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible humans (defaults to 0). Input is rounded to the nearest time step.

Probability of delivery to eligible humans

p=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Probability of this list of components being deployed, given that other constraints are met.

component

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Prophylactic treatment

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere → clearInfections

<clearInfections
    timesteps=string
    stage=("liver" or "blood" or "both")
  />

Documentation (element)

Attributes

Length of effect

timesteps=string

Units: User defined (defaults to steps)

Target stage

stage=("liver" or "blood" or "both")

SP

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SP

<SP
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SP>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

AQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → AQ

<AQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</AQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

SPAQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SPAQ

<SPAQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SPAQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

ACT

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → ACT

<ACT
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</ACT>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

QN

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → QN

<QN
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</QN>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

Probability that human is incompatible with liver-stage drug treatment

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pHumanCannotReceive

<pHumanCannotReceive
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that a human is determined to be unable to receive liver-stage drug treatment. Treatment is neither reported or given for such humans.

This is sampled once per human at birth.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Ignore liver-stage drug treatment incompatibility

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → ignoreCannotReceive

<ignoreCannotReceive
    value=boolean
  />

Documentation (element)

If true, ignore pHumanCannotReceive and consider all humans eligible for treatment; if false (or not specified), do not treat those demed incompatible with liver-stage drug treatment.

The point of this is that pHumanCannotReceive cannot be altered by changeHS interventions, but this property can be.

Attributes

Input parameter value

value=boolean

A boolean value.

Prob use in UC case

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pUseUncomplicated

<pUseUncomplicated
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

This feature is deprecated; it is suggested to use the "simple treatment" feature configured to clear liver-stage parasites, leaving this option unset or zero.

Chance of liver-stage drug treatment being used for routine treatment of an uncomplicated case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Effectiveness

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → effectivenessOnUse

<effectivenessOnUse
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that liver-stage drug treatment is effective.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

DecisionTree5Day

<DecisionTree5Day
  [ name=string ]
  >
IN ANY ORDER:
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
|   <treeUCOfficial ... /> 
|   <treeUCSelfTreat ... /> 
|   <cureRateSevere ... /> 
|   <treatmentSevere ... /> 
</DecisionTree5Day>

Documentation (type)

Besides greater flexibility, this allows treatment via PK/PD models.

Attributes

Name of case management parameterisation

name=string

Name of health system

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → DecisionTree5Day → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → DecisionTree5Day → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

treeUCOfficial

→ scenario → healthSystem → DecisionTree5Day → treeUCOfficial

<treeUCOfficial
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCOfficial>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treeUCSelfTreat

→ scenario → healthSystem → DecisionTree5Day → treeUCSelfTreat

<treeUCSelfTreat
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCSelfTreat>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Cure rate (severe cases)

→ scenario → healthSystem → DecisionTree5Day → cureRateSevere

<cureRateSevere
    value=double
  />

Documentation (element)

Min: 0 Max: 1

The probability of clearing parasites given access to appropriate (hospital) care, for a severe case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

treatmentSevere

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere

<treatmentSevere
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</treatmentSevere>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Case fatality rate for inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: Dimensionless

List of age-specific probabilities of sequelae in inpatients, during a severe bout of malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeEIR>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeEIR → timedDeployment

<timedDeployment
    eipDuration=int
    time=string
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timedDeployment>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Time

time=string

Units: User defined (defauls to steps) Min: 0

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=string ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=string

Units: User defined (default: steps) Min: 0

Default value: 0

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=string
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time of start

time=string

Units: User defined (defauls to steps) Min: 0

Insert R_0 case

<insertR_0Case
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</insertR_0Case>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → insertR_0Case → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Uninfect vectors

<uninfectVectors
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</uninfectVectors>

timedDeployment

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → uninfectVectors → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Vector population intervention

→ scenario → interventions → vectorPop

<vectorPop>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorPop>

intervention

Documentation (element)

Units: List of elements

A list of parameterisations of generic vector host-inspecific interventions.

intervention

→ scenario → interventions → vectorPop → intervention

<intervention
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

Units: List of elements

An intervention which may have various effects on the vector populations as a whole. (Not host specific.)

Multiple instances of this intervention class are allowed (multiple parameterisations, not just deployments).

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → vectorPop → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → vectorPop → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <seekingDeathRateIncrease ... /> ]
| [ <probDeathOvipositing ... /> ]
| [ <emergenceReduction ... /> ]
</anopheles>

Documentation (type)

Units: dimensionless Min: 0 Max: 1

Descriptions of the effects of vector interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Proportional increase in deaths while host searching

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease

<seekingDeathRateIncrease
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</seekingDeathRateIncrease>

decay

Documentation (element)

Units: dimensionless

Describe an effect on the increase in the death rate while host seeking (mu_vA) due to this intervention.

Enter the rate increase (i.e. if rate increases to 120% of normal, give 0.2). New death rate while seeking is old × (1 + increase) where increase is this factor given. Must have increas ≥ -1.

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

If sigma is non-zero, heterogeneity of decay is introduced via a random variable sampled from the log-normal distribution with mu and sigma as specified. Both mu and sigma default to zero when not specified. The decay rate is multiplied by this variable (effectively, the half-life is divided by it). Note that with m=0, the median of the variable and the median value of L is unchanged, and thus the time at which the median decay amongst the population of decaying objects reaches half (assuming exponential, Weibull or Hill decay) is L. With m=-½σ² (negative half sigma squared) the mean of the variable will be 1 and mean of the half-life L, but the time at which mean decay of the population has reached half may not be L.

σ (sigma)

sigma=double

Min: 0

Default value: 0

Proportion ovipositing mosquitoes killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing

<probDeathOvipositing
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probDeathOvipositing>

decay

Documentation (element)

Units: dimensionless

Describe an effect of increased mortality while ovipositing due to this intervention. Enter the probability of dying due to this intervention.

Attributes

Initial probability of killing

initial=double

Units: dimensionless Min: 0 Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Proportion of emerging pupa killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction

<emergenceReduction
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</emergenceReduction>

decay

Documentation (element)

Units: dimensionless

Describe an effect on emergence of pupa into adults: this value is the proportion of emerging pupa which are killed by this intervention.

Attributes

Initial proportion reduction

initial=double

Units: dimensionless Min: -inf Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Vector population intervention deployment

→ scenario → interventions → vectorPop → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

deploy

→ scenario → interventions → vectorPop → intervention → timed → deploy

<deploy
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Baited trap

→ scenario → interventions → vectorTrap

<vectorTrap>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorTrap>

intervention

Documentation (element)

intervention

→ scenario → interventions → vectorTrap → intervention

<intervention
  [ name=string ]
  >
IN THIS ORDER:
| ( <description ... /> )+
| [ <timed ... /> ]
</intervention>

Documentation (type)

Attributes

Descriptive name for type of trap

name=string

Optional name for this type of trap

Description

→ scenario → interventions → vectorTrap → intervention → description

<description
    mosquito=string
  >
IN THIS ORDER:
|   <relativeAvailability ... /> 
|   <decayOfAvailability ... /> 
</description>

Documentation (element)

Parameters associated with a vector trap intervention, per mosquito species.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Initial relative availability

→ scenario → interventions → vectorTrap → intervention → description → relativeAvailability

<relativeAvailability
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: inf

Describes the availiability of a trap to a host-seeking mosquito relative to an average unprotected adult.

I.e. if this parameter is 2, then each trap will on average attract twice as many mosquitoes as unprotected adults.

This is the initial availability; it may decay towards zero depending on the configured decay function.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay of availability

→ scenario → interventions → vectorTrap → intervention → description → decayOfAvailability

<decayOfAvailability
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Describes how availability decays to zero.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Vector trap intervention deployment

→ scenario → interventions → vectorTrap → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )*
</timed>

deploy

Documentation (element)

List of timed vector trap intervention deployment

deploy

→ scenario → interventions → vectorTrap → intervention → timed → deploy

<deploy
    time=string
    ratioToHumans=double
    lifespan=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Ratio to humans

ratioToHumans=double

Min: 0 Max: inf

The number of traps deployed, by this deployment, per adult human. E.g. if there are currently 100 traps and 1000 humans, then a ratio of 0.1 will increase the number of traps to 200.

Lifespan

lifespan=string

Units: Steps or Days or Years

Human-specific interventions

→ scenario → interventions → human

<human>
IN THIS ORDER:
| ( <component ... /> )+
| ( <deployment ... /> )*
</human>

Documentation (element)

Encapsulates all interventions whose effects are specific to the human host: any interventions where target humans may be selected via population-coverage, age limits and sub-population membership.

Component

→ scenario → interventions → human → component

<component
    id=string
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <screen ... /> 
| |   <treatSimple ... /> 
| |   <treatPKPD ... /> 
| |   <decisionTree ... /> 
| |   <PEV ... /> 
| |   <BSV ... /> 
| |   <TBV ... /> 
| |   <ITN ... /> 
| |   <IRS ... /> 
| |   <GVI ... /> 
| | [ <recruitmentOnly ... /> ]
| |   <clearImmunity ... /> 
| [ <subPopRemoval ... /> ]
</component>

Documentation (element)

Each element describes one component: its effects, decay of the(se) effect(s), and related stuff (e.g. description of indirect decay and of usage levels).

Attributes

Component identifier

id=string

Name of component

name=string

An informal name/description for the component

screen

→ scenario → interventions → human → component → screen

<screen
    diagnostic=string
  >
IN THIS ORDER:
| ( <positive ... /> )*
| ( <negative ... /> )*
</screen>

Documentation (type)

This can be combined with MDA to achieve mass screen and treat (MSAT) or other types of mass screening intervention.

The use of the screening itself is reported (if enabled), but not the outcome. Deployment of interventions triggered by the screening may be reported, however.

Attributes

Name of diagnostic

diagnostic=string

Name of a parameterised diagnostic (see scenario/diagnostics).

positive

→ scenario → interventions → human → component → screen → positive

<positive
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → screen → negative

<negative
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

treatSimple

→ scenario → interventions → human → component → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

treatPKPD

→ scenario → interventions → human → component → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

decisionTree

→ scenario → interventions → human → component → decisionTree

<decisionTree
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</decisionTree>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Vaccines

→ scenario → interventions → human → component → PEV

<PEV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</PEV>

Documentation (element)

Pre-erythrocytic vaccine (PEV): prevents a proportion of infections from commencing.

Documentation (type)

Description of a vaccine's effect

Decay of effect

→ scenario → interventions → human → component → PEV → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Specification of decay of efficacy. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Variance parameter for vaccine efficacy

→ scenario → interventions → human → component → PEV → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vaccines

→ scenario → interventions → human → component → BSV

<BSV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</BSV>

Documentation (element)

Blood-stage vaccine (BSV): acts as a killing factor on blood-stage parasites. Exact action depends on the within host model.

Documentation (type)

Description of a vaccine's effect

Vaccines

→ scenario → interventions → human → component → TBV

<TBV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</TBV>

Documentation (element)

Transmission-blocking vaccine (TBV): one minus this scales the probability of transmission to mosquitoes

Documentation (type)

Description of a vaccine's effect

Bed nets

→ scenario → interventions → human → component → ITN

<ITN>
IN THIS ORDER:
| [ <usage ... /> ]
|   <holeRate ... /> 
|   <ripRate ... /> 
|   <ripFactor ... /> 
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
|   <attritionOfNets ... /> 
| ( <anophelesParams ... /> )+
</ITN>

Documentation (element)

Description of bed-net interventions (ITNs, LLINs).

Proportion of time nets are used by humans

→ scenario → interventions → human → component → ITN → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of nets by humans, from 0 to 1.

At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing.

See also "propActing" (proportion of bits for which net acts).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Rate at which holes are made

→ scenario → interventions → human → component → ITN → holeRate

<holeRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Holes per annum Min: 0

The rate at which new holes are made in nets.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ ln N( log(mean)-sigma²/2, sigma² ).

Equivalent R sample: rlnorm(n, log(m) - s*s/2, s)

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rate at which holes are enlarged

→ scenario → interventions → human → component → ITN → ripRate

<ripRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Rips per existing hole per annum Min: 0

Each existing hole has a probability of being ripped bigger according to a Poisson process with this rate as (only) parameter.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ ln N( log(mean)-sigma²/2, sigma² ).

Equivalent R sample: rlnorm(n, log(m) - s*s/2, s)

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rip factor

→ scenario → interventions → human → component → ITN → ripFactor

<ripFactor
    value=double
  />

Documentation (element)

Units: none Min: 0

This factor expresses how important rips are in increasing the hole.

The hole index of a net is h + F×x where h and x are the total numbers of holes and rips respectively and F is the rip factor.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → ITN → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: mg/m² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → human → component → ITN → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of nets. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Attrition of nets

→ scenario → interventions → human → component → ITN → attritionOfNets

<attritionOfNets
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: dimensionless

Specifies the rate at which nets are disposed of over time. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Humans are removed from the intervention component's sub-population on disposal (attrition) of their nets. Currently this event is not reported.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → human → component → ITN → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <holeIndexMax ... /> ]
| EXACTLY ONE OF:
| |   <deterrency ... /> 
| |   <twoStageDeterrency ... /> 
| EXACTLY ONE OF:
| |   <preprandialKillingEffect ... /> 
| |   <preprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| |   <postprandialKillingEffect ... /> 
| |   <postprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| | [ <fecundityReduction ... /> ]
| | [ <fecundityReductionLogit ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which net acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

maximum of holed surface area that has an effect (comparable to no net)

→ scenario → interventions → human → component → ITN → anophelesParams → holeIndexMax

<holeIndexMax
    value=double
  />

Documentation (element)

Units: in same unit as holeIndex

Used by logit attacking and killing models only, holeIndexMax is a user defined maximum hole index (typically, the total surface area of a net).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency

<twoStageDeterrency>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <entering ... /> 
| |   <enteringLogit ... /> 
| EXACTLY ONE OF:
| |   <attacking ... /> 
| |   <attackingLogit ... /> 
</twoStageDeterrency>

Documentation (element)

Units: dimensionless

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

This deterrency model multiplies human attractiveness by pEnt×pAtt.

Deterrency: entering

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → entering

<entering
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless

pEnt represents the relative probability of entering due to ITNs: pEnt = exp(log(P)×p) where P is the insecticide factor and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Deterrency: entering (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → enteringLogit

<enteringLogit
    baseFactor=double
    insecticideFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: none

See parent element documentation

Insecticide factor

insecticideFactor=double

Units: none

See parent element documentation

Deterrency: attacking

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attacking

<attacking
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Deterrency: attacking (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attackingLogit

<attackingLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Pre-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Pre-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffectLogit

<preprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Post-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffectLogit

<postprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Fecundity reduction

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-B), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReductionLogit

<fecundityReductionLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-K0), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Indoor residual spraying

→ scenario → interventions → human → component → IRS

<IRS>
IN THIS ORDER:
| [ <usage ... /> ]
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
| ( <anophelesParams ... /> )+
</IRS>

Documentation (element)

Description of indoor residual spraying interventions.

Documentation (type)

Description of effect for the more complex and probably more realistic Briet model: IRS has three effects, whos strength is calculated as a function of surviving insecticide content.

Proportion of Indoor residual spraying (IRS) interventions

→ scenario → interventions → human → component → IRS → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Indoor residual spraying (IRS) interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → IRS → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: μg/cm² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → human → component → IRS → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → IRS → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → IRS → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied by exp(P×log(p)) where P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction

→ scenario → interventions → human → component → IRS → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

First, we calculate K = B + P×p where B is the base (without protection) probability of death, and P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Fecundity is multiplied by (1−K) / (1−B). It is not allowed to be greater than 1. To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Generic vector intervention

→ scenario → interventions → human → component → GVI

<GVI>
IN THIS ORDER:
| [ <usage ... /> ]
|   <decay ... /> 
| ( <anophelesParams ... /> )+
</GVI>

Documentation (element)

Note that all actions of this intervention component will decay according to a single decay function. If independant decay is wanted, a separate component can be used for each action.

Proportion of generic vector interventions

→ scenario → interventions → human → component → GVI → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Generic vector interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay

→ scenario → interventions → human → component → GVI → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Description of decay of all intervention effects. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → GVI → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <deterrency ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → GVI → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of intervention on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied this factor times survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Fecundity reduction effect

→ scenario → interventions → human → component → GVI → anophelesParams → fecundityReduction

<fecundityReduction
    value=double
  />

Documentation (element)

Min: 0

Fertility is multiplied by 1 - (fecundityReduction * decay).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Recruitment only

→ scenario → interventions → human → component → recruitmentOnly

<recruitmentOnly/>

Documentation (element)

Recruitment of a host into a sub-population.

Clear Immunity

→ scenario → interventions → human → component → clearImmunity

<clearImmunity/>

Documentation (element)

Removes all exposure-related immunitsy gained over time by hosts without removing infections (or affecting the ability to gain immunity through exposure).

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

subPopRemoval

→ scenario → interventions → human → component → subPopRemoval

<subPopRemoval
  [ onFirstBout=boolean ] DEFAULT VALUE false
  [ onFirstTreatment=boolean ] DEFAULT VALUE false
  [ onFirstInfection=boolean ] DEFAULT VALUE false
  [ afterYears=double ]
  />

Documentation (type)

ITN attrition also removes humans from sub-populations.

Attributes

Time to first episode only

onFirstBout=boolean

Default value: false

Time to first treatment only

onFirstTreatment=boolean

Default value: false

Time to first infection only

onFirstInfection=boolean

Default value: false

Remove from sub-population after

afterYears=double

Units: Years Min: 0

Deployment

→ scenario → interventions → human → deployment

<deployment
  [ name=string ]
  >
IN THIS ORDER:
| ( <component ... /> )+
| ( <condition ... /> )*
| ( <continuous ... /> )*
| ( <timed ... /> )*
</deployment>

Documentation (element)

All components deployed by this intervention are deployed to the same people (each timed or continuous deployment selects recipients and then gives each recipient all components of the intervention).

Attributes

Intervention name

name=string

Name of intervention

component

→ scenario → interventions → human → deployment → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Condition

→ scenario → interventions → human → deployment → condition

<condition
    measure=string
  [ minValue=double ]
  [ maxValue=double ]
    initialState=boolean
  />

Documentation (element)

Conditions are evaluated for the whole population, not for individual age-groups or cohorts.

This affects all types of deployment.

Attributes

Measure

measure=string

The monitoring measure to test. Not all measures are available for use.

Minimum value

minValue=double

Minimum value. If specified, the measured variable must be greater than or equal to this value for the condition to be satisfied.

Maximum value

maxValue=double

Maximum value. If specified, the measured variable must be less than or equal to this value for the condition to be satisfied.

Initial state

initialState=boolean

Whether this condition is considered true or false before updated by a survey.

Age-based (continuous) deployment

→ scenario → interventions → human → deployment → continuous

<continuous>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| ( <deploy ... /> )+
</continuous>

Documentation (element)

List of ages at which deployment takes place (through EPI, post-natal and school-based programmes, etc.).

A sub-population restriction may be added as a property of the list of continuous deployments.

restrictToSubPop

→ scenario → interventions → human → deployment → continuous → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

deploy

→ scenario → interventions → human → deployment → continuous → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    targetAgeYrs=double
  [ begin=string ]
  [ end=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention. Input is rounded to the nearest time step.

First time active

begin=string

Units: User defined (defauls to steps)

End step

end=string

Units: User defined (defauls to steps)

Mass (timed) deployment

→ scenario → interventions → human → deployment → timed

<timed>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| [ <cumulativeCoverage ... /> ]
| ( <deploy ... /> )+
</timed>

Documentation (element)

List of timed deployments of the intervention (that is, of deployment campaigns).

Cumulative deployment mode can be specified for all deployments in a timed list. To allow multiple cumulative deployment descriptions, the entire timed list may be repeated.

restrictToSubPop

→ scenario → interventions → human → deployment → timed → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

Cumulative coverage

→ scenario → interventions → human → deployment → timed → cumulativeCoverage

<cumulativeCoverage
    component=string
  />

Documentation (element)

Attributes

Component identifier

component=string

The identifier (short name) of the component used when selecting people.

deploy

→ scenario → interventions → human → deployment → timed → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    time=string
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ repeatStep=string ]
  [ repeatEnd=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Time

time=string

Units: User defined (defauls to steps) Min: 0

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0

Maximum age of eligible individuals (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible individuals (defaults to 0). Input is rounded to the nearest time step.

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Description of health system.

Documentation (type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("forced" or "dynamic")
  [ scaledAnnualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Description of entomological data

Attributes

Entomology dataset name

name=string

Name of entomology data

Transmission model mode

mode=("forced" or "dynamic")

Override annual EIR

scaledAnnualEIR=double

Units: Infectious bites per adult per year

If set, the annual EIR (for all species of vector) is scaled to this level; can be omitted if not needed.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters of the transmission model

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <seasonality ... /> 
|   <mosq ... /> 
| [ <lifeCycle ... /> ]
| [ <simpleMPD ... /> ]
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial estimate of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial estimate of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial estimate of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Seasonality of transmission

→ scenario → entomology → vector → anopheles → seasonality

<seasonality
    input=("EIR")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <fourierSeries ... /> 
| |   <monthlyValues ... /> 
| |   <dailyValues ... /> 
</seasonality>

Documentation (element)

Specifies the seasonality of transmission and optionally the level of annual transmission.

Attributes

Seasonality input

input=("EIR")

Annual EIR

annualEIR=double

Units: Inoculations per adult per annum Min: 0

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries

<fourierSeries
    EIRRotateAngle=double
  >
IN THIS ORDER:
| ( <coeffic ... /> )*
</fourierSeries>

coeffic

Documentation (element)

Units: Infectious bites per adult per day

Attributes

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: Radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Pair of Fourier coefficients

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries → coeffic

<coeffic
    a=double
    b=double
  />

Documentation (element)

A pair of Fourier series coefficients. The first element specifies a1 and b1, the second a2 and b2, etc. Any number (from 0 up) of pairs may be given.

Attributes

a_n parameter of Fourier approximation to ln(EIR)

a=double

a_n parameter of Fourier approximation to ln(EIR) for some natural number n.

b_n parameter of Fourier approximation to ln(EIR)

b=double

b_n parameter of Fourier approximation to ln(EIR) for some natural number n.

List of monthly values

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues

<monthlyValues
    smoothing=("none" or "fourier")
  >
IN THIS ORDER:
| ( <value ... /> ){12,12}
</monthlyValues>

value

Documentation (element)

Description of seasonality from monthly values. Multiple smoothing methods are possible (see smoothing attribute).

List should contain twelve entries: January to December.

Attributes

Smoothing function

smoothing=("none" or "fourier")

How the monthly values are converted into a daily sequence of values:

none: no smoothing (step function)
Fourier: a Fourier series (with terms up to a2/b2) is fit to the sequence of monthly values and used to generate a smoothed list of daily values.

Monthly value

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Monthly value

List of daily values

→ scenario → entomology → vector → anopheles → seasonality → dailyValues

<dailyValues>
IN THIS ORDER:
| ( <value ... /> ){365,365}
</dailyValues>

value

Documentation (element)

Description of seasonality from daily values.

List should contain 365 entries: 1st January to 31st December.

Daily value

→ scenario → entomology → vector → anopheles → seasonality → dailyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Daily value

Mosquito feeding cycle parameters

→ scenario → entomology → vector → anopheles → mosq

<mosq
    minInfectedThreshold=double
  >
IN ANY ORDER:
|   <mosqRestDuration ... /> 
|   <extrinsicIncubationPeriod ... /> 
|   <mosqLaidEggsSameDayProportion ... /> 
|   <mosqSeekingDuration ... /> 
|   <mosqSurvivalFeedingCycleProbability ... /> 
|   <availabilityVariance ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <mosqProbOvipositing ... /> 
|   <mosqHumanBloodIndex ... /> 
</mosq>

Documentation (element)

Parameters describing the feeding cycle and human mosquito interaction of a single species of anopheles mosquito.

Attributes

Mininum infected threshold for mosquitos

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

Duration of the resting period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqRestDuration

<mosqRestDuration
    value=int
  />

Documentation (element)

Units: Days

name:Duration of the resting period of the vector (days);

Attributes

Input parameter value

value=int

An integer value.

Extrinsic incubation period

→ scenario → entomology → vector → anopheles → mosq → extrinsicIncubationPeriod

<extrinsicIncubationPeriod
    value=int
  />

Documentation (element)

Units: Days

name:Extrinsic incubation period (days)

Attributes

Input parameter value

value=int

An integer value.

Proportion of mosquitoes host seeking on same day as ovipositing

→ scenario → entomology → vector → anopheles → mosq → mosqLaidEggsSameDayProportion

<mosqLaidEggsSameDayProportion
    value=double
  />

Documentation (element)

Units: Proportion

Proportion of mosquitoes host seeking on same day as ovipositing

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Duration of the host-seeking period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqSeekingDuration

<mosqSeekingDuration
    value=double
  />

Documentation (element)

Units: Days

Duration of the host-seeking period of the vector (days)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito survives the feeding cycle

→ scenario → entomology → vector → anopheles → mosq → mosqSurvivalFeedingCycleProbability

<mosqSurvivalFeedingCycleProbability
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito survives the feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Variance in human availability rate

→ scenario → entomology → vector → anopheles → mosq → availabilityVariance

<availabilityVariance
    value=double
  />

Documentation (element)

Variance in availability rate of humans to mosquitoes. The mean rate is calculated based on other parameters.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito succesfully bites chosen host

→ scenario → entomology → vector → anopheles → mosq → mosqProbBiting

<mosqProbBiting
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito succesfully bites chosen host

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → mosq → mosqProbFindRestSite

<mosqProbFindRestSite
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito escapes host and finds a resting place after biting

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → mosq → mosqProbResting

<mosqProbResting
    mean=double
    variance=double
  />

Documentation (element)

Probability of mosquito successfully resting after finding a resting site

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of a mosquito successfully laying eggs given that it has rested

→ scenario → entomology → vector → anopheles → mosq → mosqProbOvipositing

<mosqProbOvipositing
    value=double
  />

Documentation (element)

Probability of a mosquito successfully laying eggs given that it has rested

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human blood index

→ scenario → entomology → vector → anopheles → mosq → mosqHumanBloodIndex

<mosqHumanBloodIndex
    value=double
  />

Documentation (element)

Units: Proportion

The proportion of resting mosquitoes which fed on human blood during the last feed.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mosquito life cycle parameters

→ scenario → entomology → vector → anopheles → lifeCycle

<lifeCycle
  [ estimatedLarvalResources=double ] DEFAULT VALUE 1e8
  >
IN ANY ORDER:
|   <eggStage ... /> 
|   <larvalStage ... /> 
|   <pupalStage ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</lifeCycle>

Documentation (element)

Parameters describing the life-cycle of this species of mosquito

Attributes

Estimate of larval resources

estimatedLarvalResources=double

Units: X

Default value: 1e8

Egg stage

→ scenario → entomology → vector → anopheles → lifeCycle → eggStage

<eggStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the egg stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

larvalStage

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage

<larvalStage>
</larvalStage>

daily

Documentation (type)

Parameters for the larval stage of development

Documentation (base type)

Parameters associated with a mosquito development stage.

Daily development

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage → daily

<daily
    resourceUsage=double
    effectCompetition=double
  />

Documentation (element)

Attributes

Resource usage

resourceUsage=double

Units: X

Resource usage during larval stage of development. Units are arbitrary.

Effect of competition

effectCompetition=double

Units: none

Effect of competition over resources on development.

Pupal stage

→ scenario → entomology → vector → anopheles → lifeCycle → pupalStage

<pupalStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the pupal stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → lifeCycle → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Simple Mosq-Pop-Dynamics parameters

→ scenario → entomology → vector → anopheles → simpleMPD

<simpleMPD>
IN ANY ORDER:
|   <developmentDuration ... /> 
|   <developmentSurvival ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</simpleMPD>

Documentation (element)

Parameters describing the simple mosquito population dynamics model.

This is a simpler version of the life-cycle model, requiring less parameters and with much simpler initialisation.

Duration

→ scenario → entomology → vector → anopheles → simpleMPD → developmentDuration

<developmentDuration
    value=int
  />

Documentation (element)

Units: Days Min: 1

Duration from egg laying to emergence in days.

Attributes

Input parameter value

value=int

An integer value.

Probability of survival

→ scenario → entomology → vector → anopheles → simpleMPD → developmentSurvival

<developmentSurvival
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that mosquito survives from the egg being laid to emergence, given no resouce limitations (no density constraints).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → simpleMPD → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Alternative (non-human) host paramters

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN ANY ORDER:
|   <mosqRelativeEntoAvailability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
| [ <hostFecundityFactor ... /> ]
</nonHumanHosts>

Documentation (element)

Min: 0

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of non-human host (ξ_i)

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqRelativeEntoAvailability

<mosqRelativeEntoAvailability
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of the population of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative fecundity of biting mosquitoes

→ scenario → entomology → vector → anopheles → nonHumanHosts → hostFecundityFactor

<hostFecundityFactor
    value=double
  />

Documentation (element)

Units: Proportion

Multiplicative factor for the number of fertile eggs laid by a mosquito after biting this type of host, relative to an unprotected human.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Name of this species of non human hosts (must match up with those described per anopheles section).

Population size of non-human host species

number=double

Units: Animals

Parasite genetics

<parasiteGenetics
    samplingMode=("initial" or "tracking")
  >
IN THIS ORDER:
| ( <locus ... /> )+
</parasiteGenetics>

locus

Documentation (element)

A specification of genotypes of infection parasites.

May be omitted; in this case there is no modelling of genetic differences of infections (resistance, fitness).

Attributes

samplingMode

samplingMode=("initial" or "tracking")

Locus

→ scenario → parasiteGenetics → locus

<locus
    name=string
  >
IN THIS ORDER:
| ( <allele ... /> )+
</locus>

allele

Documentation (element)

Alleles at loci can affect fitness and resistance to any number of drugs.

Attributes

Name of locus

name=string

Name of the Locus

Allele

→ scenario → parasiteGenetics → locus → allele

<allele
    name=string
    initialFrequency=double
    fitness=double
  />

Documentation (element)

Describes an allele, or one possible genetic option of multiple at one point of variance.

Attributes

Name

name=string

Name of the allele; used to refer to it elsewhere.

Initial frequency

initialFrequency=double

Fitness factor

fitness=double

Drug parameters (PK, PD and usage)

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
|   <treatments ... /> 
|   <drugs ... /> 
</pharmacology>

Documentation (element)

Drug model parameters and drug usage parameters

Documentation (type)

A library of drug related data for the PK/PD model.

Treatments library

→ scenario → pharmacology → treatments

<treatments>
IN THIS ORDER:
| ( <schedule ... /> )+
| ( <dosages ... /> )+
</treatments>

Documentation (element)

A library of drug deployment schedules and dosages.

schedule

→ scenario → pharmacology → treatments → schedule

<schedule
    name=string
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

A schedule for the administration of drugs in a course of treatment.

Note that dose sizes are multiplied by some multiplier (see dosages) and the times of all doses may be delayed.

Attributes

Name

name=string

Name for referring to this deployment schedule

medicate

→ scenario → pharmacology → treatments → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  />

Attributes

drug

drug=string

Abbreviated name of drug compound

Drug dose (mg with multiplier)

mg=double

Units: mg per something

Quantity of drug compound in mg per something. A separate dosage table must be used when medicating, which may specify multipliers of this number based on patient age or weight.

Time of administration

hour=double

Units: Hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

dosages

→ scenario → pharmacology → treatments → dosages

<dosages
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | ( <age ... /> )+
| | ( <bodymass ... /> )+
| |   <multiply ... /> 
</dosages>

Documentation (type)

A table for selecting a dose size. There are several ways this can work: using the patient's age or body mass in a look-up table to get a multplier, or directly using body mass as the multiplier.

The doses specified in "mg" in the treatment schedule are then multiplied by this multiplier.

Attributes

Name

name=string

Name for referring to this dosage table

Look-up table (age)

→ scenario → pharmacology → treatments → dosages → age

<age
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's age.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Look-up table (weight)

→ scenario → pharmacology → treatments → dosages → bodymass

<bodymass
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's body mass.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Multiply dose

→ scenario → pharmacology → treatments → dosages → multiply

<multiply
    by=("kg")
  />

Documentation (element)

Multiply the dose by some quantity, such as patient weight.

Attributes

By what?

by=("kg")

Quantity to multiply the dose by. Only option is "kg" (patient weight in kg).

Drug library

→ scenario → pharmacology → drugs

<drugs>
IN THIS ORDER:
| ( <drug ... /> )+
</drugs>

drug

Documentation (element)

A library of drug PK/PD data.

drug

→ scenario → pharmacology → drugs → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (type)

A drug description with PK/PD parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drugs → drug → PD

<PD
  [ locus=string ]
  >
IN THIS ORDER:
| ( <phenotype ... /> )+
</PD>

phenotype

Attributes

Locus

locus=string

PD parameters for some allele / resistance phenotype

→ scenario → pharmacology → drugs → drug → PD → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

Restrict phenotype applicability to certain alleles

→ scenario → pharmacology → drugs → drug → PD → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (element)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Maximal parasite killing rate

→ scenario → pharmacology → drugs → drug → PD → phenotype → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drugs → drug → PD → phenotype → IC50

<IC50
  [ sigma=double ] DEFAULT VALUE 0
  >
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration. If sigma > 0, the IC50 is sampled for each infection from a log-normal distribution with mean of this value and the sigma value specified, i.e. X ~ log N( log(mean) - s^2 / 2, s^2 ) .

Attributes

Sigma parameter for per-infection variation of IC50

sigma=double

Default value: 0

Distribution parameter describing per-infection variation of IC50. If zero or not specified, the IC50 is not sampled. See documentation of parent element.

Slope of effect curve

→ scenario → pharmacology → drugs → drug → PD → phenotype → slope

<slope>
    double
</slope>

Documentation (element)

Units: dimensionless

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drugs → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
| EXACTLY ONE OF:
| |   <half_life ... /> 
| | IN THIS ORDER:
| | |   <k ... /> 
| | |   <m_exponent ... /> 
| [ <k_a ... /> ]
| [ <conversion ... /> ]
|   <vol_dist ... /> 
| [ <compartment2 ... /> ]
| [ <compartment3 ... /> ]
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drugs → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drugs → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate λ, calculated as λ = ln(2) / half_life. The basic form of decay is C(t) = C0 * exp(-λ*t).

Alternatively, elimination rate can be specified via k and m_exponent.

Constant associated with elimination rate (k)

→ scenario → pharmacology → drugs → drug → PK → k

<k
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

If sigma > 0, k is sampled per-human from the log-normal distribution: ln N( ln(mean) - σ^2 / 2, σ^2).

Alternatively, elimination rate can be specified via half_life.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Constant associated with elimination rate (m_exponent)

→ scenario → pharmacology → drugs → drug → PK → m_exponent

<m_exponent>
    double
</m_exponent>

Documentation (element)

Units: day^-1 Min: 0

Alternatively, elimination rate can be specified via half_life.

Note that in the case of a conversion model, this applies to both the elimination and the conversion rates.

Absorption rate constant (k_a)

→ scenario → pharmacology → drugs → drug → PK → k_a

<k_a
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Min: 0

Absorption rate parameter. Not allowed for one compartment models, but required for two and three compartment models and one compartment with conversion model (for the parent drug only).

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Conversion parameters (parent drug)

→ scenario → pharmacology → drugs → drug → PK → conversion

<conversion>
IN ANY ORDER:
|   <metabolite ... /> 
|   <rate ... /> 
|   <molRatio ... /> 
</conversion>

Documentation (element)

Configures the parent drug in a conversion model.

To use a conversion model, the parent drug should have this section defined as well as half-life or k (direct elimination; this may be zero) and k_a (absorption rate; this may be large).

Metabolite drug (abbreviation)

→ scenario → pharmacology → drugs → drug → PK → conversion → metabolite

<metabolite>
    string
</metabolite>

Documentation (element)

The abbreviation of the metabolite drug (e.g. "DHA" or "DHA_AR").

Rate of conversion

→ scenario → pharmacology → drugs → drug → PK → conversion → rate

<rate
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Rate of conversion of parent drug to metabolite.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Molecular weight ratio

→ scenario → pharmacology → drugs → drug → PK → conversion → molRatio

<molRatio>
    double
</molRatio>

Documentation (element)

Ratio of molecular weights: molecular weight of the metabolite divided by molecular weight of the parent.

Volume of Distribution (Vd)

→ scenario → pharmacology → drugs → drug → PK → vol_dist

<vol_dist
  [ sigma=double ] DEFAULT VALUE 0
  >
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Attributes

Sigma parameter for per-human variation of Vd

sigma=double

Default value: 0

Distribution parameter describing per-human variation of volume of distribution. If zero or not specified, the parameter is not sampled. See documentation of parent element.

Second compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment2

<compartment2>
IN ANY ORDER:
|   <a12 ... /> 
|   <a21 ... /> 
</compartment2>

Documentation (element)

Optional element specifying conversion parameters to- and from- a second compartment.

Absorption rate to compartment 2 (a12)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → a12

<a12
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the first periphery compartment (2). The parameter k12 = a12 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Absorption rate from compartment 2 (a21)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → a21

<a21
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the first periphery compartment (2) to the central compartment. The parameter k21 = a21 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Third compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment3

<compartment3>
IN ANY ORDER:
|   <a13 ... /> 
|   <a31 ... /> 
</compartment3>

Documentation (element)

Optional element specifying conversion parameters to- and from- a third compartment.

Absorption rate to compartment 3 (a13)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → a13

<a13
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the second periphery compartment (3). The parameter k13 = a13 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Absorption rate from compartment 3 (a31)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → a31

<a31
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the second periphery compartment (3) to the central compartment. The parameter k31 = a31 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Diagnostic parameters

→ scenario → diagnostics

<diagnostics>
IN THIS ORDER:
| ( <diagnostic ... /> )*
</diagnostics>

diagnostic

Documentation (element)

Diagnostic model parameters

diagnostic

→ scenario → diagnostics → diagnostic

<diagnostic
    name=string
  [ units=("Other" or "Garki" or "Malariatherapy") ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterministic ... /> 
| |   <stochastic ... /> 
</diagnostic>

Attributes

Name of diagnostic

name=string

Name of this diagnostic (parameterisation). May be used elsewhere in the XML document to refer to this set of diagnostic parameters.

Parasite density units / methodology

units=("Other" or "Garki" or "Malariatherapy")

Deterministic detection

→ scenario → diagnostics → diagnostic → deterministic

<deterministic
    minDensity=double
  />

Documentation (element)

Specify that an artificial deterministic test is used: outcome is positive if parasite density is at least the minimum given.

Attributes

Minimum detectible density

minDensity=double

Units: parasites/microlitre Min: 0

The minimum density at which parasites can be detected. If 0, the test outcome is always positive.

Non-deterministic detection

→ scenario → diagnostics → diagnostic → stochastic

<stochastic
    dens_50=double
    specificity=double
  />

Documentation (element)

An improved model of detection which is non-deterministic, including false positive results as well as false negatives.

Some parameterisations:

Microscopy sensitivity/specificity data in Africa; Source: expert opinion — Allan Schapira dens_50 = 20.0 specificity = .75

RDT sensitivity/specificity for Plasmodium falciparum in Africa Source: Murray et al (Clinical Microbiological Reviews, Jan. 2008) dens_50 = 50.0; specificity = .942;

Attributes

Density 50

dens_50=double

Units: parasites/microlitre Min: 0

The density at which the test outcome has a 50% chance of being positive.

Specificity

specificity=double

Units: Dimensionless Min: 0 Max: 1

The probability of a positive test outcome in the absense of parasites.

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
| [ <vivax ... /> ]
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: model/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=string
  >
IN ANY ORDER:
| [ <NeonatalMortality ... /> ]
| [ <NonMalariaFevers ... /> ]
</clinical>

Documentation (type)

Attributes

Follow-up period during which recurrence is considered a treatment failure

healthSystemMemory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

Neonatal mortality parameters

→ scenario → model → clinical → NeonatalMortality

<NeonatalMortality
    diagnostic=string
  />

Attributes

Diagnostic used to parameterise model

diagnostic=string

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
| [ <prNeedTreatmentNMF ... /> ]
| [ <prNeedTreatmentMF ... /> ]
</NonMalariaFevers>

Documentation (type)

Description of the incidence of non-malaria fever. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a non-malarial fever requires treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

Availability of humans to mosquitoes relative to an adult, categorized by age group

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ]
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

Vivax model parameters

→ scenario → model → vivax

<vivax>
IN ANY ORDER:
|   <probBloodStageInfectiousToMosq ... /> 
|   <hypnozoiteRelease ... /> 
|   <bloodStageProtectionLatency ... /> 
|   <bloodStageLengthDays ... /> 
|   <clinicalEvents ... /> 
</vivax>

Documentation (element)

This describes Vivax model parameters, and is required when using the VIVAX_SIMPLE_MODEL model option.

Probability of mosquito infection

→ scenario → model → vivax → probBloodStageInfectiousToMosq

<probBloodStageInfectiousToMosq
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

The chance of a feeding mosquito becoming infected, given that the host is patent. (This may be adjusted by transmission-blocking vaccines.)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Hypnozoite releases

→ scenario → model → vivax → hypnozoiteRelease

<hypnozoiteRelease
  [ pSecondRelease=double ] DEFAULT VALUE 0
  >
IN ANY ORDER:
|   <numberHypnozoites ... /> 
|   <firstRelease ... /> 
| [ <secondRelease ... /> ]
</hypnozoiteRelease>

Documentation (element)

Describes the number and times of hypnozoite releases.

Documentation (type)

This element defines probabilites when and how many hypnozoites are released from the liverstage into the blood.

The gap between the start of a new brood of hypnozoites and its release are defined as follows:

latentP + latentRelapseDays + randomReleaseDelay

randomReleaseDelay is based on one or two lognormal distributions, which are defined in firstRelease and optionally secondRelease.

You can define 2 release distributions, which get added together and represent the probability of hypnozoites which get released before winter (first release) or after (second release).

You can omit the secondRelease element if no release to the blood happens after winter.

Attributes

latent relapse days

pSecondRelease=double

Default value: 0

Probability of a second release. If undefined it is zero.

Number of Hypnozoites

→ scenario → model → vivax → hypnozoiteRelease → numberHypnozoites

<numberHypnozoites
    max=int
    base=double
  />

Documentation (element)

numberHypnozoites calculates the number of hypnozoites in the liver stage based on a base which is between 0 and 1.

This number is random based on the following distribution and normalized:

max ∑ (base ^ n) n = 0

Attributes

max

max=int

base

base=double

firstRelease

→ scenario → model → vivax → hypnozoiteRelease → firstRelease

<firstRelease
    mu=double
    sigma=double
    latentRelapseDays=int
  />

Documentation (base type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

latent relapse days

latentRelapseDays=int

Usually 15 days or 10 days (3 or 2 5-day timesteps).

secondRelease

→ scenario → model → vivax → hypnozoiteRelease → secondRelease

<secondRelease
    mu=double
    sigma=double
    latentRelapseDays=int
  />

Documentation (base type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

latent relapse days

latentRelapseDays=int

Usually 15 days or 10 days (3 or 2 5-day timesteps).

Blood stage protection latency

→ scenario → model → vivax → bloodStageProtectionLatency

<bloodStageProtectionLatency
    value=double
  />

Documentation (element)

Min: 0

The length of time after expiry of a blood-stage infection during which relapses from the same brood are supressed by the immune system.

This is rounded to the nearest time-step.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Blood stage length

→ scenario → model → vivax → bloodStageLengthDays

<bloodStageLengthDays
    weibullScale=double
    weibullShape=double
  />

Documentation (element)

Units: Days

Parameters used to sample the length of blood-stage infections from a Weibull distribution (scale parameter lambda, shape parameter k).

Attributes

weibullScale

weibullScale=double

weibullShape

weibullShape=double

clinicalEvents

→ scenario → model → vivax → clinicalEvents

<clinicalEvents>
IN THIS ORDER:
|   <pPrimaryInfection ... /> 
|   <pRelapseOne ... /> 
|   <pRelapseTwoPlus ... /> 
|   <pEventIsSevere ... /> 
</clinicalEvents>

Documentation (type)

This elements holds all information about probabilites for clinical events from infections and relapses.

pPrimaryInfection

→ scenario → model → vivax → clinicalEvents → pPrimaryInfection

<pPrimaryInfection
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseOne

→ scenario → model → vivax → clinicalEvents → pRelapseOne

<pRelapseOne
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseTwoPlus

→ scenario → model → vivax → clinicalEvents → pRelapseTwoPlus

<pRelapseTwoPlus
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pEventIsSevere

→ scenario → model → vivax → clinicalEvents → pEventIsSevere

<pEventIsSevere
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=string
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=string

Units: User defined (default: steps) Min: 0 Max: 20

Pre-erythrocytic latent period Can be specified in steps (e.g. 3t) or days (e.g. 15d).

parameter

→ scenario → model → parameters → parameter

<parameter
  [ name=string ]
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 38 documentation

Generated from: scenario_38.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
  [ analysisNo=int ]
    name=string
  [ wuID=int ]
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:om="http://openmalaria.org/schema/scenario_38"
    xsi:schemaLocation="http://openmalaria.org/schema/scenario_38 scenario_38.xsd"
  >
IN ANY ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entomology ... /> 
| [ <parasiteGenetics ... /> ]
| [ <pharmacology ... /> ]
| [ <diagnostics ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Name of intervention

Work unit identifier

wuID=int

Units: Number

Work unit ID. Obselete and no longer required.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Description of demography

Attributes

Name of demography data

name=string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Years Min: 0 Max: 100

Maximum age of simulated humans in years

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

list of age groups included in demography

Documentation (type)

list of age groups included in demography or surveys

Attributes

Lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Units: Percentage Min: 0 Max: 100

Percentage of human population in age group

Upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ startDate=string ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
| [ <cohorts ... /> ]
</monitoring>

Documentation (element)

Description of surveys

Attributes

Name of monitoring settings

name=string

Name of monitoring settings

Start of monitoring

startDate=string

continuous

→ scenario → monitoring → continuous

<continuous
    period=string
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Delay between reports

period=string

Units: User defined (default: steps)

Delay between reports; typically one time step but can be greater. Can be specified in steps (e.g. 1t) or days (e.g. 5d).

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions
  [ onlyNewEpisode=boolean ] DEFAULT VALUE false
  >
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See model/mon/OutputMeasures.h for a list of supported outputs. Should also be on the wiki.

Attributes

Report only for new cases

onlyNewEpisode=boolean

Default value: false

option

→ scenario → monitoring → SurveyOptions → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  [ outputNumber=int ]
  [ byAge=boolean ]
  [ byCohort=boolean ]
  [ bySpecies=boolean ]
  [ byGenotype=boolean ]
  [ byDrugType=boolean ]
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Number identifying measure in output

outputNumber=int

Report by age category

byAge=boolean

Report by cohort

byCohort=boolean

Report by mosquito species

bySpecies=boolean

Report by parasite genotype

byGenotype=boolean

Report by drug type

byDrugType=boolean

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
  [ detectionLimit=double ]
  [ diagnostic=string ]
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/microlitre Min: 0

Deprecated: limit above which a human's infection is reported as patent. Alternative: do not specify this; instead specify "diagnostic".

Name of monitoring diagnostic

diagnostic=string

Name of a parameterised diagnostic to use in surveys (see scenario/diagnostics).

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime
  [ repeatStep=string ]
  [ repeatEnd=string ]
  [ reported=boolean ] DEFAULT VALUE true
  >
    string
</surveyTime>

Documentation (element)

Units: User defined (defaults to steps) Min: 0

The simulation ends immediately after the last survey is taken.

Attributes

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

reported

reported=boolean

Default value: true

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Cohorts

→ scenario → monitoring → cohorts

<cohorts>
IN THIS ORDER:
| ( <subPop ... /> )+
</cohorts>

subPop

Documentation (element)

Allows the configuration of multiple cohorts (output segregated according to membership within specific sub-populations).

If this element is omitted, monitoring surveys cover the entire simulated human population.

It does not affect the "continuous" outputs (these never take cohorts into account).

Sub-population

→ scenario → monitoring → cohorts → subPop

<subPop
    id=string
    number=integer
  />

Documentation (element)

In the output file, the output set is identified by multiplying this number by 1000 then adding it to the age group column.

Attributes

Sub-population identifier

id=string

Textual identifier for the sub-population (i.e. for an intervention component, since sub-populations are defined as the hosts an intervention component is deployed to).

Sub-population number

number=integer

Units: dimensionless Min: 1 Max: 2097152

Number identifying a sub-population; used to define identifiers of output sets. This number must be a power of 2 (i.e. 1, 2, 4, 8, ...). See documentation of subPop element.

Preventative interventions

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfections ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <vectorPop ... /> ]
| [ <vectorTrap ... /> ]
| [ <human ... /> ]
</interventions>

Documentation (element)

Attributes

Name of intervention set

name=string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeHS>

timedDeployment

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeHS → timedDeployment

<timedDeployment
    time=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timedDeployment>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</uncomplicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

multiple

→ scenario → interventions → human → component → decisionTree → multiple

<multiple
  [ name=string ]
  >
IN THIS ORDER:
| ( <caseType ... /> )*
| ( <diagnostic ... /> )*
| ( <random ... /> )*
| ( <age ... /> )*
| ( <treatPKPD ... /> )*
| [ <treatSimple ... /> ]
| ( <deploy ... /> )*
</multiple>

Documentation (type)

A special node allowing multiple sub-trees to be evaluated.

This is different from an ordinary decision tree node in that:

a) multiple types of child can occur simultaneously (e.g. multiple types of treatment or treatment plus a 'random' sub-tree)

b) the 'noTreatment' and 'treatFailure' nodes are not allowed

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → multiple → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

firstLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → firstLine

<firstLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</firstLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

secondLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → secondLine

<secondLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</secondLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

positive

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

outcome

→ scenario → interventions → human → component → decisionTree → multiple → random → outcome

<outcome
  [ name=string ]
    p=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</outcome>

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Probability

p=double

Units: None Min: 0 Max: 1

Probability of selecting this outcome. The sum of probabilities across all outcomes must be 1.

age

→ scenario → interventions → human → component → decisionTree → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Age range

→ scenario → interventions → human → component → decisionTree → multiple → age → age

<age
  [ name=string ]
    lb=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</age>

Documentation (element)

Describes a branch, selected for patients of a certain age.

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Lower bound (inclusive)

lb=double

Min: 0

noTreatment

→ scenario → interventions → human → component → decisionTree → noTreatment

<noTreatment
  [ name=string ]
  />

Documentation (type)

An end node doing nothing. This exists to explicitly state that no treatment happens and to prevent trees from accidentally being left incomplete.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatFailure

→ scenario → interventions → human → component → decisionTree → treatFailure

<treatFailure
  [ name=string ]
  />

Documentation (type)

An end node which reports treatment but does not change parasitalogical status. This allows correct labelling of second-line cases.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → multiple → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

age

→ scenario → interventions → human → component → decisionTree → multiple → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → multiple → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → multiple → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → multiple → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</complicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: Days Min: 0 Max: unbounded

Maximum number of timesteps (including first day of case) that an individual with an uncomplicated case of malaria will remember he/she was sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial or non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of a complicated or severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
  [ name=string ]
  [ useDiagnosticUC=boolean ] DEFAULT VALUE false
  >
IN ANY ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <treatmentActions ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
</ImmediateOutcomes>

Documentation (type)

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Name of case management parameterisation

name=string

Name of health system

useDiagnosticUC

useDiagnosticUC=boolean

Default value: false

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Description of drug regimen.

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Artemisinine based combination therapy

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Quinine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0 Max: 1name:P(self-treat)

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Effectiveness of treatment for non-compliant patients

treatmentActions

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions

<treatmentActions>
IN ANY ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
</treatmentActions>

CQ
SP
AQ
SPAQ
ACT
QN

CQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ

<CQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</CQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

deploy

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy

<deploy
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ p=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| ( <component ... /> )+
</deploy>

component

Attributes

Maximum age of eligible humans

maxAge=double

Units: Years Min: 0

Maximum age of eligible humans (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible humans

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible humans (defaults to 0). Input is rounded to the nearest time step.

Probability of delivery to eligible humans

p=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Probability of this list of components being deployed, given that other constraints are met.

component

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Prophylactic treatment

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere → clearInfections

<clearInfections
    timesteps=string
    stage=("liver" or "blood" or "both")
  />

Documentation (element)

Attributes

Length of effect

timesteps=string

Units: User defined (defaults to steps)

Target stage

stage=("liver" or "blood" or "both")

SP

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SP

<SP
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SP>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

AQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → AQ

<AQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</AQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

SPAQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SPAQ

<SPAQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SPAQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

ACT

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → ACT

<ACT
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</ACT>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

QN

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → QN

<QN
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</QN>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

Probability that human is incompatible with liver-stage drug treatment

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pHumanCannotReceive

<pHumanCannotReceive
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that a human is determined to be unable to receive liver-stage drug treatment. Treatment is neither reported or given for such humans.

This is sampled once per human at birth.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Ignore liver-stage drug treatment incompatibility

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → ignoreCannotReceive

<ignoreCannotReceive
    value=boolean
  />

Documentation (element)

If true, ignore pHumanCannotReceive and consider all humans eligible for treatment; if false (or not specified), do not treat those demed incompatible with liver-stage drug treatment.

The point of this is that pHumanCannotReceive cannot be altered by changeHS interventions, but this property can be.

Attributes

Input parameter value

value=boolean

A boolean value.

Prob use in UC case

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pUseUncomplicated

<pUseUncomplicated
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

This feature is deprecated; it is suggested to use the "simple treatment" feature configured to clear liver-stage parasites, leaving this option unset or zero.

Chance of liver-stage drug treatment being used for routine treatment of an uncomplicated case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Effectiveness

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → effectivenessOnUse

<effectivenessOnUse
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that liver-stage drug treatment is effective.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

DecisionTree5Day

<DecisionTree5Day
  [ name=string ]
  >
IN ANY ORDER:
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
|   <treeUCOfficial ... /> 
|   <treeUCSelfTreat ... /> 
|   <cureRateSevere ... /> 
|   <treatmentSevere ... /> 
</DecisionTree5Day>

Documentation (type)

Besides greater flexibility, this allows treatment via PK/PD models.

Attributes

Name of case management parameterisation

name=string

Name of health system

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → DecisionTree5Day → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → DecisionTree5Day → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

treeUCOfficial

→ scenario → healthSystem → DecisionTree5Day → treeUCOfficial

<treeUCOfficial
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCOfficial>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treeUCSelfTreat

→ scenario → healthSystem → DecisionTree5Day → treeUCSelfTreat

<treeUCSelfTreat
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCSelfTreat>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Cure rate (severe cases)

→ scenario → healthSystem → DecisionTree5Day → cureRateSevere

<cureRateSevere
    value=double
  />

Documentation (element)

Min: 0 Max: 1

The probability of clearing parasites given access to appropriate (hospital) care, for a severe case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

treatmentSevere

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere

<treatmentSevere
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</treatmentSevere>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Case fatality rate for inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: Dimensionless

List of age-specific probabilities of sequelae in inpatients, during a severe bout of malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeEIR>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeEIR → timedDeployment

<timedDeployment
    eipDuration=int
    time=string
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timedDeployment>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Time

time=string

Units: User defined (defauls to steps) Min: 0

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=string ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=string

Units: User defined (default: steps) Min: 0

Default value: 0

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=string
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time of start

time=string

Units: User defined (defauls to steps) Min: 0

Insert R_0 case

<insertR_0Case
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</insertR_0Case>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → insertR_0Case → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Uninfect vectors

<uninfectVectors
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</uninfectVectors>

timedDeployment

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → uninfectVectors → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Vector population intervention

→ scenario → interventions → vectorPop

<vectorPop>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorPop>

intervention

Documentation (element)

Units: List of elements

A list of parameterisations of generic vector host-inspecific interventions.

intervention

→ scenario → interventions → vectorPop → intervention

<intervention
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

Units: List of elements

An intervention which may have various effects on the vector populations as a whole. (Not host specific.)

Multiple instances of this intervention class are allowed (multiple parameterisations, not just deployments).

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → vectorPop → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → vectorPop → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <seekingDeathRateIncrease ... /> ]
| [ <probDeathOvipositing ... /> ]
| [ <emergenceReduction ... /> ]
</anopheles>

Documentation (type)

Units: dimensionless Min: 0 Max: 1

Descriptions of the effects of vector interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Proportional increase in deaths while host searching

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease

<seekingDeathRateIncrease
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</seekingDeathRateIncrease>

decay

Documentation (element)

Units: dimensionless

Describe an effect on the increase in the death rate while host seeking (mu_vA) due to this intervention.

Enter the rate increase (i.e. if rate increases to 120% of normal, give 0.2). New death rate while seeking is old × (1 + increase) where increase is this factor given. Must have increas ≥ -1.

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Proportion ovipositing mosquitoes killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing

<probDeathOvipositing
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probDeathOvipositing>

decay

Documentation (element)

Units: dimensionless

Describe an effect of increased mortality while ovipositing due to this intervention. Enter the probability of dying due to this intervention.

Attributes

Initial probability of killing

initial=double

Units: dimensionless Min: 0 Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Proportion of emerging pupa killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction

<emergenceReduction
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</emergenceReduction>

decay

Documentation (element)

Units: dimensionless

Describe an effect on emergence of pupa into adults: this value is the proportion of emerging pupa which are killed by this intervention.

Attributes

Initial proportion reduction

initial=double

Units: dimensionless Min: -inf Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Vector population intervention deployment

→ scenario → interventions → vectorPop → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

deploy

→ scenario → interventions → vectorPop → intervention → timed → deploy

<deploy
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Baited trap

→ scenario → interventions → vectorTrap

<vectorTrap>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorTrap>

intervention

Documentation (element)

intervention

→ scenario → interventions → vectorTrap → intervention

<intervention
  [ name=string ]
  >
IN THIS ORDER:
| ( <description ... /> )+
| [ <timed ... /> ]
</intervention>

Documentation (type)

Attributes

Descriptive name for type of trap

name=string

Optional name for this type of trap

Description

→ scenario → interventions → vectorTrap → intervention → description

<description
    mosquito=string
  >
IN THIS ORDER:
|   <relativeAvailability ... /> 
|   <decayOfAvailability ... /> 
</description>

Documentation (element)

Parameters associated with a vector trap intervention, per mosquito species.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Initial relative availability

→ scenario → interventions → vectorTrap → intervention → description → relativeAvailability

<relativeAvailability
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: inf

Describes the availiability of a trap to a host-seeking mosquito relative to an average unprotected adult.

I.e. if this parameter is 2, then each trap will on average attract twice as many mosquitoes as unprotected adults.

This is the initial availability; it may decay towards zero depending on the configured decay function.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay of availability

→ scenario → interventions → vectorTrap → intervention → description → decayOfAvailability

<decayOfAvailability
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Describes how availability decays to zero.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Vector trap intervention deployment

→ scenario → interventions → vectorTrap → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )*
</timed>

deploy

Documentation (element)

List of timed vector trap intervention deployment

deploy

→ scenario → interventions → vectorTrap → intervention → timed → deploy

<deploy
    time=string
    ratioToHumans=double
    lifespan=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Ratio to humans

ratioToHumans=double

Min: 0 Max: inf

The number of traps deployed, by this deployment, per adult human. E.g. if there are currently 100 traps and 1000 humans, then a ratio of 0.1 will increase the number of traps to 200.

Lifespan

lifespan=string

Units: Steps or Days or Years

Human-specific interventions

→ scenario → interventions → human

<human>
IN THIS ORDER:
| ( <component ... /> )+
| ( <deployment ... /> )*
</human>

Documentation (element)

Encapsulates all interventions whose effects are specific to the human host: any interventions where target humans may be selected via population-coverage, age limits and sub-population membership.

Component

→ scenario → interventions → human → component

<component
    id=string
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <screen ... /> 
| |   <treatSimple ... /> 
| |   <treatPKPD ... /> 
| |   <decisionTree ... /> 
| |   <PEV ... /> 
| |   <BSV ... /> 
| |   <TBV ... /> 
| |   <ITN ... /> 
| |   <IRS ... /> 
| |   <GVI ... /> 
| | [ <recruitmentOnly ... /> ]
| |   <clearImmunity ... /> 
| [ <subPopRemoval ... /> ]
</component>

Documentation (element)

Each element describes one component: its effects, decay of the(se) effect(s), and related stuff (e.g. description of indirect decay and of usage levels).

Attributes

Component identifier

id=string

Name of component

name=string

An informal name/description for the component

screen

→ scenario → interventions → human → component → screen

<screen
    diagnostic=string
  >
IN THIS ORDER:
| ( <positive ... /> )*
| ( <negative ... /> )*
</screen>

Documentation (type)

This can be combined with MDA to achieve mass screen and treat (MSAT) or other types of mass screening intervention.

The use of the screening itself is reported (if enabled), but not the outcome. Deployment of interventions triggered by the screening may be reported, however.

Attributes

Name of diagnostic

diagnostic=string

Name of a parameterised diagnostic (see scenario/diagnostics).

positive

→ scenario → interventions → human → component → screen → positive

<positive
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → screen → negative

<negative
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

treatSimple

→ scenario → interventions → human → component → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

treatPKPD

→ scenario → interventions → human → component → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

decisionTree

→ scenario → interventions → human → component → decisionTree

<decisionTree
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</decisionTree>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Vaccines

→ scenario → interventions → human → component → PEV

<PEV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</PEV>

Documentation (element)

Pre-erythrocytic vaccine (PEV): prevents a proportion of infections from commencing.

Documentation (type)

Description of a vaccine's effect

Decay of effect

→ scenario → interventions → human → component → PEV → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Specification of decay of efficacy. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Variance parameter for vaccine efficacy

→ scenario → interventions → human → component → PEV → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vaccines

→ scenario → interventions → human → component → BSV

<BSV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</BSV>

Documentation (element)

Blood-stage vaccine (BSV): acts as a killing factor on blood-stage parasites. Exact action depends on the within host model.

Documentation (type)

Description of a vaccine's effect

Vaccines

→ scenario → interventions → human → component → TBV

<TBV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</TBV>

Documentation (element)

Transmission-blocking vaccine (TBV): one minus this scales the probability of transmission to mosquitoes

Documentation (type)

Description of a vaccine's effect

Bed nets

→ scenario → interventions → human → component → ITN

<ITN>
IN THIS ORDER:
| [ <usage ... /> ]
|   <holeRate ... /> 
|   <ripRate ... /> 
|   <ripFactor ... /> 
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
|   <attritionOfNets ... /> 
| ( <anophelesParams ... /> )+
</ITN>

Documentation (element)

Description of bed-net interventions (ITNs, LLINs).

Proportion of time nets are used by humans

→ scenario → interventions → human → component → ITN → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of nets by humans, from 0 to 1.

At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing.

See also "propActing" (proportion of bits for which net acts).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Rate at which holes are made

→ scenario → interventions → human → component → ITN → holeRate

<holeRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Holes per annum Min: 0

The rate at which new holes are made in nets.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ ln N( log(mean)-sigma²/2, sigma² ).

Equivalent R sample: rlnorm(n, log(m) - s*s/2, s)

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rate at which holes are enlarged

→ scenario → interventions → human → component → ITN → ripRate

<ripRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Rips per existing hole per annum Min: 0

Each existing hole has a probability of being ripped bigger according to a Poisson process with this rate as (only) parameter.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ ln N( log(mean)-sigma²/2, sigma² ).

Equivalent R sample: rlnorm(n, log(m) - s*s/2, s)

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rip factor

→ scenario → interventions → human → component → ITN → ripFactor

<ripFactor
    value=double
  />

Documentation (element)

Units: none Min: 0

This factor expresses how important rips are in increasing the hole.

The hole index of a net is h + F×x where h and x are the total numbers of holes and rips respectively and F is the rip factor.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → ITN → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: mg/m² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → human → component → ITN → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of nets. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Attrition of nets

→ scenario → interventions → human → component → ITN → attritionOfNets

<attritionOfNets
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: dimensionless

Specifies the rate at which nets are disposed of over time. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Humans are removed from the intervention component's sub-population on disposal (attrition) of their nets. Currently this event is not reported.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → human → component → ITN → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <holeIndexMax ... /> ]
| EXACTLY ONE OF:
| |   <deterrency ... /> 
| |   <twoStageDeterrency ... /> 
| EXACTLY ONE OF:
| |   <preprandialKillingEffect ... /> 
| |   <preprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| |   <postprandialKillingEffect ... /> 
| |   <postprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| | [ <fecundityReduction ... /> ]
| | [ <fecundityReductionLogit ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which net acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

maximum of holed surface area that has an effect (comparable to no net)

→ scenario → interventions → human → component → ITN → anophelesParams → holeIndexMax

<holeIndexMax
    value=double
  />

Documentation (element)

Units: in same unit as holeIndex

Used by logit attacking and killing models only, holeIndexMax is a user defined maximum hole index (typically, the total surface area of a net).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency

<twoStageDeterrency>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <entering ... /> 
| |   <enteringLogit ... /> 
| EXACTLY ONE OF:
| |   <attacking ... /> 
| |   <attackingLogit ... /> 
</twoStageDeterrency>

Documentation (element)

Units: dimensionless

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

This deterrency model multiplies human attractiveness by pEnt×pAtt.

Deterrency: entering

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → entering

<entering
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless

pEnt represents the relative probability of entering due to ITNs: pEnt = exp(log(P)×p) where P is the insecticide factor and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Deterrency: entering (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → enteringLogit

<enteringLogit
    baseFactor=double
    insecticideFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: none

See parent element documentation

Insecticide factor

insecticideFactor=double

Units: none

See parent element documentation

Deterrency: attacking

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attacking

<attacking
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Deterrency: attacking (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attackingLogit

<attackingLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Pre-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Pre-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffectLogit

<preprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Post-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffectLogit

<postprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Fecundity reduction

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-B), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction (logit)

→ scenario → interventions → human → component → ITN → anophelesParams → fecundityReductionLogit

<fecundityReductionLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Effect of net on fertility of mosquitoes who survive feeding on a protected human, relative to an unprotected human.

Fertility (number of eggs laid) is multiplied by (1-K) / (1-K0), similar to killing effects. This is not allowed to be greater than 1.

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Indoor residual spraying

→ scenario → interventions → human → component → IRS

<IRS>
IN THIS ORDER:
| [ <usage ... /> ]
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
| ( <anophelesParams ... /> )+
</IRS>

Documentation (element)

Description of indoor residual spraying interventions.

Documentation (type)

Description of effect for the more complex and probably more realistic Briet model: IRS has three effects, whos strength is calculated as a function of surviving insecticide content.

Proportion of Indoor residual spraying (IRS) interventions

→ scenario → interventions → human → component → IRS → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Indoor residual spraying (IRS) interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → IRS → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: μg/cm² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → human → component → IRS → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → IRS → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → IRS → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied by exp(P×log(p)) where P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Fecundity reduction

→ scenario → interventions → human → component → IRS → anophelesParams → fecundityReduction

<fecundityReduction
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

First, we calculate K = B + P×p where B is the base (without protection) probability of death, and P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Fecundity is multiplied by (1−K) / (1−B). It is not allowed to be greater than 1. To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Generic vector intervention

→ scenario → interventions → human → component → GVI

<GVI>
IN THIS ORDER:
| [ <usage ... /> ]
|   <decay ... /> 
| ( <anophelesParams ... /> )+
</GVI>

Documentation (element)

Note that all actions of this intervention component will decay according to a single decay function. If independant decay is wanted, a separate component can be used for each action.

Proportion of generic vector interventions

→ scenario → interventions → human → component → GVI → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Generic vector interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay

→ scenario → interventions → human → component → GVI → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Description of decay of all intervention effects. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → GVI → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <deterrency ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
| [ <fecundityReduction ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → GVI → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of intervention on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied this factor times survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Fecundity reduction effect

→ scenario → interventions → human → component → GVI → anophelesParams → fecundityReduction

<fecundityReduction
    value=double
  />

Documentation (element)

Min: 0

Fertility is multiplied by 1 - (fecundityReduction * decay).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Recruitment only

→ scenario → interventions → human → component → recruitmentOnly

<recruitmentOnly/>

Documentation (element)

Recruitment of a host into a sub-population.

Clear Immunity

→ scenario → interventions → human → component → clearImmunity

<clearImmunity/>

Documentation (element)

Removes all exposure-related immunitsy gained over time by hosts without removing infections (or affecting the ability to gain immunity through exposure).

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

subPopRemoval

→ scenario → interventions → human → component → subPopRemoval

<subPopRemoval
  [ onFirstBout=boolean ] DEFAULT VALUE false
  [ onFirstTreatment=boolean ] DEFAULT VALUE false
  [ onFirstInfection=boolean ] DEFAULT VALUE false
  [ afterYears=double ]
  />

Documentation (type)

ITN attrition also removes humans from sub-populations.

Attributes

Time to first episode only

onFirstBout=boolean

Default value: false

Time to first treatment only

onFirstTreatment=boolean

Default value: false

Time to first infection only

onFirstInfection=boolean

Default value: false

Remove from sub-population after

afterYears=double

Units: Years Min: 0

Deployment

→ scenario → interventions → human → deployment

<deployment
  [ name=string ]
  >
IN THIS ORDER:
| ( <component ... /> )+
| ( <condition ... /> )*
| ( <continuous ... /> )*
| ( <timed ... /> )*
</deployment>

Documentation (element)

All components deployed by this intervention are deployed to the same people (each timed or continuous deployment selects recipients and then gives each recipient all components of the intervention).

Attributes

Intervention name

name=string

Name of intervention

component

→ scenario → interventions → human → deployment → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Condition

→ scenario → interventions → human → deployment → condition

<condition
    measure=string
  [ minValue=double ]
  [ maxValue=double ]
    initialState=boolean
  />

Documentation (element)

Conditions are evaluated for the whole population, not for individual age-groups or cohorts.

This affects all types of deployment.

Attributes

Measure

measure=string

The monitoring measure to test. Not all measures are available for use.

Minimum value

minValue=double

Minimum value. If specified, the measured variable must be greater than or equal to this value for the condition to be satisfied.

Maximum value

maxValue=double

Maximum value. If specified, the measured variable must be less than or equal to this value for the condition to be satisfied.

Initial state

initialState=boolean

Whether this condition is considered true or false before updated by a survey.

Age-based (continuous) deployment

→ scenario → interventions → human → deployment → continuous

<continuous>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| ( <deploy ... /> )+
</continuous>

Documentation (element)

List of ages at which deployment takes place (through EPI, post-natal and school-based programmes, etc.).

A sub-population restriction may be added as a property of the list of continuous deployments.

restrictToSubPop

→ scenario → interventions → human → deployment → continuous → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

deploy

→ scenario → interventions → human → deployment → continuous → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    targetAgeYrs=double
  [ begin=string ]
  [ end=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention. Input is rounded to the nearest time step.

First time active

begin=string

Units: User defined (defauls to steps)

End step

end=string

Units: User defined (defauls to steps)

Mass (timed) deployment

→ scenario → interventions → human → deployment → timed

<timed>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| [ <cumulativeCoverage ... /> ]
| ( <deploy ... /> )+
</timed>

Documentation (element)

List of timed deployments of the intervention (that is, of deployment campaigns).

Cumulative deployment mode can be specified for all deployments in a timed list. To allow multiple cumulative deployment descriptions, the entire timed list may be repeated.

restrictToSubPop

→ scenario → interventions → human → deployment → timed → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

Cumulative coverage

→ scenario → interventions → human → deployment → timed → cumulativeCoverage

<cumulativeCoverage
    component=string
  />

Documentation (element)

Attributes

Component identifier

component=string

The identifier (short name) of the component used when selecting people.

deploy

→ scenario → interventions → human → deployment → timed → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    time=string
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ repeatStep=string ]
  [ repeatEnd=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Time

time=string

Units: User defined (defauls to steps) Min: 0

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0

Maximum age of eligible individuals (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible individuals (defaults to 0). Input is rounded to the nearest time step.

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Description of health system.

Documentation (type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("forced" or "dynamic")
  [ scaledAnnualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Description of entomological data

Attributes

Entomology dataset name

name=string

Name of entomology data

Transmission model mode

mode=("forced" or "dynamic")

Override annual EIR

scaledAnnualEIR=double

Units: Infectious bites per adult per year

If set, the annual EIR (for all species of vector) is scaled to this level; can be omitted if not needed.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters of the transmission model

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <seasonality ... /> 
|   <mosq ... /> 
| [ <lifeCycle ... /> ]
| [ <simpleMPD ... /> ]
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial estimate of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial estimate of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial estimate of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Seasonality of transmission

→ scenario → entomology → vector → anopheles → seasonality

<seasonality
    input=("EIR")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <fourierSeries ... /> 
| |   <monthlyValues ... /> 
| |   <dailyValues ... /> 
</seasonality>

Documentation (element)

Specifies the seasonality of transmission and optionally the level of annual transmission.

Attributes

Seasonality input

input=("EIR")

Annual EIR

annualEIR=double

Units: Inoculations per adult per annum Min: 0

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries

<fourierSeries
    EIRRotateAngle=double
  >
IN THIS ORDER:
| ( <coeffic ... /> )*
</fourierSeries>

coeffic

Documentation (element)

Units: Infectious bites per adult per day

Attributes

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: Radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Pair of Fourier coefficients

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries → coeffic

<coeffic
    a=double
    b=double
  />

Documentation (element)

A pair of Fourier series coefficients. The first element specifies a1 and b1, the second a2 and b2, etc. Any number (from 0 up) of pairs may be given.

Attributes

a_n parameter of Fourier approximation to ln(EIR)

a=double

a_n parameter of Fourier approximation to ln(EIR) for some natural number n.

b_n parameter of Fourier approximation to ln(EIR)

b=double

b_n parameter of Fourier approximation to ln(EIR) for some natural number n.

List of monthly values

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues

<monthlyValues
    smoothing=("none" or "fourier")
  >
IN THIS ORDER:
| ( <value ... /> ){12,12}
</monthlyValues>

value

Documentation (element)

Description of seasonality from monthly values. Multiple smoothing methods are possible (see smoothing attribute).

List should contain twelve entries: January to December.

Attributes

Smoothing function

smoothing=("none" or "fourier")

How the monthly values are converted into a daily sequence of values:

none: no smoothing (step function)
Fourier: a Fourier series (with terms up to a2/b2) is fit to the sequence of monthly values and used to generate a smoothed list of daily values.

Monthly value

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Monthly value

List of daily values

→ scenario → entomology → vector → anopheles → seasonality → dailyValues

<dailyValues>
IN THIS ORDER:
| ( <value ... /> ){365,365}
</dailyValues>

value

Documentation (element)

Description of seasonality from daily values.

List should contain 365 entries: 1st January to 31st December.

Daily value

→ scenario → entomology → vector → anopheles → seasonality → dailyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Daily value

Mosquito feeding cycle parameters

→ scenario → entomology → vector → anopheles → mosq

<mosq
    minInfectedThreshold=double
  >
IN ANY ORDER:
|   <mosqRestDuration ... /> 
|   <extrinsicIncubationPeriod ... /> 
|   <mosqLaidEggsSameDayProportion ... /> 
|   <mosqSeekingDuration ... /> 
|   <mosqSurvivalFeedingCycleProbability ... /> 
|   <availabilityVariance ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <mosqProbOvipositing ... /> 
|   <mosqHumanBloodIndex ... /> 
</mosq>

Documentation (element)

Parameters describing the feeding cycle and human mosquito interaction of a single species of anopheles mosquito.

Attributes

Mininum infected threshold for mosquitos

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

Duration of the resting period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqRestDuration

<mosqRestDuration
    value=int
  />

Documentation (element)

Units: Days

name:Duration of the resting period of the vector (days);

Attributes

Input parameter value

value=int

An integer value.

Extrinsic incubation period

→ scenario → entomology → vector → anopheles → mosq → extrinsicIncubationPeriod

<extrinsicIncubationPeriod
    value=int
  />

Documentation (element)

Units: Days

name:Extrinsic incubation period (days)

Attributes

Input parameter value

value=int

An integer value.

Proportion of mosquitoes host seeking on same day as ovipositing

→ scenario → entomology → vector → anopheles → mosq → mosqLaidEggsSameDayProportion

<mosqLaidEggsSameDayProportion
    value=double
  />

Documentation (element)

Units: Proportion

Proportion of mosquitoes host seeking on same day as ovipositing

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Duration of the host-seeking period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqSeekingDuration

<mosqSeekingDuration
    value=double
  />

Documentation (element)

Units: Days

Duration of the host-seeking period of the vector (days)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito survives the feeding cycle

→ scenario → entomology → vector → anopheles → mosq → mosqSurvivalFeedingCycleProbability

<mosqSurvivalFeedingCycleProbability
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito survives the feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Variance in human availability rate

→ scenario → entomology → vector → anopheles → mosq → availabilityVariance

<availabilityVariance
    value=double
  />

Documentation (element)

Variance in availability rate of humans to mosquitoes. The mean rate is calculated based on other parameters.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito succesfully bites chosen host

→ scenario → entomology → vector → anopheles → mosq → mosqProbBiting

<mosqProbBiting
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito succesfully bites chosen host

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → mosq → mosqProbFindRestSite

<mosqProbFindRestSite
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito escapes host and finds a resting place after biting

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → mosq → mosqProbResting

<mosqProbResting
    mean=double
    variance=double
  />

Documentation (element)

Probability of mosquito successfully resting after finding a resting site

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of a mosquito successfully laying eggs given that it has rested

→ scenario → entomology → vector → anopheles → mosq → mosqProbOvipositing

<mosqProbOvipositing
    value=double
  />

Documentation (element)

Probability of a mosquito successfully laying eggs given that it has rested

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human blood index

→ scenario → entomology → vector → anopheles → mosq → mosqHumanBloodIndex

<mosqHumanBloodIndex
    value=double
  />

Documentation (element)

Units: Proportion

The proportion of resting mosquitoes which fed on human blood during the last feed.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mosquito life cycle parameters

→ scenario → entomology → vector → anopheles → lifeCycle

<lifeCycle
  [ estimatedLarvalResources=double ] DEFAULT VALUE 1e8
  >
IN ANY ORDER:
|   <eggStage ... /> 
|   <larvalStage ... /> 
|   <pupalStage ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</lifeCycle>

Documentation (element)

Parameters describing the life-cycle of this species of mosquito

Attributes

Estimate of larval resources

estimatedLarvalResources=double

Units: X

Default value: 1e8

Egg stage

→ scenario → entomology → vector → anopheles → lifeCycle → eggStage

<eggStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the egg stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

larvalStage

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage

<larvalStage>
</larvalStage>

daily

Documentation (type)

Parameters for the larval stage of development

Documentation (base type)

Parameters associated with a mosquito development stage.

Daily development

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage → daily

<daily
    resourceUsage=double
    effectCompetition=double
  />

Documentation (element)

Attributes

Resource usage

resourceUsage=double

Units: X

Resource usage during larval stage of development. Units are arbitrary.

Effect of competition

effectCompetition=double

Units: none

Effect of competition over resources on development.

Pupal stage

→ scenario → entomology → vector → anopheles → lifeCycle → pupalStage

<pupalStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the pupal stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → lifeCycle → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Simple Mosq-Pop-Dynamics parameters

→ scenario → entomology → vector → anopheles → simpleMPD

<simpleMPD>
IN ANY ORDER:
|   <developmentDuration ... /> 
|   <developmentSurvival ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</simpleMPD>

Documentation (element)

Parameters describing the simple mosquito population dynamics model.

This is a simpler version of the life-cycle model, requiring less parameters and with much simpler initialisation.

Duration

→ scenario → entomology → vector → anopheles → simpleMPD → developmentDuration

<developmentDuration
    value=int
  />

Documentation (element)

Units: Days Min: 1

Duration from egg laying to emergence in days.

Attributes

Input parameter value

value=int

An integer value.

Probability of survival

→ scenario → entomology → vector → anopheles → simpleMPD → developmentSurvival

<developmentSurvival
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that mosquito survives from the egg being laid to emergence, given no resouce limitations (no density constraints).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → simpleMPD → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Alternative (non-human) host paramters

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN ANY ORDER:
|   <mosqRelativeEntoAvailability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
| [ <hostFecundityFactor ... /> ]
</nonHumanHosts>

Documentation (element)

Min: 0

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of non-human host (ξ_i)

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqRelativeEntoAvailability

<mosqRelativeEntoAvailability
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of the population of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative fecundity of biting mosquitoes

→ scenario → entomology → vector → anopheles → nonHumanHosts → hostFecundityFactor

<hostFecundityFactor
    value=double
  />

Documentation (element)

Units: Proportion

Multiplicative factor for the number of fertile eggs laid by a mosquito after biting this type of host, relative to an unprotected human.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Name of this species of non human hosts (must match up with those described per anopheles section).

Population size of non-human host species

number=double

Units: Animals

Parasite genetics

<parasiteGenetics
    samplingMode=("initial" or "tracking")
  >
IN THIS ORDER:
| ( <locus ... /> )+
</parasiteGenetics>

locus

Documentation (element)

A specification of genotypes of infection parasites.

May be omitted; in this case there is no modelling of genetic differences of infections (resistance, fitness).

Attributes

samplingMode

samplingMode=("initial" or "tracking")

Locus

→ scenario → parasiteGenetics → locus

<locus
    name=string
  >
IN THIS ORDER:
| ( <allele ... /> )+
</locus>

allele

Documentation (element)

Alleles at loci can affect fitness and resistance to any number of drugs.

Attributes

Name of locus

name=string

Name of the Locus

Allele

→ scenario → parasiteGenetics → locus → allele

<allele
    name=string
    initialFrequency=double
    fitness=double
  />

Documentation (element)

Describes an allele, or one possible genetic option of multiple at one point of variance.

Attributes

Name

name=string

Name of the allele; used to refer to it elsewhere.

Initial frequency

initialFrequency=double

Fitness factor

fitness=double

Drug parameters (PK, PD and usage)

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
|   <treatments ... /> 
|   <drugs ... /> 
</pharmacology>

Documentation (element)

Drug model parameters and drug usage parameters

Documentation (type)

A library of drug related data for the PK/PD model.

Treatments library

→ scenario → pharmacology → treatments

<treatments>
IN THIS ORDER:
| ( <schedule ... /> )+
| ( <dosages ... /> )+
</treatments>

Documentation (element)

A library of drug deployment schedules and dosages.

schedule

→ scenario → pharmacology → treatments → schedule

<schedule
    name=string
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

A schedule for the administration of drugs in a course of treatment.

Note that dose sizes are multiplied by some multiplier (see dosages) and the times of all doses may be delayed.

Attributes

Name

name=string

Name for referring to this deployment schedule

medicate

→ scenario → pharmacology → treatments → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  />

Attributes

drug

drug=string

Abbreviated name of drug compound

Drug dose (mg with multiplier)

mg=double

Units: mg per something

Quantity of drug compound in mg per something. A separate dosage table must be used when medicating, which may specify multipliers of this number based on patient age or weight.

Time of administration

hour=double

Units: Hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

dosages

→ scenario → pharmacology → treatments → dosages

<dosages
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | ( <age ... /> )+
| | ( <bodymass ... /> )+
| |   <multiply ... /> 
</dosages>

Documentation (type)

A table for selecting a dose size. There are several ways this can work: using the patient's age or body mass in a look-up table to get a multplier, or directly using body mass as the multiplier.

The doses specified in "mg" in the treatment schedule are then multiplied by this multiplier.

Attributes

Name

name=string

Name for referring to this dosage table

Look-up table (age)

→ scenario → pharmacology → treatments → dosages → age

<age
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's age.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Look-up table (weight)

→ scenario → pharmacology → treatments → dosages → bodymass

<bodymass
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's body mass.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Multiply dose

→ scenario → pharmacology → treatments → dosages → multiply

<multiply
    by=("kg")
  />

Documentation (element)

Multiply the dose by some quantity, such as patient weight.

Attributes

By what?

by=("kg")

Quantity to multiply the dose by. Only option is "kg" (patient weight in kg).

Drug library

→ scenario → pharmacology → drugs

<drugs>
IN THIS ORDER:
| ( <drug ... /> )+
</drugs>

drug

Documentation (element)

A library of drug PK/PD data.

drug

→ scenario → pharmacology → drugs → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (type)

A drug description with PK/PD parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drugs → drug → PD

<PD
  [ locus=string ]
  >
IN THIS ORDER:
| ( <phenotype ... /> )+
</PD>

phenotype

Attributes

Locus

locus=string

PD parameters for some allele / resistance phenotype

→ scenario → pharmacology → drugs → drug → PD → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

Restrict phenotype applicability to certain alleles

→ scenario → pharmacology → drugs → drug → PD → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (element)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Maximal parasite killing rate

→ scenario → pharmacology → drugs → drug → PD → phenotype → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drugs → drug → PD → phenotype → IC50

<IC50
  [ sigma=double ] DEFAULT VALUE 0
  >
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Attributes

Sigma parameter for per-infection variation of IC50

sigma=double

Default value: 0

Distribution parameter describing per-infection variation of IC50. If zero or not specified, the IC50 is not sampled. See documentation of parent element.

Slope of effect curve

→ scenario → pharmacology → drugs → drug → PD → phenotype → slope

<slope>
    double
</slope>

Documentation (element)

Units: dimensionless

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drugs → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
| EXACTLY ONE OF:
| |   <half_life ... /> 
| | IN THIS ORDER:
| | |   <k ... /> 
| | |   <m_exponent ... /> 
| [ <k_a ... /> ]
| [ <conversion ... /> ]
|   <vol_dist ... /> 
| [ <compartment2 ... /> ]
| [ <compartment3 ... /> ]
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drugs → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drugs → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate λ, calculated as λ = ln(2) / half_life. The basic form of decay is C(t) = C0 * exp(-λ*t).

Alternatively, elimination rate can be specified via k and m_exponent.

Constant associated with elimination rate (k)

→ scenario → pharmacology → drugs → drug → PK → k

<k
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

If sigma > 0, k is sampled per-human from the log-normal distribution: ln N( ln(mean) - σ^2 / 2, σ^2).

Alternatively, elimination rate can be specified via half_life.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Constant associated with elimination rate (m_exponent)

→ scenario → pharmacology → drugs → drug → PK → m_exponent

<m_exponent>
    double
</m_exponent>

Documentation (element)

Units: day^-1 Min: 0

Alternatively, elimination rate can be specified via half_life.

Note that in the case of a conversion model, this applies to both the elimination and the conversion rates.

Absorption rate constant (k_a)

→ scenario → pharmacology → drugs → drug → PK → k_a

<k_a
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Min: 0

Absorption rate parameter. Not allowed for one compartment models, but required for two and three compartment models and one compartment with conversion model (for the parent drug only).

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Conversion parameters (parent drug)

→ scenario → pharmacology → drugs → drug → PK → conversion

<conversion>
IN ANY ORDER:
|   <metabolite ... /> 
|   <rate ... /> 
|   <molRatio ... /> 
</conversion>

Documentation (element)

Configures the parent drug in a conversion model.

To use a conversion model, the parent drug should have this section defined as well as half-life or k (direct elimination; this may be zero) and k_a (absorption rate; this may be large).

Metabolite drug (abbreviation)

→ scenario → pharmacology → drugs → drug → PK → conversion → metabolite

<metabolite>
    string
</metabolite>

Documentation (element)

The abbreviation of the metabolite drug (e.g. "DHA" or "DHA_AR").

Rate of conversion

→ scenario → pharmacology → drugs → drug → PK → conversion → rate

<rate
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Rate of conversion of parent drug to metabolite.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Molecular weight ratio

→ scenario → pharmacology → drugs → drug → PK → conversion → molRatio

<molRatio>
    double
</molRatio>

Documentation (element)

Ratio of molecular weights: molecular weight of the metabolite divided by molecular weight of the parent.

Volume of Distribution (Vd)

→ scenario → pharmacology → drugs → drug → PK → vol_dist

<vol_dist
  [ sigma=double ] DEFAULT VALUE 0
  >
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Attributes

Sigma parameter for per-human variation of Vd

sigma=double

Default value: 0

Distribution parameter describing per-human variation of volume of distribution. If zero or not specified, the parameter is not sampled. See documentation of parent element.

Second compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment2

<compartment2>
IN ANY ORDER:
|   <a12 ... /> 
|   <a21 ... /> 
</compartment2>

Documentation (element)

Optional element specifying conversion parameters to- and from- a second compartment.

Absorption rate to compartment 2 (a12)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → a12

<a12
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the first periphery compartment (2). The parameter k12 = a12 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Absorption rate from compartment 2 (a21)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → a21

<a21
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the first periphery compartment (2) to the central compartment. The parameter k21 = a21 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Third compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment3

<compartment3>
IN ANY ORDER:
|   <a13 ... /> 
|   <a31 ... /> 
</compartment3>

Documentation (element)

Optional element specifying conversion parameters to- and from- a third compartment.

Absorption rate to compartment 3 (a13)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → a13

<a13
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the second periphery compartment (3). The parameter k13 = a13 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Absorption rate from compartment 3 (a31)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → a31

<a31
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the second periphery compartment (3) to the central compartment. The parameter k31 = a31 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Diagnostic parameters

→ scenario → diagnostics

<diagnostics>
IN THIS ORDER:
| ( <diagnostic ... /> )*
</diagnostics>

diagnostic

Documentation (element)

Diagnostic model parameters

diagnostic

→ scenario → diagnostics → diagnostic

<diagnostic
    name=string
  [ units=("Other" or "Garki" or "Malariatherapy") ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterministic ... /> 
| |   <stochastic ... /> 
</diagnostic>

Attributes

Name of diagnostic

name=string

Name of this diagnostic (parameterisation). May be used elsewhere in the XML document to refer to this set of diagnostic parameters.

Parasite density units / methodology

units=("Other" or "Garki" or "Malariatherapy")

Deterministic detection

→ scenario → diagnostics → diagnostic → deterministic

<deterministic
    minDensity=double
  />

Documentation (element)

Specify that an artificial deterministic test is used: outcome is positive if parasite density is at least the minimum given.

Attributes

Minimum detectible density

minDensity=double

Units: parasites/microlitre Min: 0

The minimum density at which parasites can be detected. If 0, the test outcome is always positive.

Non-deterministic detection

→ scenario → diagnostics → diagnostic → stochastic

<stochastic
    dens_50=double
    specificity=double
  />

Documentation (element)

An improved model of detection which is non-deterministic, including false positive results as well as false negatives.

Some parameterisations:

Microscopy sensitivity/specificity data in Africa; Source: expert opinion — Allan Schapira dens_50 = 20.0 specificity = .75

RDT sensitivity/specificity for Plasmodium falciparum in Africa Source: Murray et al (Clinical Microbiological Reviews, Jan. 2008) dens_50 = 50.0; specificity = .942;

Attributes

Density 50

dens_50=double

Units: parasites/microlitre Min: 0

The density at which the test outcome has a 50% chance of being positive.

Specificity

specificity=double

Units: Dimensionless Min: 0 Max: 1

The probability of a positive test outcome in the absense of parasites.

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
| [ <vivax ... /> ]
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: model/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=string
  >
IN ANY ORDER:
| [ <NeonatalMortality ... /> ]
| [ <NonMalariaFevers ... /> ]
</clinical>

Documentation (type)

Attributes

Follow-up period during which recurrence is considered a treatment failure

healthSystemMemory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

Neonatal mortality parameters

→ scenario → model → clinical → NeonatalMortality

<NeonatalMortality
    diagnostic=string
  />

Attributes

Diagnostic used to parameterise model

diagnostic=string

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
| [ <prNeedTreatmentNMF ... /> ]
| [ <prNeedTreatmentMF ... /> ]
</NonMalariaFevers>

Documentation (type)

Description of the incidence of non-malaria fever. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a non-malarial fever requires treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

Availability of humans to mosquitoes relative to an adult, categorized by age group

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ]
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

Vivax model parameters

→ scenario → model → vivax

<vivax>
IN ANY ORDER:
|   <probBloodStageInfectiousToMosq ... /> 
|   <hypnozoiteRelease ... /> 
|   <bloodStageProtectionLatency ... /> 
|   <bloodStageLengthDays ... /> 
|   <clinicalEvents ... /> 
</vivax>

Documentation (element)

This describes Vivax model parameters, and is required when using the VIVAX_SIMPLE_MODEL model option.

Probability of mosquito infection

→ scenario → model → vivax → probBloodStageInfectiousToMosq

<probBloodStageInfectiousToMosq
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

The chance of a feeding mosquito becoming infected, given that the host is patent. (This may be adjusted by transmission-blocking vaccines.)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Hypnozoite releases

→ scenario → model → vivax → hypnozoiteRelease

<hypnozoiteRelease
  [ pSecondRelease=double ] DEFAULT VALUE 0
  >
IN ANY ORDER:
|   <numberHypnozoites ... /> 
|   <firstRelease ... /> 
| [ <secondRelease ... /> ]
</hypnozoiteRelease>

Documentation (element)

Describes the number and times of hypnozoite releases.

Documentation (type)

This element defines probabilites when and how many hypnozoites are released from the liverstage into the blood.

The gap between the start of a new brood of hypnozoites and its release are defined as follows:

latentP + latentRelapseDays + randomReleaseDelay

randomReleaseDelay is based on one or two lognormal distributions, which are defined in firstRelease and optionally secondRelease.

You can define 2 release distributions, which get added together and represent the probability of hypnozoites which get released before winter (first release) or after (second release).

You can omit the secondRelease element if no release to the blood happens after winter.

Attributes

latent relapse days

pSecondRelease=double

Default value: 0

Probability of a second release. If undefined it is zero.

Number of Hypnozoites

→ scenario → model → vivax → hypnozoiteRelease → numberHypnozoites

<numberHypnozoites
    max=int
    base=double
  />

Documentation (element)

numberHypnozoites calculates the number of hypnozoites in the liver stage based on a base which is between 0 and 1.

This number is random based on the following distribution and normalized:

max ∑ (base ^ n) n = 0

Attributes

max

max=int

base

base=double

firstRelease

→ scenario → model → vivax → hypnozoiteRelease → firstRelease

<firstRelease
    mu=double
    sigma=double
    latentRelapseDays=int
  />

Documentation (base type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

latent relapse days

latentRelapseDays=int

Usually 15 days or 10 days (3 or 2 5-day timesteps).

secondRelease

→ scenario → model → vivax → hypnozoiteRelease → secondRelease

<secondRelease
    mu=double
    sigma=double
    latentRelapseDays=int
  />

Documentation (base type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

latent relapse days

latentRelapseDays=int

Usually 15 days or 10 days (3 or 2 5-day timesteps).

Blood stage protection latency

→ scenario → model → vivax → bloodStageProtectionLatency

<bloodStageProtectionLatency
    value=double
  />

Documentation (element)

Min: 0

The length of time after expiry of a blood-stage infection during which relapses from the same brood are supressed by the immune system.

This is rounded to the nearest time-step.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Blood stage length

→ scenario → model → vivax → bloodStageLengthDays

<bloodStageLengthDays
    weibullScale=double
    weibullShape=double
  />

Documentation (element)

Units: Days

Parameters used to sample the length of blood-stage infections from a Weibull distribution (scale parameter lambda, shape parameter k).

Attributes

weibullScale

weibullScale=double

weibullShape

weibullShape=double

clinicalEvents

→ scenario → model → vivax → clinicalEvents

<clinicalEvents>
IN THIS ORDER:
|   <pPrimaryInfection ... /> 
|   <pRelapseOne ... /> 
|   <pRelapseTwoPlus ... /> 
|   <pEventIsSevere ... /> 
</clinicalEvents>

Documentation (type)

This elements holds all information about probabilites for clinical events from infections and relapses.

pPrimaryInfection

→ scenario → model → vivax → clinicalEvents → pPrimaryInfection

<pPrimaryInfection
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseOne

→ scenario → model → vivax → clinicalEvents → pRelapseOne

<pRelapseOne
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseTwoPlus

→ scenario → model → vivax → clinicalEvents → pRelapseTwoPlus

<pRelapseTwoPlus
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pEventIsSevere

→ scenario → model → vivax → clinicalEvents → pEventIsSevere

<pEventIsSevere
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=string
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=string

Units: User defined (default: steps) Min: 0 Max: 20

Pre-erythrocytic latent period Can be specified in steps (e.g. 3t) or days (e.g. 15d).

parameter

→ scenario → model → parameters → parameter

<parameter
  [ name=string ]
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 37 documentation

Generated from: scenario_37.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
  [ analysisNo=int ]
    name=string
  [ wuID=int ]
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:om="http://openmalaria.org/schema/scenario_37"
    xsi:schemaLocation="http://openmalaria.org/schema/scenario_37 scenario_37.xsd"
  >
IN ANY ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entomology ... /> 
| [ <parasiteGenetics ... /> ]
| [ <pharmacology ... /> ]
| [ <diagnostics ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Name of intervention

Work unit identifier

wuID=int

Units: Number

Work unit ID. Obselete and no longer required.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Description of demography

Attributes

Name of demography data

name=string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Years Min: 0 Max: 100

Maximum age of simulated humans in years

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

list of age groups included in demography

Documentation (type)

list of age groups included in demography or surveys

Attributes

Lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Units: Percentage Min: 0 Max: 100

Percentage of human population in age group

Upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ startDate=string ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
| [ <cohorts ... /> ]
</monitoring>

Documentation (element)

Description of surveys

Attributes

Name of monitoring settings

name=string

Name of monitoring settings

Start of monitoring

startDate=string

continuous

→ scenario → monitoring → continuous

<continuous
    period=string
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Delay between reports

period=string

Units: User defined (default: steps)

Delay between reports; typically one time step but can be greater. Can be specified in steps (e.g. 1t) or days (e.g. 5d).

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions
  [ onlyNewEpisode=boolean ] DEFAULT VALUE false
  >
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See model/mon/OutputMeasures.h for a list of supported outputs. Should also be on the wiki.

Attributes

Report only for new cases

onlyNewEpisode=boolean

Default value: false

option

→ scenario → monitoring → SurveyOptions → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  [ outputNumber=int ]
  [ byAge=boolean ]
  [ byCohort=boolean ]
  [ bySpecies=boolean ]
  [ byGenotype=boolean ]
  [ byDrugType=boolean ]
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Number identifying measure in output

outputNumber=int

Report by age category

byAge=boolean

Report by cohort

byCohort=boolean

Report by mosquito species

bySpecies=boolean

Report by parasite genotype

byGenotype=boolean

Report by drug type

byDrugType=boolean

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
  [ detectionLimit=double ]
  [ diagnostic=string ]
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/microlitre Min: 0

Deprecated: limit above which a human's infection is reported as patent. Alternative: do not specify this; instead specify "diagnostic".

Name of monitoring diagnostic

diagnostic=string

Name of a parameterised diagnostic to use in surveys (see scenario/diagnostics).

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime
  [ repeatStep=string ]
  [ repeatEnd=string ]
  [ reported=boolean ] DEFAULT VALUE true
  >
    string
</surveyTime>

Documentation (element)

Units: User defined (defaults to steps) Min: 0

The simulation ends immediately after the last survey is taken.

Attributes

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

reported

reported=boolean

Default value: true

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Cohorts

→ scenario → monitoring → cohorts

<cohorts>
IN THIS ORDER:
| ( <subPop ... /> )+
</cohorts>

subPop

Documentation (element)

Allows the configuration of multiple cohorts (output segregated according to membership within specific sub-populations).

If this element is omitted, monitoring surveys cover the entire simulated human population.

It does not affect the "continuous" outputs (these never take cohorts into account).

Sub-population

→ scenario → monitoring → cohorts → subPop

<subPop
    id=string
    number=integer
  />

Documentation (element)

In the output file, the output set is identified by multiplying this number by 1000 then adding it to the age group column.

Attributes

Sub-population identifier

id=string

Textual identifier for the sub-population (i.e. for an intervention component, since sub-populations are defined as the hosts an intervention component is deployed to).

Sub-population number

number=integer

Units: dimensionless Min: 1 Max: 2097152

Number identifying a sub-population; used to define identifiers of output sets. This number must be a power of 2 (i.e. 1, 2, 4, 8, ...). See documentation of subPop element.

Preventative interventions

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfections ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <vectorPop ... /> ]
| [ <vectorTrap ... /> ]
| [ <human ... /> ]
</interventions>

Documentation (element)

Attributes

Name of intervention set

name=string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeHS>

timedDeployment

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeHS → timedDeployment

<timedDeployment
    time=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timedDeployment>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</uncomplicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

multiple

→ scenario → interventions → human → component → decisionTree → multiple

<multiple
  [ name=string ]
  >
IN THIS ORDER:
| ( <caseType ... /> )*
| ( <diagnostic ... /> )*
| ( <random ... /> )*
| ( <age ... /> )*
| ( <treatPKPD ... /> )*
| [ <treatSimple ... /> ]
| ( <deploy ... /> )*
</multiple>

Documentation (type)

A special node allowing multiple sub-trees to be evaluated.

This is different from an ordinary decision tree node in that:

a) multiple types of child can occur simultaneously (e.g. multiple types of treatment or treatment plus a 'random' sub-tree)

b) the 'noTreatment' and 'treatFailure' nodes are not allowed

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → multiple → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

firstLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → firstLine

<firstLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</firstLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

secondLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → secondLine

<secondLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</secondLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

positive

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

outcome

→ scenario → interventions → human → component → decisionTree → multiple → random → outcome

<outcome
  [ name=string ]
    p=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</outcome>

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Probability

p=double

Units: None Min: 0 Max: 1

Probability of selecting this outcome. The sum of probabilities across all outcomes must be 1.

age

→ scenario → interventions → human → component → decisionTree → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Age range

→ scenario → interventions → human → component → decisionTree → multiple → age → age

<age
  [ name=string ]
    lb=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</age>

Documentation (element)

Describes a branch, selected for patients of a certain age.

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Lower bound (inclusive)

lb=double

Min: 0

noTreatment

→ scenario → interventions → human → component → decisionTree → noTreatment

<noTreatment
  [ name=string ]
  />

Documentation (type)

An end node doing nothing. This exists to explicitly state that no treatment happens and to prevent trees from accidentally being left incomplete.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatFailure

→ scenario → interventions → human → component → decisionTree → treatFailure

<treatFailure
  [ name=string ]
  />

Documentation (type)

An end node which reports treatment but does not change parasitalogical status. This allows correct labelling of second-line cases.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → multiple → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

age

→ scenario → interventions → human → component → decisionTree → multiple → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → multiple → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → multiple → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → multiple → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</complicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: Days Min: 0 Max: unbounded

Maximum number of timesteps (including first day of case) that an individual with an uncomplicated case of malaria will remember he/she was sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial or non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of a complicated or severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
  [ name=string ]
  [ useDiagnosticUC=boolean ] DEFAULT VALUE false
  >
IN ANY ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <treatmentActions ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
</ImmediateOutcomes>

Documentation (type)

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Name of case management parameterisation

name=string

Name of health system

useDiagnosticUC

useDiagnosticUC=boolean

Default value: false

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Description of drug regimen.

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Artemisinine based combination therapy

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Quinine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0 Max: 1name:P(self-treat)

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Effectiveness of treatment for non-compliant patients

treatmentActions

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions

<treatmentActions>
IN ANY ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
</treatmentActions>

CQ
SP
AQ
SPAQ
ACT
QN

CQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ

<CQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</CQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

deploy

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy

<deploy
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ p=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| ( <component ... /> )+
</deploy>

component

Attributes

Maximum age of eligible humans

maxAge=double

Units: Years Min: 0

Maximum age of eligible humans (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible humans

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible humans (defaults to 0). Input is rounded to the nearest time step.

Probability of delivery to eligible humans

p=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Probability of this list of components being deployed, given that other constraints are met.

component

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Prophylactic treatment

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere → clearInfections

<clearInfections
    timesteps=string
    stage=("liver" or "blood" or "both")
  />

Documentation (element)

Attributes

Length of effect

timesteps=string

Units: User defined (defaults to steps)

Target stage

stage=("liver" or "blood" or "both")

SP

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SP

<SP
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SP>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

AQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → AQ

<AQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</AQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

SPAQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SPAQ

<SPAQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SPAQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

ACT

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → ACT

<ACT
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</ACT>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

QN

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → QN

<QN
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</QN>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

Probability that human is incompatible with liver-stage drug treatment

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pHumanCannotReceive

<pHumanCannotReceive
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that a human is determined to be unable to receive liver-stage drug treatment. Treatment is neither reported or given for such humans.

This is sampled once per human at birth.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Ignore liver-stage drug treatment incompatibility

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → ignoreCannotReceive

<ignoreCannotReceive
    value=boolean
  />

Documentation (element)

If true, ignore pHumanCannotReceive and consider all humans eligible for treatment; if false (or not specified), do not treat those demed incompatible with liver-stage drug treatment.

The point of this is that pHumanCannotReceive cannot be altered by changeHS interventions, but this property can be.

Attributes

Input parameter value

value=boolean

A boolean value.

Prob use in UC case

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pUseUncomplicated

<pUseUncomplicated
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

This feature is deprecated; it is suggested to use the "simple treatment" feature configured to clear liver-stage parasites, leaving this option unset or zero.

Chance of liver-stage drug treatment being used for routine treatment of an uncomplicated case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Effectiveness

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → effectivenessOnUse

<effectivenessOnUse
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that liver-stage drug treatment is effective.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

DecisionTree5Day

<DecisionTree5Day
  [ name=string ]
  >
IN ANY ORDER:
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
|   <treeUCOfficial ... /> 
|   <treeUCSelfTreat ... /> 
|   <cureRateSevere ... /> 
|   <treatmentSevere ... /> 
</DecisionTree5Day>

Documentation (type)

Besides greater flexibility, this allows treatment via PK/PD models.

Attributes

Name of case management parameterisation

name=string

Name of health system

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → DecisionTree5Day → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → DecisionTree5Day → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

treeUCOfficial

→ scenario → healthSystem → DecisionTree5Day → treeUCOfficial

<treeUCOfficial
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCOfficial>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treeUCSelfTreat

→ scenario → healthSystem → DecisionTree5Day → treeUCSelfTreat

<treeUCSelfTreat
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCSelfTreat>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Cure rate (severe cases)

→ scenario → healthSystem → DecisionTree5Day → cureRateSevere

<cureRateSevere
    value=double
  />

Documentation (element)

Min: 0 Max: 1

The probability of clearing parasites given access to appropriate (hospital) care, for a severe case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

treatmentSevere

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere

<treatmentSevere
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</treatmentSevere>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Case fatality rate for inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: Dimensionless

List of age-specific probabilities of sequelae in inpatients, during a severe bout of malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeEIR>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeEIR → timedDeployment

<timedDeployment
    eipDuration=int
    time=string
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timedDeployment>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Time

time=string

Units: User defined (defauls to steps) Min: 0

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=string ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=string

Units: User defined (default: steps) Min: 0

Default value: 0

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=string
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time of start

time=string

Units: User defined (defauls to steps) Min: 0

Insert R_0 case

<insertR_0Case
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</insertR_0Case>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → insertR_0Case → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Uninfect vectors

<uninfectVectors
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</uninfectVectors>

timedDeployment

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → uninfectVectors → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Vector population intervention

→ scenario → interventions → vectorPop

<vectorPop>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorPop>

intervention

Documentation (element)

Units: List of elements

A list of parameterisations of generic vector host-inspecific interventions.

intervention

→ scenario → interventions → vectorPop → intervention

<intervention
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

Units: List of elements

An intervention which may have various effects on the vector populations as a whole. (Not host specific.)

Multiple instances of this intervention class are allowed (multiple parameterisations, not just deployments).

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → vectorPop → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → vectorPop → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <seekingDeathRateIncrease ... /> ]
| [ <probDeathOvipositing ... /> ]
| [ <emergenceReduction ... /> ]
</anopheles>

Documentation (type)

Units: dimensionless Min: 0 Max: 1

Descriptions of the effects of vector interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Proportional increase in deaths while host searching

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease

<seekingDeathRateIncrease
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</seekingDeathRateIncrease>

decay

Documentation (element)

Units: dimensionless

Describe an effect on the increase in the death rate while host seeking (mu_vA) due to this intervention.

Enter the rate increase (i.e. if rate increases to 120% of normal, give 0.2). New death rate while seeking is old × (1 + increase) where increase is this factor given. Must have increas ≥ -1.

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Proportion ovipositing mosquitoes killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing

<probDeathOvipositing
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probDeathOvipositing>

decay

Documentation (element)

Units: dimensionless

Describe an effect of increased mortality while ovipositing due to this intervention. Enter the probability of dying due to this intervention.

Attributes

Initial probability of killing

initial=double

Units: dimensionless Min: 0 Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Proportion of emerging pupa killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction

<emergenceReduction
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</emergenceReduction>

decay

Documentation (element)

Units: dimensionless

Describe an effect on emergence of pupa into adults: this value is the proportion of emerging pupa which are killed by this intervention.

Attributes

Initial proportion reduction

initial=double

Units: dimensionless Min: -inf Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Vector population intervention deployment

→ scenario → interventions → vectorPop → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

deploy

→ scenario → interventions → vectorPop → intervention → timed → deploy

<deploy
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Baited trap

→ scenario → interventions → vectorTrap

<vectorTrap>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorTrap>

intervention

Documentation (element)

intervention

→ scenario → interventions → vectorTrap → intervention

<intervention
  [ name=string ]
  >
IN THIS ORDER:
| ( <description ... /> )+
| [ <timed ... /> ]
</intervention>

Documentation (type)

Attributes

Descriptive name for type of trap

name=string

Optional name for this type of trap

Description

→ scenario → interventions → vectorTrap → intervention → description

<description
    mosquito=string
  >
IN THIS ORDER:
|   <relativeAvailability ... /> 
|   <decayOfAvailability ... /> 
</description>

Documentation (element)

Parameters associated with a vector trap intervention, per mosquito species.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Initial relative availability

→ scenario → interventions → vectorTrap → intervention → description → relativeAvailability

<relativeAvailability
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: inf

Describes the availiability of a trap to a host-seeking mosquito relative to an average unprotected adult.

I.e. if this parameter is 2, then each trap will on average attract twice as many mosquitoes as unprotected adults.

This is the initial availability; it may decay towards zero depending on the configured decay function.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay of availability

→ scenario → interventions → vectorTrap → intervention → description → decayOfAvailability

<decayOfAvailability
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Describes how availability decays to zero.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Vector trap intervention deployment

→ scenario → interventions → vectorTrap → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )*
</timed>

deploy

Documentation (element)

List of timed vector trap intervention deployment

deploy

→ scenario → interventions → vectorTrap → intervention → timed → deploy

<deploy
    time=string
    ratioToHumans=double
    lifespan=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Ratio to humans

ratioToHumans=double

Min: 0 Max: inf

The number of traps deployed, by this deployment, per adult human. E.g. if there are currently 100 traps and 1000 humans, then a ratio of 0.1 will increase the number of traps to 200.

Lifespan

lifespan=string

Units: Steps or Days or Years

Human-specific interventions

→ scenario → interventions → human

<human>
IN THIS ORDER:
| ( <component ... /> )+
| ( <deployment ... /> )*
</human>

Documentation (element)

Encapsulates all interventions whose effects are specific to the human host: any interventions where target humans may be selected via population-coverage, age limits and sub-population membership.

Component

→ scenario → interventions → human → component

<component
    id=string
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <screen ... /> 
| |   <treatSimple ... /> 
| |   <treatPKPD ... /> 
| |   <decisionTree ... /> 
| |   <PEV ... /> 
| |   <BSV ... /> 
| |   <TBV ... /> 
| |   <ITN ... /> 
| |   <IRS ... /> 
| |   <GVI ... /> 
| | [ <recruitmentOnly ... /> ]
| |   <clearImmunity ... /> 
| [ <subPopRemoval ... /> ]
</component>

Documentation (element)

Each element describes one component: its effects, decay of the(se) effect(s), and related stuff (e.g. description of indirect decay and of usage levels).

Attributes

Component identifier

id=string

Name of component

name=string

An informal name/description for the component

screen

→ scenario → interventions → human → component → screen

<screen
    diagnostic=string
  >
IN THIS ORDER:
| ( <positive ... /> )*
| ( <negative ... /> )*
</screen>

Documentation (type)

This can be combined with MDA to achieve mass screen and treat (MSAT) or other types of mass screening intervention.

The use of the screening itself is reported (if enabled), but not the outcome. Deployment of interventions triggered by the screening may be reported, however.

Attributes

Name of diagnostic

diagnostic=string

Name of a parameterised diagnostic (see scenario/diagnostics).

positive

→ scenario → interventions → human → component → screen → positive

<positive
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → screen → negative

<negative
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

treatSimple

→ scenario → interventions → human → component → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

treatPKPD

→ scenario → interventions → human → component → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

decisionTree

→ scenario → interventions → human → component → decisionTree

<decisionTree
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</decisionTree>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Vaccines

→ scenario → interventions → human → component → PEV

<PEV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</PEV>

Documentation (element)

Pre-erythrocytic vaccine (PEV): prevents a proportion of infections from commencing.

Documentation (type)

Description of a vaccine's effect

Decay of effect

→ scenario → interventions → human → component → PEV → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Specification of decay of efficacy. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Variance parameter for vaccine efficacy

→ scenario → interventions → human → component → PEV → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vaccines

→ scenario → interventions → human → component → BSV

<BSV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</BSV>

Documentation (element)

Blood-stage vaccine (BSV): acts as a killing factor on blood-stage parasites. Exact action depends on the within host model.

Documentation (type)

Description of a vaccine's effect

Vaccines

→ scenario → interventions → human → component → TBV

<TBV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</TBV>

Documentation (element)

Transmission-blocking vaccine (TBV): one minus this scales the probability of transmission to mosquitoes

Documentation (type)

Description of a vaccine's effect

Bed nets

→ scenario → interventions → human → component → ITN

<ITN>
IN THIS ORDER:
| [ <usage ... /> ]
|   <holeRate ... /> 
|   <ripRate ... /> 
|   <ripFactor ... /> 
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
|   <attritionOfNets ... /> 
| ( <anophelesParams ... /> )+
</ITN>

Documentation (element)

Description of bed-net interventions (ITNs, LLINs).

Proportion of time nets are used by humans

→ scenario → interventions → human → component → ITN → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of nets by humans, from 0 to 1.

At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing.

See also "propActing" (proportion of bits for which net acts).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Rate at which holes are made

→ scenario → interventions → human → component → ITN → holeRate

<holeRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Holes per annum Min: 0

The rate at which new holes are made in nets.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ ln N( log(mean)-sigma²/2, sigma² ).

Equivalent R sample: rlnorm(n, log(m) - s*s/2, s)

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rate at which holes are enlarged

→ scenario → interventions → human → component → ITN → ripRate

<ripRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Rips per existing hole per annum Min: 0

Each existing hole has a probability of being ripped bigger according to a Poisson process with this rate as (only) parameter.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ ln N( log(mean)-sigma²/2, sigma² ).

Equivalent R sample: rlnorm(n, log(m) - s*s/2, s)

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rip factor

→ scenario → interventions → human → component → ITN → ripFactor

<ripFactor
    value=double
  />

Documentation (element)

Units: none Min: 0

This factor expresses how important rips are in increasing the hole.

The hole index of a net is h + F×x where h and x are the total numbers of holes and rips respectively and F is the rip factor.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → ITN → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: mg/m² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → human → component → ITN → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of nets. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Attrition of nets

→ scenario → interventions → human → component → ITN → attritionOfNets

<attritionOfNets
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: dimensionless

Specifies the rate at which nets are disposed of over time. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Humans are removed from the intervention component's sub-population on disposal (attrition) of their nets. Currently this event is not reported.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → human → component → ITN → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <holeIndexMax ... /> ]
| EXACTLY ONE OF:
| |   <deterrency ... /> 
| |   <twoStageDeterrency ... /> 
| EXACTLY ONE OF:
| |   <preprandialKillingEffect ... /> 
| |   <preprandialKillingEffectLogit ... /> 
| EXACTLY ONE OF:
| |   <postprandialKillingEffect ... /> 
| |   <postprandialKillingEffectLogit ... /> 
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which net acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

maximum of holed surface area that has an effect (comparable to no net)

→ scenario → interventions → human → component → ITN → anophelesParams → holeIndexMax

<holeIndexMax
    value=double
  />

Documentation (element)

Units: in same unit as holeIndex

Used by logit attacking and killing models only, holeIndexMax is a user defined maximum hole index (typically, the total surface area of a net).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency

<twoStageDeterrency>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <entering ... /> 
| |   <enteringLogit ... /> 
| EXACTLY ONE OF:
| |   <attacking ... /> 
| |   <attackingLogit ... /> 
</twoStageDeterrency>

Documentation (element)

Units: dimensionless

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

This deterrency model multiplies human attractiveness by pEnt×pAtt.

Deterrency: entering

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → entering

<entering
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless

pEnt represents the relative probability of entering due to ITNs: pEnt = exp(log(P)×p) where P is the insecticide factor and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Deterrency: entering (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → enteringLogit

<enteringLogit
    baseFactor=double
    insecticideFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: none

See parent element documentation

Insecticide factor

insecticideFactor=double

Units: none

See parent element documentation

Deterrency: attacking

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attacking

<attacking
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Deterrency: attacking (logit model)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attackingLogit

<attackingLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Pre-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Pre-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffectLogit

<preprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Post-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffectLogit

<postprandialKillingEffectLogit
    baseFactor=double
    insecticideFactor=double
    holeFactor=double
    interactionFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Base factor

baseFactor=double

Units: dimensionless

Logit of the probability (e.g. of death, of entry, of attacking) without intervention.

Insecticide factor

insecticideFactor=double

Units: none

Coefficient of log(insecticide content+1) in a generalized linear model with logit link function.

Hole factor

holeFactor=double

Units: none

Coefficient of log(total holed surface area (in cm2) +1) in a generalized linear model with logit link function.

Interaction factor

interactionFactor=double

Units: none

Coefficient of the interaction term of log(total holed surface area (in cm2) +1) with log(insecticide content+1) in a generalized linear model with logit link function.

Indoor residual spraying

→ scenario → interventions → human → component → IRS

<IRS>
IN THIS ORDER:
| [ <usage ... /> ]
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
| ( <anophelesParams ... /> )+
</IRS>

Documentation (element)

Description of indoor residual spraying interventions.

Documentation (type)

Description of effect for the more complex and probably more realistic Briet model: IRS has three effects, whos strength is calculated as a function of surviving insecticide content.

Proportion of Indoor residual spraying (IRS) interventions

→ scenario → interventions → human → component → IRS → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Indoor residual spraying (IRS) interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → IRS → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: μg/cm² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → human → component → IRS → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → IRS → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → IRS → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied by exp(P×log(p)) where P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Generic vector intervention

→ scenario → interventions → human → component → GVI

<GVI>
IN THIS ORDER:
| [ <usage ... /> ]
|   <decay ... /> 
| ( <anophelesParams ... /> )+
</GVI>

Documentation (element)

Note that all actions of this intervention component will decay according to a single decay function. If independant decay is wanted, a separate component can be used for each action.

Proportion of generic vector interventions

→ scenario → interventions → human → component → GVI → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Generic vector interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay

→ scenario → interventions → human → component → GVI → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Description of decay of all intervention effects. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → GVI → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <deterrency ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → GVI → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied this factor times survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Recruitment only

→ scenario → interventions → human → component → recruitmentOnly

<recruitmentOnly/>

Documentation (element)

Recruitment of a host into a sub-population.

Clear Immunity

→ scenario → interventions → human → component → clearImmunity

<clearImmunity/>

Documentation (element)

Removes all exposure-related immunitsy gained over time by hosts without removing infections (or affecting the ability to gain immunity through exposure).

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

subPopRemoval

→ scenario → interventions → human → component → subPopRemoval

<subPopRemoval
  [ onFirstBout=boolean ] DEFAULT VALUE false
  [ onFirstTreatment=boolean ] DEFAULT VALUE false
  [ onFirstInfection=boolean ] DEFAULT VALUE false
  [ afterYears=double ]
  />

Documentation (type)

ITN attrition also removes humans from sub-populations.

Attributes

Time to first episode only

onFirstBout=boolean

Default value: false

Time to first treatment only

onFirstTreatment=boolean

Default value: false

Time to first infection only

onFirstInfection=boolean

Default value: false

Remove from sub-population after

afterYears=double

Units: Years Min: 0

Deployment

→ scenario → interventions → human → deployment

<deployment
  [ name=string ]
  >
IN THIS ORDER:
| ( <component ... /> )+
| ( <condition ... /> )*
| ( <continuous ... /> )*
| ( <timed ... /> )*
</deployment>

Documentation (element)

All components deployed by this intervention are deployed to the same people (each timed or continuous deployment selects recipients and then gives each recipient all components of the intervention).

Attributes

Intervention name

name=string

Name of intervention

component

→ scenario → interventions → human → deployment → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Condition

→ scenario → interventions → human → deployment → condition

<condition
    measure=string
  [ minValue=double ]
  [ maxValue=double ]
    initialState=boolean
  />

Documentation (element)

Conditions are evaluated for the whole population, not for individual age-groups or cohorts.

This affects all types of deployment.

Attributes

Measure

measure=string

The monitoring measure to test. Not all measures are available for use.

Minimum value

minValue=double

Minimum value. If specified, the measured variable must be greater than or equal to this value for the condition to be satisfied.

Maximum value

maxValue=double

Maximum value. If specified, the measured variable must be less than or equal to this value for the condition to be satisfied.

Initial state

initialState=boolean

Whether this condition is considered true or false before updated by a survey.

Age-based (continuous) deployment

→ scenario → interventions → human → deployment → continuous

<continuous>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| ( <deploy ... /> )+
</continuous>

Documentation (element)

List of ages at which deployment takes place (through EPI, post-natal and school-based programmes, etc.).

A sub-population restriction may be added as a property of the list of continuous deployments.

restrictToSubPop

→ scenario → interventions → human → deployment → continuous → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

deploy

→ scenario → interventions → human → deployment → continuous → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    targetAgeYrs=double
  [ begin=string ]
  [ end=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention. Input is rounded to the nearest time step.

First time active

begin=string

Units: User defined (defauls to steps)

End step

end=string

Units: User defined (defauls to steps)

Mass (timed) deployment

→ scenario → interventions → human → deployment → timed

<timed>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| [ <cumulativeCoverage ... /> ]
| ( <deploy ... /> )+
</timed>

Documentation (element)

List of timed deployments of the intervention (that is, of deployment campaigns).

Cumulative deployment mode can be specified for all deployments in a timed list. To allow multiple cumulative deployment descriptions, the entire timed list may be repeated.

restrictToSubPop

→ scenario → interventions → human → deployment → timed → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

Cumulative coverage

→ scenario → interventions → human → deployment → timed → cumulativeCoverage

<cumulativeCoverage
    component=string
  />

Documentation (element)

Attributes

Component identifier

component=string

The identifier (short name) of the component used when selecting people.

deploy

→ scenario → interventions → human → deployment → timed → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    time=string
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ repeatStep=string ]
  [ repeatEnd=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Time

time=string

Units: User defined (defauls to steps) Min: 0

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0

Maximum age of eligible individuals (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible individuals (defaults to 0). Input is rounded to the nearest time step.

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Description of health system.

Documentation (type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("forced" or "dynamic")
  [ scaledAnnualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Description of entomological data

Attributes

Entomology dataset name

name=string

Name of entomology data

Transmission model mode

mode=("forced" or "dynamic")

Override annual EIR

scaledAnnualEIR=double

Units: Infectious bites per adult per year

If set, the annual EIR (for all species of vector) is scaled to this level; can be omitted if not needed.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters of the transmission model

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <seasonality ... /> 
|   <mosq ... /> 
| [ <lifeCycle ... /> ]
| [ <simpleMPD ... /> ]
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial estimate of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial estimate of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial estimate of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Seasonality of transmission

→ scenario → entomology → vector → anopheles → seasonality

<seasonality
    input=("EIR")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <fourierSeries ... /> 
| |   <monthlyValues ... /> 
| |   <dailyValues ... /> 
</seasonality>

Documentation (element)

Specifies the seasonality of transmission and optionally the level of annual transmission.

Attributes

Seasonality input

input=("EIR")

Annual EIR

annualEIR=double

Units: Inoculations per adult per annum Min: 0

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries

<fourierSeries
    EIRRotateAngle=double
  >
IN THIS ORDER:
| ( <coeffic ... /> )*
</fourierSeries>

coeffic

Documentation (element)

Units: Infectious bites per adult per day

Attributes

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: Radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Pair of Fourier coefficients

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries → coeffic

<coeffic
    a=double
    b=double
  />

Documentation (element)

A pair of Fourier series coefficients. The first element specifies a1 and b1, the second a2 and b2, etc. Any number (from 0 up) of pairs may be given.

Attributes

a_n parameter of Fourier approximation to ln(EIR)

a=double

a_n parameter of Fourier approximation to ln(EIR) for some natural number n.

b_n parameter of Fourier approximation to ln(EIR)

b=double

b_n parameter of Fourier approximation to ln(EIR) for some natural number n.

List of monthly values

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues

<monthlyValues
    smoothing=("none" or "fourier")
  >
IN THIS ORDER:
| ( <value ... /> ){12,12}
</monthlyValues>

value

Documentation (element)

Description of seasonality from monthly values. Multiple smoothing methods are possible (see smoothing attribute).

List should contain twelve entries: January to December.

Attributes

Smoothing function

smoothing=("none" or "fourier")

How the monthly values are converted into a daily sequence of values:

none: no smoothing (step function)
Fourier: a Fourier series (with terms up to a2/b2) is fit to the sequence of monthly values and used to generate a smoothed list of daily values.

Monthly value

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Monthly value

List of daily values

→ scenario → entomology → vector → anopheles → seasonality → dailyValues

<dailyValues>
IN THIS ORDER:
| ( <value ... /> ){365,365}
</dailyValues>

value

Documentation (element)

Description of seasonality from daily values.

List should contain 365 entries: 1st January to 31st December.

Daily value

→ scenario → entomology → vector → anopheles → seasonality → dailyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Daily value

Mosquito feeding cycle parameters

→ scenario → entomology → vector → anopheles → mosq

<mosq
    minInfectedThreshold=double
  >
IN ANY ORDER:
|   <mosqRestDuration ... /> 
|   <extrinsicIncubationPeriod ... /> 
|   <mosqLaidEggsSameDayProportion ... /> 
|   <mosqSeekingDuration ... /> 
|   <mosqSurvivalFeedingCycleProbability ... /> 
|   <availabilityVariance ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <mosqProbOvipositing ... /> 
|   <mosqHumanBloodIndex ... /> 
</mosq>

Documentation (element)

Parameters describing the feeding cycle and human mosquito interaction of a single species of anopheles mosquito.

Attributes

Mininum infected threshold for mosquitos

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

Duration of the resting period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqRestDuration

<mosqRestDuration
    value=int
  />

Documentation (element)

Units: Days

name:Duration of the resting period of the vector (days);

Attributes

Input parameter value

value=int

An integer value.

Extrinsic incubation period

→ scenario → entomology → vector → anopheles → mosq → extrinsicIncubationPeriod

<extrinsicIncubationPeriod
    value=int
  />

Documentation (element)

Units: Days

name:Extrinsic incubation period (days)

Attributes

Input parameter value

value=int

An integer value.

Proportion of mosquitoes host seeking on same day as ovipositing

→ scenario → entomology → vector → anopheles → mosq → mosqLaidEggsSameDayProportion

<mosqLaidEggsSameDayProportion
    value=double
  />

Documentation (element)

Units: Proportion

Proportion of mosquitoes host seeking on same day as ovipositing

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Duration of the host-seeking period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqSeekingDuration

<mosqSeekingDuration
    value=double
  />

Documentation (element)

Units: Days

Duration of the host-seeking period of the vector (days)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito survives the feeding cycle

→ scenario → entomology → vector → anopheles → mosq → mosqSurvivalFeedingCycleProbability

<mosqSurvivalFeedingCycleProbability
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito survives the feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Variance in human availability rate

→ scenario → entomology → vector → anopheles → mosq → availabilityVariance

<availabilityVariance
    value=double
  />

Documentation (element)

Variance in availability rate of humans to mosquitoes. The mean rate is calculated based on other parameters.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito succesfully bites chosen host

→ scenario → entomology → vector → anopheles → mosq → mosqProbBiting

<mosqProbBiting
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito succesfully bites chosen host

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → mosq → mosqProbFindRestSite

<mosqProbFindRestSite
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito escapes host and finds a resting place after biting

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → mosq → mosqProbResting

<mosqProbResting
    mean=double
    variance=double
  />

Documentation (element)

Probability of mosquito successfully resting after finding a resting site

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of a mosquito successfully laying eggs given that it has rested

→ scenario → entomology → vector → anopheles → mosq → mosqProbOvipositing

<mosqProbOvipositing
    value=double
  />

Documentation (element)

Probability of a mosquito successfully laying eggs given that it has rested

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human blood index

→ scenario → entomology → vector → anopheles → mosq → mosqHumanBloodIndex

<mosqHumanBloodIndex
    value=double
  />

Documentation (element)

Units: Proportion

The proportion of resting mosquitoes which fed on human blood during the last feed.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mosquito life cycle parameters

→ scenario → entomology → vector → anopheles → lifeCycle

<lifeCycle
  [ estimatedLarvalResources=double ] DEFAULT VALUE 1e8
  >
IN ANY ORDER:
|   <eggStage ... /> 
|   <larvalStage ... /> 
|   <pupalStage ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</lifeCycle>

Documentation (element)

Parameters describing the life-cycle of this species of mosquito

Attributes

Estimate of larval resources

estimatedLarvalResources=double

Units: X

Default value: 1e8

Egg stage

→ scenario → entomology → vector → anopheles → lifeCycle → eggStage

<eggStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the egg stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

larvalStage

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage

<larvalStage>
</larvalStage>

daily

Documentation (type)

Parameters for the larval stage of development

Documentation (base type)

Parameters associated with a mosquito development stage.

Daily development

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage → daily

<daily
    resourceUsage=double
    effectCompetition=double
  />

Documentation (element)

Attributes

Resource usage

resourceUsage=double

Units: X

Resource usage during larval stage of development. Units are arbitrary.

Effect of competition

effectCompetition=double

Units: none

Effect of competition over resources on development.

Pupal stage

→ scenario → entomology → vector → anopheles → lifeCycle → pupalStage

<pupalStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the pupal stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → lifeCycle → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Simple Mosq-Pop-Dynamics parameters

→ scenario → entomology → vector → anopheles → simpleMPD

<simpleMPD>
IN ANY ORDER:
|   <developmentDuration ... /> 
|   <developmentSurvival ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</simpleMPD>

Documentation (element)

Parameters describing the simple mosquito population dynamics model.

This is a simpler version of the life-cycle model, requiring less parameters and with much simpler initialisation.

Duration

→ scenario → entomology → vector → anopheles → simpleMPD → developmentDuration

<developmentDuration
    value=int
  />

Documentation (element)

Units: Days Min: 1

Duration from egg laying to emergence in days.

Attributes

Input parameter value

value=int

An integer value.

Probability of survival

→ scenario → entomology → vector → anopheles → simpleMPD → developmentSurvival

<developmentSurvival
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that mosquito survives from the egg being laid to emergence, given no resouce limitations (no density constraints).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → simpleMPD → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Alternative (non-human) host paramters

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN ANY ORDER:
|   <mosqRelativeEntoAvailability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
</nonHumanHosts>

Documentation (element)

Min: 0

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of non-human host (ξ_i)

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqRelativeEntoAvailability

<mosqRelativeEntoAvailability
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of the population of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Name of this species of non human hosts (must match up with those described per anopheles section).

Population size of non-human host species

number=double

Units: Animals

Parasite genetics

<parasiteGenetics
    samplingMode=("initial" or "tracking")
  >
IN THIS ORDER:
| ( <locus ... /> )+
</parasiteGenetics>

locus

Documentation (element)

A specification of genotypes of infection parasites.

May be omitted; in this case there is no modelling of genetic differences of infections (resistance, fitness).

Attributes

samplingMode

samplingMode=("initial" or "tracking")

Locus

→ scenario → parasiteGenetics → locus

<locus
    name=string
  >
IN THIS ORDER:
| ( <allele ... /> )+
</locus>

allele

Documentation (element)

Alleles at loci can affect fitness and resistance to any number of drugs.

Attributes

Name of locus

name=string

Name of the Locus

Allele

→ scenario → parasiteGenetics → locus → allele

<allele
    name=string
    initialFrequency=double
    fitness=double
  />

Documentation (element)

Describes an allele, or one possible genetic option of multiple at one point of variance.

Attributes

Name

name=string

Name of the allele; used to refer to it elsewhere.

Initial frequency

initialFrequency=double

Fitness factor

fitness=double

Drug parameters (PK, PD and usage)

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
|   <treatments ... /> 
|   <drugs ... /> 
</pharmacology>

Documentation (element)

Drug model parameters and drug usage parameters

Documentation (type)

A library of drug related data for the PK/PD model.

Treatments library

→ scenario → pharmacology → treatments

<treatments>
IN THIS ORDER:
| ( <schedule ... /> )+
| ( <dosages ... /> )+
</treatments>

Documentation (element)

A library of drug deployment schedules and dosages.

schedule

→ scenario → pharmacology → treatments → schedule

<schedule
    name=string
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

A schedule for the administration of drugs in a course of treatment.

Note that dose sizes are multiplied by some multiplier (see dosages) and the times of all doses may be delayed.

Attributes

Name

name=string

Name for referring to this deployment schedule

medicate

→ scenario → pharmacology → treatments → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  />

Attributes

drug

drug=string

Abbreviated name of drug compound

Drug dose (mg with multiplier)

mg=double

Units: mg per something

Quantity of drug compound in mg per something. A separate dosage table must be used when medicating, which may specify multipliers of this number based on patient age or weight.

Time of administration

hour=double

Units: Hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

dosages

→ scenario → pharmacology → treatments → dosages

<dosages
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | ( <age ... /> )+
| | ( <bodymass ... /> )+
| |   <multiply ... /> 
</dosages>

Documentation (type)

A table for selecting a dose size. There are several ways this can work: using the patient's age or body mass in a look-up table to get a multplier, or directly using body mass as the multiplier.

The doses specified in "mg" in the treatment schedule are then multiplied by this multiplier.

Attributes

Name

name=string

Name for referring to this dosage table

Look-up table (age)

→ scenario → pharmacology → treatments → dosages → age

<age
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's age.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Look-up table (weight)

→ scenario → pharmacology → treatments → dosages → bodymass

<bodymass
    lowerbound=double
    dose_mult=double
  />

Documentation (element)

Select dose multiplier from a look-up table using the patient's body mass.

Documentation (type)

A look-up table which uses patient age (in years) or weight (in kg) to find a multiplier.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years or kg Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in "mg") is multiplied by this value for patients falling into this range when this dosage table is used.

Multiply dose

→ scenario → pharmacology → treatments → dosages → multiply

<multiply
    by=("kg")
  />

Documentation (element)

Multiply the dose by some quantity, such as patient weight.

Attributes

By what?

by=("kg")

Quantity to multiply the dose by. Only option is "kg" (patient weight in kg).

Drug library

→ scenario → pharmacology → drugs

<drugs>
IN THIS ORDER:
| ( <drug ... /> )+
</drugs>

drug

Documentation (element)

A library of drug PK/PD data.

drug

→ scenario → pharmacology → drugs → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (type)

A drug description with PK/PD parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drugs → drug → PD

<PD
  [ locus=string ]
  >
IN THIS ORDER:
| ( <phenotype ... /> )+
</PD>

phenotype

Attributes

Locus

locus=string

PD parameters for some allele / resistance phenotype

→ scenario → pharmacology → drugs → drug → PD → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

Restrict phenotype applicability to certain alleles

→ scenario → pharmacology → drugs → drug → PD → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (element)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Maximal parasite killing rate

→ scenario → pharmacology → drugs → drug → PD → phenotype → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drugs → drug → PD → phenotype → IC50

<IC50
  [ sigma=double ] DEFAULT VALUE 0
  >
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Attributes

Sigma parameter for per-infection variation of IC50

sigma=double

Default value: 0

Distribution parameter describing per-infection variation of IC50. If zero or not specified, the IC50 is not sampled. See documentation of parent element.

Slope of effect curve

→ scenario → pharmacology → drugs → drug → PD → phenotype → slope

<slope>
    double
</slope>

Documentation (element)

Units: dimensionless

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drugs → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
| EXACTLY ONE OF:
| |   <half_life ... /> 
| | IN THIS ORDER:
| | |   <k ... /> 
| | |   <m_exponent ... /> 
| [ <k_a ... /> ]
| [ <conversion ... /> ]
|   <vol_dist ... /> 
| [ <compartment2 ... /> ]
| [ <compartment3 ... /> ]
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drugs → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drugs → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate λ, calculated as λ = ln(2) / half_life. The basic form of decay is C(t) = C0 * exp(-λ*t).

Alternatively, elimination rate can be specified via k and m_exponent.

Constant associated with elimination rate (k)

→ scenario → pharmacology → drugs → drug → PK → k

<k
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

If sigma > 0, k is sampled per-human from the log-normal distribution: ln N( ln(mean) - σ^2 / 2, σ^2).

Alternatively, elimination rate can be specified via half_life.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Constant associated with elimination rate (m_exponent)

→ scenario → pharmacology → drugs → drug → PK → m_exponent

<m_exponent>
    double
</m_exponent>

Documentation (element)

Units: day^-1 Min: 0

Alternatively, elimination rate can be specified via half_life.

Note that in the case of a conversion model, this applies to both the elimination and the conversion rates.

Absorption rate constant (k_a)

→ scenario → pharmacology → drugs → drug → PK → k_a

<k_a
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Min: 0

Absorption rate parameter. Not allowed for one compartment models, but required for two and three compartment models and one compartment with conversion model (for the parent drug only).

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Conversion parameters (parent drug)

→ scenario → pharmacology → drugs → drug → PK → conversion

<conversion>
IN ANY ORDER:
|   <metabolite ... /> 
|   <rate ... /> 
|   <molRatio ... /> 
</conversion>

Documentation (element)

Configures the parent drug in a conversion model.

To use a conversion model, the parent drug should have this section defined as well as half-life or k (direct elimination; this may be zero) and k_a (absorption rate; this may be large).

Metabolite drug (abbreviation)

→ scenario → pharmacology → drugs → drug → PK → conversion → metabolite

<metabolite>
    string
</metabolite>

Documentation (element)

The abbreviation of the metabolite drug (e.g. "DHA" or "DHA_AR").

Rate of conversion

→ scenario → pharmacology → drugs → drug → PK → conversion → rate

<rate
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Rate of conversion of parent drug to metabolite.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Molecular weight ratio

→ scenario → pharmacology → drugs → drug → PK → conversion → molRatio

<molRatio>
    double
</molRatio>

Documentation (element)

Ratio of molecular weights: molecular weight of the metabolite divided by molecular weight of the parent.

Volume of Distribution (Vd)

→ scenario → pharmacology → drugs → drug → PK → vol_dist

<vol_dist
  [ sigma=double ] DEFAULT VALUE 0
  >
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Attributes

Sigma parameter for per-human variation of Vd

sigma=double

Default value: 0

Distribution parameter describing per-human variation of volume of distribution. If zero or not specified, the parameter is not sampled. See documentation of parent element.

Second compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment2

<compartment2>
IN ANY ORDER:
|   <a12 ... /> 
|   <a21 ... /> 
</compartment2>

Documentation (element)

Optional element specifying conversion parameters to- and from- a second compartment.

Absorption rate to compartment 2 (a12)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → a12

<a12
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the first periphery compartment (2). The parameter k12 = a12 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Absorption rate from compartment 2 (a21)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → a21

<a21
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the first periphery compartment (2) to the central compartment. The parameter k21 = a21 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Third compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment3

<compartment3>
IN ANY ORDER:
|   <a13 ... /> 
|   <a31 ... /> 
</compartment3>

Documentation (element)

Optional element specifying conversion parameters to- and from- a third compartment.

Absorption rate to compartment 3 (a13)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → a13

<a13
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the second periphery compartment (3). The parameter k13 = a13 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Absorption rate from compartment 3 (a31)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → a31

<a31
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the second periphery compartment (3) to the central compartment. The parameter k31 = a31 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Diagnostic parameters

→ scenario → diagnostics

<diagnostics>
IN THIS ORDER:
| ( <diagnostic ... /> )*
</diagnostics>

diagnostic

Documentation (element)

Diagnostic model parameters

diagnostic

→ scenario → diagnostics → diagnostic

<diagnostic
    name=string
  [ units=("Other" or "Garki" or "Malariatherapy") ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterministic ... /> 
| |   <stochastic ... /> 
</diagnostic>

Attributes

Name of diagnostic

name=string

Name of this diagnostic (parameterisation). May be used elsewhere in the XML document to refer to this set of diagnostic parameters.

Parasite density units / methodology

units=("Other" or "Garki" or "Malariatherapy")

Deterministic detection

→ scenario → diagnostics → diagnostic → deterministic

<deterministic
    minDensity=double
  />

Documentation (element)

Specify that an artificial deterministic test is used: outcome is positive if parasite density is at least the minimum given.

Attributes

Minimum detectible density

minDensity=double

Units: parasites/microlitre Min: 0

The minimum density at which parasites can be detected. If 0, the test outcome is always positive.

Non-deterministic detection

→ scenario → diagnostics → diagnostic → stochastic

<stochastic
    dens_50=double
    specificity=double
  />

Documentation (element)

An improved model of detection which is non-deterministic, including false positive results as well as false negatives.

Some parameterisations:

Microscopy sensitivity/specificity data in Africa; Source: expert opinion — Allan Schapira dens_50 = 20.0 specificity = .75

RDT sensitivity/specificity for Plasmodium falciparum in Africa Source: Murray et al (Clinical Microbiological Reviews, Jan. 2008) dens_50 = 50.0; specificity = .942;

Attributes

Density 50

dens_50=double

Units: parasites/microlitre Min: 0

The density at which the test outcome has a 50% chance of being positive.

Specificity

specificity=double

Units: Dimensionless Min: 0 Max: 1

The probability of a positive test outcome in the absense of parasites.

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
| [ <vivax ... /> ]
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: model/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=string
  >
IN ANY ORDER:
| [ <NeonatalMortality ... /> ]
| [ <NonMalariaFevers ... /> ]
</clinical>

Documentation (type)

Attributes

Follow-up period during which recurrence is considered a treatment failure

healthSystemMemory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

Neonatal mortality parameters

→ scenario → model → clinical → NeonatalMortality

<NeonatalMortality
    diagnostic=string
  />

Attributes

Diagnostic used to parameterise model

diagnostic=string

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
| [ <prNeedTreatmentNMF ... /> ]
| [ <prNeedTreatmentMF ... /> ]
</NonMalariaFevers>

Documentation (type)

Description of the incidence of non-malaria fever. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a non-malarial fever requires treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

Availability of humans to mosquitoes relative to an adult, categorized by age group

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ]
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

Vivax model parameters

→ scenario → model → vivax

<vivax>
IN ANY ORDER:
|   <probBloodStageInfectiousToMosq ... /> 
|   <hypnozoiteRelease ... /> 
|   <bloodStageProtectionLatency ... /> 
|   <bloodStageLengthDays ... /> 
|   <clinicalEvents ... /> 
</vivax>

Documentation (element)

This describes Vivax model parameters, and is required when using the VIVAX_SIMPLE_MODEL model option.

Probability of mosquito infection

→ scenario → model → vivax → probBloodStageInfectiousToMosq

<probBloodStageInfectiousToMosq
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

The chance of a feeding mosquito becoming infected, given that the host is patent. (This may be adjusted by transmission-blocking vaccines.)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Hypnozoite releases

→ scenario → model → vivax → hypnozoiteRelease

<hypnozoiteRelease
  [ pSecondRelease=double ] DEFAULT VALUE 0
  >
IN ANY ORDER:
|   <numberHypnozoites ... /> 
|   <firstRelease ... /> 
| [ <secondRelease ... /> ]
</hypnozoiteRelease>

Documentation (element)

Describes the number and times of hypnozoite releases.

Documentation (type)

This element defines probabilites when and how many hypnozoites are released from the liverstage into the blood.

The gap between the start of a new brood of hypnozoites and its release are defined as follows:

latentP + latentRelapseDays + randomReleaseDelay

randomReleaseDelay is based on one or two lognormal distributions, which are defined in firstRelease and optionally secondRelease.

You can define 2 release distributions, which get added together and represent the probability of hypnozoites which get released before winter (first release) or after (second release).

You can omit the secondRelease element if no release to the blood happens after winter.

Attributes

latent relapse days

pSecondRelease=double

Default value: 0

Probability of a second release. If undefined it is zero.

Number of Hypnozoites

→ scenario → model → vivax → hypnozoiteRelease → numberHypnozoites

<numberHypnozoites
    max=int
    base=double
  />

Documentation (element)

numberHypnozoites calculates the number of hypnozoites in the liver stage based on a base which is between 0 and 1.

This number is random based on the following distribution and normalized:

max ∑ (base ^ n) n = 0

Attributes

max

max=int

base

base=double

firstRelease

→ scenario → model → vivax → hypnozoiteRelease → firstRelease

<firstRelease
    mu=double
    sigma=double
    latentRelapseDays=int
  />

Documentation (base type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

latent relapse days

latentRelapseDays=int

Usually 15 days or 10 days (3 or 2 5-day timesteps).

secondRelease

→ scenario → model → vivax → hypnozoiteRelease → secondRelease

<secondRelease
    mu=double
    sigma=double
    latentRelapseDays=int
  />

Documentation (base type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

latent relapse days

latentRelapseDays=int

Usually 15 days or 10 days (3 or 2 5-day timesteps).

Blood stage protection latency

→ scenario → model → vivax → bloodStageProtectionLatency

<bloodStageProtectionLatency
    value=double
  />

Documentation (element)

Min: 0

The length of time after expiry of a blood-stage infection during which relapses from the same brood are supressed by the immune system.

This is rounded to the nearest time-step.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Blood stage length

→ scenario → model → vivax → bloodStageLengthDays

<bloodStageLengthDays
    weibullScale=double
    weibullShape=double
  />

Documentation (element)

Units: Days

Parameters used to sample the length of blood-stage infections from a Weibull distribution (scale parameter lambda, shape parameter k).

Attributes

weibullScale

weibullScale=double

weibullShape

weibullShape=double

clinicalEvents

→ scenario → model → vivax → clinicalEvents

<clinicalEvents>
IN THIS ORDER:
|   <pPrimaryInfection ... /> 
|   <pRelapseOne ... /> 
|   <pRelapseTwoPlus ... /> 
|   <pEventIsSevere ... /> 
</clinicalEvents>

Documentation (type)

This elements holds all information about probabilites for clinical events from infections and relapses.

pPrimaryInfection

→ scenario → model → vivax → clinicalEvents → pPrimaryInfection

<pPrimaryInfection
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseOne

→ scenario → model → vivax → clinicalEvents → pRelapseOne

<pRelapseOne
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseTwoPlus

→ scenario → model → vivax → clinicalEvents → pRelapseTwoPlus

<pRelapseTwoPlus
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pEventIsSevere

→ scenario → model → vivax → clinicalEvents → pEventIsSevere

<pEventIsSevere
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=string
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=string

Units: User defined (default: steps) Min: 0 Max: 20

Pre-erythrocytic latent period Can be specified in steps (e.g. 3t) or days (e.g. 15d).

parameter

→ scenario → model → parameters → parameter

<parameter
  [ name=string ]
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 36 documentation

Generated from: scenario_36.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
  [ analysisNo=int ]
    name=string
  [ wuID=int ]
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:om="http://openmalaria.org/schema/scenario_36"
    xsi:schemaLocation="http://openmalaria.org/schema/scenario_36 scenario_36.xsd"
  >
IN ANY ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entomology ... /> 
| [ <parasiteGenetics ... /> ]
| [ <pharmacology ... /> ]
| [ <diagnostics ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Name of intervention

Work unit identifier

wuID=int

Units: Number

Work unit ID. Obselete and no longer required.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Description of demography

Attributes

Name of demography data

name=string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Years Min: 0 Max: 100

Maximum age of simulated humans in years

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

list of age groups included in demography

Documentation (type)

list of age groups included in demography or surveys

Attributes

Lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Units: Percentage Min: 0 Max: 100

Percentage of human population in age group

Upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ startDate=string ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
| [ <cohorts ... /> ]
</monitoring>

Documentation (element)

Description of surveys

Attributes

Name of monitoring settings

name=string

Name of monitoring settings

Start of monitoring

startDate=string

continuous

→ scenario → monitoring → continuous

<continuous
    period=string
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Delay between reports

period=string

Units: User defined (default: steps)

Delay between reports; typically one time step but can be greater. Can be specified in steps (e.g. 1t) or days (e.g. 5d).

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions
  [ onlyNewEpisode=boolean ] DEFAULT VALUE false
  >
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See model/mon/OutputMeasures.h for a list of supported outputs. Should also be on the wiki.

Attributes

Report only for new cases

onlyNewEpisode=boolean

Default value: false

option

→ scenario → monitoring → SurveyOptions → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  [ outputNumber=int ]
  [ byAge=boolean ]
  [ byCohort=boolean ]
  [ bySpecies=boolean ]
  [ byGenotype=boolean ]
  [ byDrugType=boolean ]
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Number identifying measure in output

outputNumber=int

Report by age category

byAge=boolean

Report by cohort

byCohort=boolean

Report by mosquito species

bySpecies=boolean

Report by parasite genotype

byGenotype=boolean

Report by drug type

byDrugType=boolean

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
  [ detectionLimit=double ]
  [ diagnostic=string ]
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/microlitre Min: 0

Deprecated: limit above which a human's infection is reported as patent. Alternative: do not specify this; instead specify "diagnostic".

Name of monitoring diagnostic

diagnostic=string

Name of a parameterised diagnostic to use in surveys (see scenario/diagnostics).

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime
  [ repeatStep=string ]
  [ repeatEnd=string ]
  [ reported=boolean ] DEFAULT VALUE true
  >
    string
</surveyTime>

Documentation (element)

Units: User defined (defaults to steps) Min: 0

The simulation ends immediately after the last survey is taken.

Attributes

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

reported

reported=boolean

Default value: true

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Cohorts

→ scenario → monitoring → cohorts

<cohorts>
IN THIS ORDER:
| ( <subPop ... /> )+
</cohorts>

subPop

Documentation (element)

Allows the configuration of multiple cohorts (output segregated according to membership within specific sub-populations).

If this element is omitted, monitoring surveys cover the entire simulated human population.

It does not affect the "continuous" outputs (these never take cohorts into account).

Sub-population

→ scenario → monitoring → cohorts → subPop

<subPop
    id=string
    number=integer
  />

Documentation (element)

In the output file, the output set is identified by multiplying this number by 1000 then adding it to the age group column.

Attributes

Sub-population identifier

id=string

Textual identifier for the sub-population (i.e. for an intervention component, since sub-populations are defined as the hosts an intervention component is deployed to).

Sub-population number

number=integer

Units: dimensionless Min: 1 Max: 2097152

Number identifying a sub-population; used to define identifiers of output sets. This number must be a power of 2 (i.e. 1, 2, 4, 8, ...). See documentation of subPop element.

Preventative interventions

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfections ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <vectorPop ... /> ]
| [ <vectorTrap ... /> ]
| [ <human ... /> ]
</interventions>

Documentation (element)

Attributes

Name of intervention set

name=string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeHS>

timedDeployment

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeHS → timedDeployment

<timedDeployment
    time=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timedDeployment>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</uncomplicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

multiple

→ scenario → interventions → human → component → decisionTree → multiple

<multiple
  [ name=string ]
  >
IN THIS ORDER:
| ( <caseType ... /> )*
| ( <diagnostic ... /> )*
| ( <random ... /> )*
| ( <age ... /> )*
| ( <treatPKPD ... /> )*
| [ <treatSimple ... /> ]
| ( <deploy ... /> )*
</multiple>

Documentation (type)

A special node allowing multiple sub-trees to be evaluated.

This is different from an ordinary decision tree node in that:

a) multiple types of child can occur simultaneously (e.g. multiple types of treatment or treatment plus a 'random' sub-tree)

b) the 'noTreatment' and 'treatFailure' nodes are not allowed

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → multiple → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

firstLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → firstLine

<firstLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</firstLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

secondLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → secondLine

<secondLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</secondLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

positive

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

outcome

→ scenario → interventions → human → component → decisionTree → multiple → random → outcome

<outcome
  [ name=string ]
    p=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</outcome>

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Probability

p=double

Units: None Min: 0 Max: 1

Probability of selecting this outcome. The sum of probabilities across all outcomes must be 1.

age

→ scenario → interventions → human → component → decisionTree → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Age range

→ scenario → interventions → human → component → decisionTree → multiple → age → age

<age
  [ name=string ]
    lb=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</age>

Documentation (element)

Describes a branch, selected for patients of a certain age.

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Lower bound (inclusive)

lb=double

Min: 0

noTreatment

→ scenario → interventions → human → component → decisionTree → noTreatment

<noTreatment
  [ name=string ]
  />

Documentation (type)

An end node doing nothing. This exists to explicitly state that no treatment happens and to prevent trees from accidentally being left incomplete.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatFailure

→ scenario → interventions → human → component → decisionTree → treatFailure

<treatFailure
  [ name=string ]
  />

Documentation (type)

An end node which reports treatment but does not change parasitalogical status. This allows correct labelling of second-line cases.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → multiple → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

age

→ scenario → interventions → human → component → decisionTree → multiple → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → multiple → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → multiple → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → multiple → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</complicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: Days Min: 0 Max: unbounded

Maximum number of timesteps (including first day of case) that an individual with an uncomplicated case of malaria will remember he/she was sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial or non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of a complicated or severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
  [ name=string ]
  [ useDiagnosticUC=boolean ] DEFAULT VALUE false
  >
IN ANY ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <treatmentActions ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
</ImmediateOutcomes>

Documentation (type)

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Name of case management parameterisation

name=string

Name of health system

useDiagnosticUC

useDiagnosticUC=boolean

Default value: false

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Description of drug regimen.

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Artemisinine based combination therapy

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Quinine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0 Max: 1name:P(self-treat)

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Effectiveness of treatment for non-compliant patients

treatmentActions

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions

<treatmentActions>
IN ANY ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
</treatmentActions>

CQ
SP
AQ
SPAQ
ACT
QN

CQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ

<CQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</CQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

deploy

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy

<deploy
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ p=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| ( <component ... /> )+
</deploy>

component

Attributes

Maximum age of eligible humans

maxAge=double

Units: Years Min: 0

Maximum age of eligible humans (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible humans

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible humans (defaults to 0). Input is rounded to the nearest time step.

Probability of delivery to eligible humans

p=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Probability of this list of components being deployed, given that other constraints are met.

component

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Prophylactic treatment

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere → clearInfections

<clearInfections
    timesteps=string
    stage=("liver" or "blood" or "both")
  />

Documentation (element)

Attributes

Length of effect

timesteps=string

Units: User defined (defaults to steps)

Target stage

stage=("liver" or "blood" or "both")

SP

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SP

<SP
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SP>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

AQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → AQ

<AQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</AQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

SPAQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SPAQ

<SPAQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SPAQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

ACT

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → ACT

<ACT
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</ACT>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

QN

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → QN

<QN
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</QN>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

Probability that human is incompatible with liver-stage drug treatment

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pHumanCannotReceive

<pHumanCannotReceive
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that a human is determined to be unable to receive liver-stage drug treatment. Treatment is neither reported or given for such humans.

This is sampled once per human at birth.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Ignore liver-stage drug treatment incompatibility

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → ignoreCannotReceive

<ignoreCannotReceive
    value=boolean
  />

Documentation (element)

If true, ignore pHumanCannotReceive and consider all humans eligible for treatment; if false (or not specified), do not treat those demed incompatible with liver-stage drug treatment.

The point of this is that pHumanCannotReceive cannot be altered by changeHS interventions, but this property can be.

Attributes

Input parameter value

value=boolean

A boolean value.

Prob use in UC case

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pUseUncomplicated

<pUseUncomplicated
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

This feature is deprecated; it is suggested to use the "simple treatment" feature configured to clear liver-stage parasites, leaving this option unset or zero.

Chance of liver-stage drug treatment being used for routine treatment of an uncomplicated case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Effectiveness

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → effectivenessOnUse

<effectivenessOnUse
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that liver-stage drug treatment is effective.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

DecisionTree5Day

<DecisionTree5Day
  [ name=string ]
  >
IN ANY ORDER:
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
|   <treeUCOfficial ... /> 
|   <treeUCSelfTreat ... /> 
|   <cureRateSevere ... /> 
|   <treatmentSevere ... /> 
</DecisionTree5Day>

Documentation (type)

Besides greater flexibility, this allows treatment via PK/PD models.

Attributes

Name of case management parameterisation

name=string

Name of health system

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → DecisionTree5Day → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → DecisionTree5Day → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

treeUCOfficial

→ scenario → healthSystem → DecisionTree5Day → treeUCOfficial

<treeUCOfficial
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCOfficial>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treeUCSelfTreat

→ scenario → healthSystem → DecisionTree5Day → treeUCSelfTreat

<treeUCSelfTreat
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCSelfTreat>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Cure rate (severe cases)

→ scenario → healthSystem → DecisionTree5Day → cureRateSevere

<cureRateSevere
    value=double
  />

Documentation (element)

Min: 0 Max: 1

The probability of clearing parasites given access to appropriate (hospital) care, for a severe case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

treatmentSevere

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere

<treatmentSevere
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</treatmentSevere>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Case fatality rate for inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: Dimensionless

List of age-specific probabilities of sequelae in inpatients, during a severe bout of malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeEIR>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeEIR → timedDeployment

<timedDeployment
    eipDuration=int
    time=string
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timedDeployment>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Time

time=string

Units: User defined (defauls to steps) Min: 0

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=string ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=string

Units: User defined (default: steps) Min: 0

Default value: 0

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=string
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time of start

time=string

Units: User defined (defauls to steps) Min: 0

Insert R_0 case

<insertR_0Case
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</insertR_0Case>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → insertR_0Case → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Uninfect vectors

<uninfectVectors
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</uninfectVectors>

timedDeployment

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → uninfectVectors → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Vector population intervention

→ scenario → interventions → vectorPop

<vectorPop>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorPop>

intervention

Documentation (element)

Units: List of elements

A list of parameterisations of generic vector host-inspecific interventions.

intervention

→ scenario → interventions → vectorPop → intervention

<intervention
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

Units: List of elements

An intervention which may have various effects on the vector populations as a whole. (Not host specific.)

Multiple instances of this intervention class are allowed (multiple parameterisations, not just deployments).

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → vectorPop → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → vectorPop → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <seekingDeathRateIncrease ... /> ]
| [ <probDeathOvipositing ... /> ]
| [ <emergenceReduction ... /> ]
</anopheles>

Documentation (type)

Units: dimensionless Min: 0 Max: 1

Descriptions of the effects of vector interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Proportional increase in deaths while host searching

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease

<seekingDeathRateIncrease
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</seekingDeathRateIncrease>

decay

Documentation (element)

Units: dimensionless

Describe an effect on the increase in the death rate while host seeking (mu_vA) due to this intervention.

Enter the rate increase (i.e. if rate increases to 120% of normal, give 0.2). New death rate while seeking is old × (1 + increase) where increase is this factor given. Must have increas ≥ -1.

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Proportion ovipositing mosquitoes killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing

<probDeathOvipositing
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probDeathOvipositing>

decay

Documentation (element)

Units: dimensionless

Describe an effect of increased mortality while ovipositing due to this intervention. Enter the probability of dying due to this intervention.

Attributes

Initial probability of killing

initial=double

Units: dimensionless Min: 0 Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Proportion of emerging pupa killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction

<emergenceReduction
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</emergenceReduction>

decay

Documentation (element)

Units: dimensionless

Describe an effect on emergence of pupa into adults: this value is the proportion of emerging pupa which are killed by this intervention.

Attributes

Initial proportion reduction

initial=double

Units: dimensionless Min: -inf Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Vector population intervention deployment

→ scenario → interventions → vectorPop → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

deploy

→ scenario → interventions → vectorPop → intervention → timed → deploy

<deploy
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Baited trap

→ scenario → interventions → vectorTrap

<vectorTrap>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorTrap>

intervention

Documentation (element)

intervention

→ scenario → interventions → vectorTrap → intervention

<intervention
  [ name=string ]
  >
IN THIS ORDER:
| ( <description ... /> )+
| [ <timed ... /> ]
</intervention>

Documentation (type)

Attributes

Descriptive name for type of trap

name=string

Optional name for this type of trap

Description

→ scenario → interventions → vectorTrap → intervention → description

<description
    mosquito=string
  >
IN THIS ORDER:
|   <relativeAvailability ... /> 
|   <decayOfAvailability ... /> 
</description>

Documentation (element)

Parameters associated with a vector trap intervention, per mosquito species.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Initial relative availability

→ scenario → interventions → vectorTrap → intervention → description → relativeAvailability

<relativeAvailability
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: inf

Describes the availiability of a trap to a host-seeking mosquito relative to an average unprotected adult.

I.e. if this parameter is 2, then each trap will on average attract twice as many mosquitoes as unprotected adults.

This is the initial availability; it may decay towards zero depending on the configured decay function.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay of availability

→ scenario → interventions → vectorTrap → intervention → description → decayOfAvailability

<decayOfAvailability
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Describes how availability decays to zero.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Vector trap intervention deployment

→ scenario → interventions → vectorTrap → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )*
</timed>

deploy

Documentation (element)

List of timed vector trap intervention deployment

deploy

→ scenario → interventions → vectorTrap → intervention → timed → deploy

<deploy
    time=string
    ratioToHumans=double
    lifespan=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Ratio to humans

ratioToHumans=double

Min: 0 Max: inf

The number of traps deployed, by this deployment, per adult human. E.g. if there are currently 100 traps and 1000 humans, then a ratio of 0.1 will increase the number of traps to 200.

Lifespan

lifespan=string

Units: Steps or Days or Years

Human-specific interventions

→ scenario → interventions → human

<human>
IN THIS ORDER:
| ( <component ... /> )+
| ( <deployment ... /> )*
</human>

Documentation (element)

Encapsulates all interventions whose effects are specific to the human host: any interventions where target humans may be selected via population-coverage, age limits and sub-population membership.

Component

→ scenario → interventions → human → component

<component
    id=string
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <screen ... /> 
| |   <treatSimple ... /> 
| |   <treatPKPD ... /> 
| |   <decisionTree ... /> 
| |   <PEV ... /> 
| |   <BSV ... /> 
| |   <TBV ... /> 
| |   <ITN ... /> 
| |   <IRS ... /> 
| |   <GVI ... /> 
| | [ <recruitmentOnly ... /> ]
| |   <clearImmunity ... /> 
| [ <subPopRemoval ... /> ]
</component>

Documentation (element)

Each element describes one component: its effects, decay of the(se) effect(s), and related stuff (e.g. description of indirect decay and of usage levels).

Attributes

Component identifier

id=string

Name of component

name=string

An informal name/description for the component

screen

→ scenario → interventions → human → component → screen

<screen
    diagnostic=string
  >
IN THIS ORDER:
| ( <positive ... /> )*
| ( <negative ... /> )*
</screen>

Documentation (type)

This can be combined with MDA to achieve mass screen and treat (MSAT) or other types of mass screening intervention.

The use of the screening itself is reported (if enabled), but not the outcome. Deployment of interventions triggered by the screening may be reported, however.

Attributes

Name of diagnostic

diagnostic=string

Name of a parameterised diagnostic (see scenario/diagnostics).

positive

→ scenario → interventions → human → component → screen → positive

<positive
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → screen → negative

<negative
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

treatSimple

→ scenario → interventions → human → component → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

treatPKPD

→ scenario → interventions → human → component → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

decisionTree

→ scenario → interventions → human → component → decisionTree

<decisionTree
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</decisionTree>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Vaccines

→ scenario → interventions → human → component → PEV

<PEV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</PEV>

Documentation (element)

Pre-erythrocytic vaccine (PEV): prevents a proportion of infections from commencing.

Documentation (type)

Description of a vaccine's effect

Decay of effect

→ scenario → interventions → human → component → PEV → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Specification of decay of efficacy. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Variance parameter for vaccine efficacy

→ scenario → interventions → human → component → PEV → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vaccines

→ scenario → interventions → human → component → BSV

<BSV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</BSV>

Documentation (element)

Blood-stage vaccine (BSV): acts as a killing factor on blood-stage parasites. Exact action depends on the within host model.

Documentation (type)

Description of a vaccine's effect

Vaccines

→ scenario → interventions → human → component → TBV

<TBV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</TBV>

Documentation (element)

Transmission-blocking vaccine (TBV): one minus this scales the probability of transmission to mosquitoes

Documentation (type)

Description of a vaccine's effect

Bed nets

→ scenario → interventions → human → component → ITN

<ITN>
IN THIS ORDER:
| [ <usage ... /> ]
|   <holeRate ... /> 
|   <ripRate ... /> 
|   <ripFactor ... /> 
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
|   <attritionOfNets ... /> 
| ( <anophelesParams ... /> )+
</ITN>

Documentation (element)

Description of bed-net interventions (ITNs, LLINs).

Proportion of time nets are used by humans

→ scenario → interventions → human → component → ITN → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of nets by humans, from 0 to 1.

At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing.

See also "propActing" (proportion of bits for which net acts).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Rate at which holes are made

→ scenario → interventions → human → component → ITN → holeRate

<holeRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Holes per annum Min: 0

The rate at which new holes are made in nets.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ ln N( log(mean)-sigma²/2, sigma² ).

Equivalent R sample: rlnorm(n, log(m) - s*s/2, s)

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rate at which holes are enlarged

→ scenario → interventions → human → component → ITN → ripRate

<ripRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Rips per existing hole per annum Min: 0

Each existing hole has a probability of being ripped bigger according to a Poisson process with this rate as (only) parameter.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ ln N( log(mean)-sigma²/2, sigma² ).

Equivalent R sample: rlnorm(n, log(m) - s*s/2, s)

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rip factor

→ scenario → interventions → human → component → ITN → ripFactor

<ripFactor
    value=double
  />

Documentation (element)

Units: none Min: 0

This factor expresses how important rips are in increasing the hole.

The hole index of a net is h + F×x where h and x are the total numbers of holes and rips respectively and F is the rip factor.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → ITN → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: mg/m² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → human → component → ITN → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of nets. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Attrition of nets

→ scenario → interventions → human → component → ITN → attritionOfNets

<attritionOfNets
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: dimensionless

Specifies the rate at which nets are disposed of over time. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Humans are removed from the intervention component's sub-population on disposal (attrition) of their nets. Currently this event is not reported.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → human → component → ITN → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterrency ... /> 
| |   <twoStageDeterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which net acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency

<twoStageDeterrency>
IN ANY ORDER:
|   <entering ... /> 
|   <attacking ... /> 
</twoStageDeterrency>

Documentation (element)

Units: dimensionless

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

This deterrency model multiplies human attractiveness by pEnt×pAtt divided by a base factor to normalise the output to 1 when there are no nets.

RA (entering)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → entering

<entering
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless

pEnt represents the relative probability of entering due to ITNs: pEnt = exp(log(P)×p) where P is the insecticide factor and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

RA (attacking)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attacking

<attacking
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless

pAtt represents the relative probability of attacking a human after entering a house due to ITNs (i.e. of feeding/dying vs. flying off): pAtt = B + H×h + P×p + I×h×p where B is the base (without net) probability; H, P and I are the hole, insecticide and interaction factors respectively, h=exp(-holeIndex×holeScalingFactor) and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Pre-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Indoor residual spraying

→ scenario → interventions → human → component → IRS

<IRS>
IN THIS ORDER:
| [ <usage ... /> ]
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
| ( <anophelesParams ... /> )+
</IRS>

Documentation (element)

Description of indoor residual spraying interventions.

Documentation (type)

Description of effect for the more complex and probably more realistic Briet model: IRS has three effects, whos strength is calculated as a function of surviving insecticide content.

Proportion of Indoor residual spraying (IRS) interventions

→ scenario → interventions → human → component → IRS → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Indoor residual spraying (IRS) interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → IRS → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: μg/cm² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → human → component → IRS → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → IRS → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → IRS → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied by exp(P×log(p)) where P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Generic vector intervention

→ scenario → interventions → human → component → GVI

<GVI>
IN THIS ORDER:
| [ <usage ... /> ]
|   <decay ... /> 
| ( <anophelesParams ... /> )+
</GVI>

Documentation (element)

Note that all actions of this intervention component will decay according to a single decay function. If independant decay is wanted, a separate component can be used for each action.

Proportion of generic vector interventions

→ scenario → interventions → human → component → GVI → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Generic vector interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay

→ scenario → interventions → human → component → GVI → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Description of decay of all intervention effects. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → GVI → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <deterrency ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → GVI → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied this factor times survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Recruitment only

→ scenario → interventions → human → component → recruitmentOnly

<recruitmentOnly/>

Documentation (element)

Recruitment of a host into a sub-population.

Clear Immunity

→ scenario → interventions → human → component → clearImmunity

<clearImmunity/>

Documentation (element)

Removes all exposure-related immunitsy gained over time by hosts without removing infections (or affecting the ability to gain immunity through exposure).

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

subPopRemoval

→ scenario → interventions → human → component → subPopRemoval

<subPopRemoval
  [ onFirstBout=boolean ] DEFAULT VALUE false
  [ onFirstTreatment=boolean ] DEFAULT VALUE false
  [ onFirstInfection=boolean ] DEFAULT VALUE false
  [ afterYears=double ]
  />

Documentation (type)

ITN attrition also removes humans from sub-populations.

Attributes

Time to first episode only

onFirstBout=boolean

Default value: false

Time to first treatment only

onFirstTreatment=boolean

Default value: false

Time to first infection only

onFirstInfection=boolean

Default value: false

Remove from sub-population after

afterYears=double

Units: Years Min: 0

Deployment

→ scenario → interventions → human → deployment

<deployment
  [ name=string ]
  >
IN THIS ORDER:
| ( <component ... /> )+
| ( <condition ... /> )*
| ( <continuous ... /> )*
| ( <timed ... /> )*
</deployment>

Documentation (element)

All components deployed by this intervention are deployed to the same people (each timed or continuous deployment selects recipients and then gives each recipient all components of the intervention).

Attributes

Intervention name

name=string

Name of intervention

component

→ scenario → interventions → human → deployment → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Condition

→ scenario → interventions → human → deployment → condition

<condition
    measure=string
  [ minValue=double ]
  [ maxValue=double ]
    initialState=boolean
  />

Documentation (element)

Conditions are evaluated for the whole population, not for individual age-groups or cohorts.

This affects all types of deployment.

Attributes

Measure

measure=string

The monitoring measure to test. Not all measures are available for use.

Minimum value

minValue=double

Minimum value. If specified, the measured variable must be greater than this value for the condition to be satisfied.

Maximum value

maxValue=double

Maximum value. If specified, the measured variable must be less than this value for the condition to be satisfied.

Initial state

initialState=boolean

Whether this condition is considered true or false before updated by a survey.

Age-based (continuous) deployment

→ scenario → interventions → human → deployment → continuous

<continuous>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| ( <deploy ... /> )+
</continuous>

Documentation (element)

List of ages at which deployment takes place (through EPI, post-natal and school-based programmes, etc.).

A sub-population restriction may be added as a property of the list of continuous deployments.

restrictToSubPop

→ scenario → interventions → human → deployment → continuous → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

deploy

→ scenario → interventions → human → deployment → continuous → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    targetAgeYrs=double
  [ begin=string ]
  [ end=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention. Input is rounded to the nearest time step.

First time active

begin=string

Units: User defined (defauls to steps)

End step

end=string

Units: User defined (defauls to steps)

Mass (timed) deployment

→ scenario → interventions → human → deployment → timed

<timed>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| [ <cumulativeCoverage ... /> ]
| ( <deploy ... /> )+
</timed>

Documentation (element)

List of timed deployments of the intervention (that is, of deployment campaigns).

Cumulative deployment mode can be specified for all deployments in a timed list. To allow multiple cumulative deployment descriptions, the entire timed list may be repeated.

restrictToSubPop

→ scenario → interventions → human → deployment → timed → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

Cumulative coverage

→ scenario → interventions → human → deployment → timed → cumulativeCoverage

<cumulativeCoverage
    component=string
  />

Documentation (element)

Attributes

Component identifier

component=string

The identifier (short name) of the component used when selecting people.

deploy

→ scenario → interventions → human → deployment → timed → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    time=string
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ repeatStep=string ]
  [ repeatEnd=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Time

time=string

Units: User defined (defauls to steps) Min: 0

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0

Maximum age of eligible individuals (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible individuals (defaults to 0). Input is rounded to the nearest time step.

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Description of health system.

Documentation (type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("forced" or "dynamic")
  [ scaledAnnualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Description of entomological data

Attributes

Entomology dataset name

name=string

Name of entomology data

Transmission model mode

mode=("forced" or "dynamic")

Override annual EIR

scaledAnnualEIR=double

Units: Infectious bites per adult per year

If set, the annual EIR (for all species of vector) is scaled to this level; can be omitted if not needed.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters of the transmission model

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <seasonality ... /> 
|   <mosq ... /> 
| [ <lifeCycle ... /> ]
| [ <simpleMPD ... /> ]
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial estimate of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial estimate of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial estimate of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Seasonality of transmission

→ scenario → entomology → vector → anopheles → seasonality

<seasonality
    input=("EIR")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <fourierSeries ... /> 
| |   <monthlyValues ... /> 
| |   <dailyValues ... /> 
</seasonality>

Documentation (element)

Specifies the seasonality of transmission and optionally the level of annual transmission.

Attributes

Seasonality input

input=("EIR")

Annual EIR

annualEIR=double

Units: Inoculations per adult per annum Min: 0

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries

<fourierSeries
    EIRRotateAngle=double
  >
IN THIS ORDER:
| ( <coeffic ... /> )*
</fourierSeries>

coeffic

Documentation (element)

Units: Infectious bites per adult per day

Attributes

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: Radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Pair of Fourier coefficients

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries → coeffic

<coeffic
    a=double
    b=double
  />

Documentation (element)

A pair of Fourier series coefficients. The first element specifies a1 and b1, the second a2 and b2, etc. Any number (from 0 up) of pairs may be given.

Attributes

a_n parameter of Fourier approximation to ln(EIR)

a=double

a_n parameter of Fourier approximation to ln(EIR) for some natural number n.

b_n parameter of Fourier approximation to ln(EIR)

b=double

b_n parameter of Fourier approximation to ln(EIR) for some natural number n.

List of monthly values

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues

<monthlyValues
    smoothing=("none" or "fourier")
  >
IN THIS ORDER:
| ( <value ... /> ){12,12}
</monthlyValues>

value

Documentation (element)

Description of seasonality from monthly values. Multiple smoothing methods are possible (see smoothing attribute).

List should contain twelve entries: January to December.

Attributes

Smoothing function

smoothing=("none" or "fourier")

How the monthly values are converted into a daily sequence of values:

none: no smoothing (step function)
Fourier: a Fourier series (with terms up to a2/b2) is fit to the sequence of monthly values and used to generate a smoothed list of daily values.

Monthly value

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Monthly value

List of daily values

→ scenario → entomology → vector → anopheles → seasonality → dailyValues

<dailyValues>
IN THIS ORDER:
| ( <value ... /> ){365,365}
</dailyValues>

value

Documentation (element)

Description of seasonality from daily values.

List should contain 365 entries: 1st January to 31st December.

Daily value

→ scenario → entomology → vector → anopheles → seasonality → dailyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Daily value

Mosquito feeding cycle parameters

→ scenario → entomology → vector → anopheles → mosq

<mosq
    minInfectedThreshold=double
  >
IN ANY ORDER:
|   <mosqRestDuration ... /> 
|   <extrinsicIncubationPeriod ... /> 
|   <mosqLaidEggsSameDayProportion ... /> 
|   <mosqSeekingDuration ... /> 
|   <mosqSurvivalFeedingCycleProbability ... /> 
|   <availabilityVariance ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <mosqProbOvipositing ... /> 
|   <mosqHumanBloodIndex ... /> 
</mosq>

Documentation (element)

Parameters describing the feeding cycle and human mosquito interaction of a single species of anopheles mosquito.

Attributes

Mininum infected threshold for mosquitos

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

Duration of the resting period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqRestDuration

<mosqRestDuration
    value=int
  />

Documentation (element)

Units: Days

name:Duration of the resting period of the vector (days);

Attributes

Input parameter value

value=int

An integer value.

Extrinsic incubation period

→ scenario → entomology → vector → anopheles → mosq → extrinsicIncubationPeriod

<extrinsicIncubationPeriod
    value=int
  />

Documentation (element)

Units: Days

name:Extrinsic incubation period (days)

Attributes

Input parameter value

value=int

An integer value.

Proportion of mosquitoes host seeking on same day as ovipositing

→ scenario → entomology → vector → anopheles → mosq → mosqLaidEggsSameDayProportion

<mosqLaidEggsSameDayProportion
    value=double
  />

Documentation (element)

Units: Proportion

Proportion of mosquitoes host seeking on same day as ovipositing

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Duration of the host-seeking period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqSeekingDuration

<mosqSeekingDuration
    value=double
  />

Documentation (element)

Units: Days

Duration of the host-seeking period of the vector (days)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito survives the feeding cycle

→ scenario → entomology → vector → anopheles → mosq → mosqSurvivalFeedingCycleProbability

<mosqSurvivalFeedingCycleProbability
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito survives the feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Variance in human availability rate

→ scenario → entomology → vector → anopheles → mosq → availabilityVariance

<availabilityVariance
    value=double
  />

Documentation (element)

Variance in availability rate of humans to mosquitoes. The mean rate is calculated based on other parameters.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito succesfully bites chosen host

→ scenario → entomology → vector → anopheles → mosq → mosqProbBiting

<mosqProbBiting
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito succesfully bites chosen host

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → mosq → mosqProbFindRestSite

<mosqProbFindRestSite
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito escapes host and finds a resting place after biting

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → mosq → mosqProbResting

<mosqProbResting
    mean=double
    variance=double
  />

Documentation (element)

Probability of mosquito successfully resting after finding a resting site

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of a mosquito successfully laying eggs given that it has rested

→ scenario → entomology → vector → anopheles → mosq → mosqProbOvipositing

<mosqProbOvipositing
    value=double
  />

Documentation (element)

Probability of a mosquito successfully laying eggs given that it has rested

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human blood index

→ scenario → entomology → vector → anopheles → mosq → mosqHumanBloodIndex

<mosqHumanBloodIndex
    value=double
  />

Documentation (element)

Units: Proportion

The proportion of resting mosquitoes which fed on human blood during the last feed.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mosquito life cycle parameters

→ scenario → entomology → vector → anopheles → lifeCycle

<lifeCycle
  [ estimatedLarvalResources=double ] DEFAULT VALUE 1e8
  >
IN ANY ORDER:
|   <eggStage ... /> 
|   <larvalStage ... /> 
|   <pupalStage ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</lifeCycle>

Documentation (element)

Parameters describing the life-cycle of this species of mosquito

Attributes

Estimate of larval resources

estimatedLarvalResources=double

Units: X

Default value: 1e8

Egg stage

→ scenario → entomology → vector → anopheles → lifeCycle → eggStage

<eggStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the egg stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

larvalStage

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage

<larvalStage>
</larvalStage>

daily

Documentation (type)

Parameters for the larval stage of development

Documentation (base type)

Parameters associated with a mosquito development stage.

Daily development

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage → daily

<daily
    resourceUsage=double
    effectCompetition=double
  />

Documentation (element)

Attributes

Resource usage

resourceUsage=double

Units: X

Resource usage during larval stage of development. Units are arbitrary.

Effect of competition

effectCompetition=double

Units: none

Effect of competition over resources on development.

Pupal stage

→ scenario → entomology → vector → anopheles → lifeCycle → pupalStage

<pupalStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the pupal stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → lifeCycle → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Simple Mosq-Pop-Dynamics parameters

→ scenario → entomology → vector → anopheles → simpleMPD

<simpleMPD>
IN ANY ORDER:
|   <developmentDuration ... /> 
|   <developmentSurvival ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</simpleMPD>

Documentation (element)

Parameters describing the simple mosquito population dynamics model.

This is a simpler version of the life-cycle model, requiring less parameters and with much simpler initialisation.

Duration

→ scenario → entomology → vector → anopheles → simpleMPD → developmentDuration

<developmentDuration
    value=int
  />

Documentation (element)

Units: Days Min: 1

Duration from egg laying to emergence in days.

Attributes

Input parameter value

value=int

An integer value.

Probability of survival

→ scenario → entomology → vector → anopheles → simpleMPD → developmentSurvival

<developmentSurvival
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that mosquito survives from the egg being laid to emergence, given no resouce limitations (no density constraints).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → simpleMPD → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Alternative (non-human) host paramters

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN ANY ORDER:
|   <mosqRelativeEntoAvailability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
</nonHumanHosts>

Documentation (element)

Min: 0

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of non-human host (ξ_i)

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqRelativeEntoAvailability

<mosqRelativeEntoAvailability
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Name of this species of non human hosts (must match up with those described per anopheles section).

Population size of alternative host species

number=double

Units: Number

Population size of this non-human host.

Parasite genetics

<parasiteGenetics
    samplingMode=("initial" or "tracking")
  >
IN THIS ORDER:
| ( <locus ... /> )+
</parasiteGenetics>

locus

Documentation (element)

A specification of genotypes of infection parasites.

May be omitted; in this case there is no modelling of genetic differences of infections (resistance, fitness).

Attributes

samplingMode

samplingMode=("initial" or "tracking")

Locus

→ scenario → parasiteGenetics → locus

<locus
    name=string
  >
IN THIS ORDER:
| ( <allele ... /> )+
</locus>

allele

Documentation (element)

Alleles at loci can affect fitness and resistance to any number of drugs.

Attributes

Name of locus

name=string

Name of the Locus

Allele

→ scenario → parasiteGenetics → locus → allele

<allele
    name=string
    initialFrequency=double
    fitness=double
  />

Documentation (element)

Describes an allele, or one possible genetic option of multiple at one point of variance.

Attributes

Name

name=string

Name of the allele; used to refer to it elsewhere.

Initial frequency

initialFrequency=double

Fitness factor

fitness=double

Drug parameters (PK, PD and usage)

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
|   <treatments ... /> 
|   <drugs ... /> 
</pharmacology>

Documentation (element)

Drug model parameters and drug usage parameters

Documentation (type)

A library of drug related data for the PK/PD model.

Treatments library

→ scenario → pharmacology → treatments

<treatments>
IN THIS ORDER:
| ( <schedule ... /> )+
| ( <dosages ... /> )+
</treatments>

Documentation (element)

A library of drug deployment schedules and dosages.

schedule

→ scenario → pharmacology → treatments → schedule

<schedule
    name=string
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

A schedule for the administration of drugs in a course of treatment.

Note that dose sizes are multiplied by some multiplier (see dosages) and the times of all doses may be delayed.

Attributes

Name

name=string

Name for referring to this deployment schedule

medicate

→ scenario → pharmacology → treatments → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  />

Attributes

drug

drug=string

Abbreviated name of drug compound

Drug dose (mg with multiplier)

mg=double

Units: mg per something

Quantity of drug compound in mg per something. A separate dosage table must be used when medicating, which may specify multipliers of this number based on patient age or weight.

Time of administration

hour=double

Units: Hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

dosages

→ scenario → pharmacology → treatments → dosages

<dosages
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | ( <age ... /> )+
| | ( <bodymass ... /> )+
| |   <multiply ... /> 
</dosages>

Documentation (type)

A table for selecting a dose size given an age.

Attributes

Name

name=string

Name for referring to this dosage table

age

→ scenario → pharmacology → treatments → dosages → age

<age
    lowerbound=double
    dose_mult=double
  />

Documentation (type)

Gives a dose multiplier for an age or body mass range.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in mg) is multiplied by this value for patients falling into this age range when this dosage table is used.

bodymass

→ scenario → pharmacology → treatments → dosages → bodymass

<bodymass
    lowerbound=double
    dose_mult=double
  />

Documentation (type)

Gives a dose multiplier for an age or body mass range.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in mg) is multiplied by this value for patients falling into this age range when this dosage table is used.

Multiply dose

→ scenario → pharmacology → treatments → dosages → multiply

<multiply
    by=("kg")
  />

Documentation (element)

Multiply the dose by some quantity, such as patient weight.

Attributes

By what?

by=("kg")

Quantity to multiply the dose by. Only option is "kg" (patient weight in kg).

Drug library

→ scenario → pharmacology → drugs

<drugs>
IN THIS ORDER:
| ( <drug ... /> )+
</drugs>

drug

Documentation (element)

A library of drug PK/PD data.

drug

→ scenario → pharmacology → drugs → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (type)

A drug description with PK/PD parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drugs → drug → PD

<PD
  [ locus=string ]
  >
IN THIS ORDER:
| ( <phenotype ... /> )+
</PD>

phenotype

Attributes

Locus

locus=string

PD parameters for some allele / resistance phenotype

→ scenario → pharmacology → drugs → drug → PD → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

Restrict phenotype applicability to certain alleles

→ scenario → pharmacology → drugs → drug → PD → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (element)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Maximal parasite killing rate

→ scenario → pharmacology → drugs → drug → PD → phenotype → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drugs → drug → PD → phenotype → IC50

<IC50
  [ sigma=double ] DEFAULT VALUE 0
  >
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Attributes

Sigma parameter for per-infection variation of IC50

sigma=double

Default value: 0

Distribution parameter describing per-infection variation of IC50. If zero or not specified, the IC50 is not sampled. See documentation of parent element.

Slope of effect curve

→ scenario → pharmacology → drugs → drug → PD → phenotype → slope

<slope>
    double
</slope>

Documentation (element)

Units: dimensionless

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drugs → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
| EXACTLY ONE OF:
| |   <half_life ... /> 
| | IN THIS ORDER:
| | |   <k ... /> 
| | |   <m_exponent ... /> 
| [ <k_a ... /> ]
| [ <conversion ... /> ]
|   <vol_dist ... /> 
| [ <compartment2 ... /> ]
| [ <compartment3 ... /> ]
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drugs → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drugs → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate λ, calculated as λ = ln(2) / half_life. The basic form of decay is C(t) = C0 * exp(-λ*t).

Alternatively, elimination rate can be specified via k and m_exponent.

Constant associated with elimination rate (k)

→ scenario → pharmacology → drugs → drug → PK → k

<k
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

If sigma > 0, k is sampled per-human from the log-normal distribution: ln N( ln(mean) - σ^2 / 2, σ^2).

Alternatively, elimination rate can be specified via half_life.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Constant associated with elimination rate (m_exponent)

→ scenario → pharmacology → drugs → drug → PK → m_exponent

<m_exponent>
    double
</m_exponent>

Documentation (element)

Units: day^-1 Min: 0

Alternatively, elimination rate can be specified via half_life.

Note that in the case of a conversion model, this applies to both the elimination and the conversion rates.

Absorption rate constant (k_a)

→ scenario → pharmacology → drugs → drug → PK → k_a

<k_a
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Min: 0

Absorption rate parameter. Not allowed for one compartment models, but required for two and three compartment models and one compartment with conversion model (for the parent drug only).

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Conversion parameters (parent drug)

→ scenario → pharmacology → drugs → drug → PK → conversion

<conversion>
IN ANY ORDER:
|   <metabolite ... /> 
|   <rate ... /> 
|   <molRatio ... /> 
</conversion>

Documentation (element)

Configures the parent drug in a conversion model.

To use a conversion model, the parent drug should have this section defined as well as half-life or k (direct elimination; this may be zero) and k_a (absorption rate; this may be large).

Metabolite drug (abbreviation)

→ scenario → pharmacology → drugs → drug → PK → conversion → metabolite

<metabolite>
    string
</metabolite>

Documentation (element)

The abbreviation of the metabolite drug (e.g. "DHA" or "DHA_AR").

Rate of conversion

→ scenario → pharmacology → drugs → drug → PK → conversion → rate

<rate
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Rate of conversion of parent drug to metabolite.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Molecular weight ratio

→ scenario → pharmacology → drugs → drug → PK → conversion → molRatio

<molRatio>
    double
</molRatio>

Documentation (element)

Ratio of molecular weights: molecular weight of the metabolite divided by molecular weight of the parent.

Volume of Distribution (Vd)

→ scenario → pharmacology → drugs → drug → PK → vol_dist

<vol_dist
  [ sigma=double ] DEFAULT VALUE 0
  >
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Attributes

Sigma parameter for per-human variation of Vd

sigma=double

Default value: 0

Distribution parameter describing per-human variation of volume of distribution. If zero or not specified, the parameter is not sampled. See documentation of parent element.

Second compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment2

<compartment2>
IN ANY ORDER:
|   <a12 ... /> 
|   <a21 ... /> 
</compartment2>

Documentation (element)

Optional element specifying conversion parameters to- and from- a second compartment.

Absorption rate to compartment 2 (a12)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → a12

<a12
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the first periphery compartment (2). The parameter k12 = a12 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Absorption rate from compartment 2 (a21)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → a21

<a21
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the first periphery compartment (2) to the central compartment. The parameter k21 = a21 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Third compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment3

<compartment3>
IN ANY ORDER:
|   <a13 ... /> 
|   <a31 ... /> 
</compartment3>

Documentation (element)

Optional element specifying conversion parameters to- and from- a third compartment.

Absorption rate to compartment 3 (a13)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → a13

<a13
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the second periphery compartment (3). The parameter k13 = a13 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Absorption rate from compartment 3 (a31)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → a31

<a31
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the second periphery compartment (3) to the central compartment. The parameter k31 = a31 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Diagnostic parameters

→ scenario → diagnostics

<diagnostics>
IN THIS ORDER:
| ( <diagnostic ... /> )*
</diagnostics>

diagnostic

Documentation (element)

Diagnostic model parameters

diagnostic

→ scenario → diagnostics → diagnostic

<diagnostic
    name=string
  [ units=("Other" or "Garki" or "Malariatherapy") ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterministic ... /> 
| |   <stochastic ... /> 
</diagnostic>

Attributes

Name of diagnostic

name=string

Name of this diagnostic (parameterisation). May be used elsewhere in the XML document to refer to this set of diagnostic parameters.

Parasite density units / methodology

units=("Other" or "Garki" or "Malariatherapy")

Deterministic detection

→ scenario → diagnostics → diagnostic → deterministic

<deterministic
    minDensity=double
  />

Documentation (element)

Specify that an artificial deterministic test is used: outcome is positive if parasite density is at least the minimum given.

Attributes

Minimum detectible density

minDensity=double

Units: parasites/microlitre Min: 0

The minimum density at which parasites can be detected. If 0, the test outcome is always positive.

Non-deterministic detection

→ scenario → diagnostics → diagnostic → stochastic

<stochastic
    dens_50=double
    specificity=double
  />

Documentation (element)

An improved model of detection which is non-deterministic, including false positive results as well as false negatives.

Some parameterisations:

Microscopy sensitivity/specificity data in Africa; Source: expert opinion — Allan Schapira dens_50 = 20.0 specificity = .75

RDT sensitivity/specificity for Plasmodium falciparum in Africa Source: Murray et al (Clinical Microbiological Reviews, Jan. 2008) dens_50 = 50.0; specificity = .942;

Attributes

Density 50

dens_50=double

Units: parasites/microlitre Min: 0

The density at which the test outcome has a 50% chance of being positive.

Specificity

specificity=double

Units: Dimensionless Min: 0 Max: 1

The probability of a positive test outcome in the absense of parasites.

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
| [ <vivax ... /> ]
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: model/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=string
  >
IN ANY ORDER:
| [ <NeonatalMortality ... /> ]
| [ <NonMalariaFevers ... /> ]
</clinical>

Documentation (type)

Attributes

Follow-up period during which recurrence is considered a treatment failure

healthSystemMemory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

Neonatal mortality parameters

→ scenario → model → clinical → NeonatalMortality

<NeonatalMortality
    diagnostic=string
  />

Attributes

Diagnostic used to parameterise model

diagnostic=string

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
| [ <prNeedTreatmentNMF ... /> ]
| [ <prNeedTreatmentMF ... /> ]
</NonMalariaFevers>

Documentation (type)

Description of the incidence of non-malaria fever. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a non-malarial fever requires treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

Availability of humans to mosquitoes relative to an adult, categorized by age group

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ]
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

vivax

→ scenario → model → vivax

<vivax>
IN ANY ORDER:
|   <probBloodStageInfectiousToMosq ... /> 
|   <hypnozoiteRelease ... /> 
|   <bloodStageProtectionLatency ... /> 
|   <bloodStageLengthDays ... /> 
|   <clinicalEvents ... /> 
</vivax>

probBloodStageInfectiousToMosq

→ scenario → model → vivax → probBloodStageInfectiousToMosq

<probBloodStageInfectiousToMosq
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

hypnozoiteRelease

→ scenario → model → vivax → hypnozoiteRelease

<hypnozoiteRelease
  [ pSecondRelease=double ] DEFAULT VALUE 0
  >
IN ANY ORDER:
|   <numberHypnozoites ... /> 
|   <firstRelease ... /> 
| [ <secondRelease ... /> ]
</hypnozoiteRelease>

Documentation (type)

This element defines probabilites when and how many hypnozoites are released from the liverstage into the blood.

The gap between the start of a new brood of hypnozoites and its release are defined as follows:

latentP + latentRelapseDays + randomReleaseDelay

randomReleaseDelay is based on one or two lognormal distributions, which are defined in firstRelease and optionally secondRelease.

You can define 2 release distributions, which get added together and represent the probability of hypnozoites which get released before winter (first release) or after (second release).

You can omit the secondRelease element if no release to the blood happens after winter.

Attributes

latent relapse days

pSecondRelease=double

Default value: 0

Probability of a second release. If undefined it is zero.

Number of Hypnozoites

→ scenario → model → vivax → hypnozoiteRelease → numberHypnozoites

<numberHypnozoites
    max=int
    base=double
  />

Documentation (element)

numberHypnozoites calculates the number of hypnozoites in the liver stage based on a base which is between 0 and 1.

This number is random based on the following distribution and normalized:

max ∑ (base ^ n) n = 0

Attributes

max

max=int

base

base=double

firstRelease

→ scenario → model → vivax → hypnozoiteRelease → firstRelease

<firstRelease
    mu=double
    sigma=double
    latentRelapseDays=int
  />

Documentation (base type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

latent relapse days

latentRelapseDays=int

Usually 15 days or 10 days (3 or 2 5-day timesteps).

secondRelease

→ scenario → model → vivax → hypnozoiteRelease → secondRelease

<secondRelease
    mu=double
    sigma=double
    latentRelapseDays=int
  />

Documentation (base type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

latent relapse days

latentRelapseDays=int

Usually 15 days or 10 days (3 or 2 5-day timesteps).

bloodStageProtectionLatency

→ scenario → model → vivax → bloodStageProtectionLatency

<bloodStageProtectionLatency
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

bloodStageLengthDays

→ scenario → model → vivax → bloodStageLengthDays

<bloodStageLengthDays
    weibullScale=double
    weibullShape=double
  />

Attributes

weibullScale

weibullScale=double

weibullShape

weibullShape=double

clinicalEvents

→ scenario → model → vivax → clinicalEvents

<clinicalEvents>
IN THIS ORDER:
|   <pPrimaryInfection ... /> 
|   <pRelapseOne ... /> 
|   <pRelapseTwoPlus ... /> 
|   <pEventIsSevere ... /> 
</clinicalEvents>

Documentation (type)

This elements holds all information about probabilites for clinical events from infections and relapses.

pPrimaryInfection

→ scenario → model → vivax → clinicalEvents → pPrimaryInfection

<pPrimaryInfection
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseOne

→ scenario → model → vivax → clinicalEvents → pRelapseOne

<pRelapseOne
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseTwoPlus

→ scenario → model → vivax → clinicalEvents → pRelapseTwoPlus

<pRelapseTwoPlus
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pEventIsSevere

→ scenario → model → vivax → clinicalEvents → pEventIsSevere

<pEventIsSevere
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=string
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=string

Units: User defined (default: steps) Min: 0 Max: 20

Pre-erythrocytic latent period Can be specified in steps (e.g. 3t) or days (e.g. 15d).

parameter

→ scenario → model → parameters → parameter

<parameter
  [ name=string ]
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 35 documentation

Generated from: scenario_35.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
  [ analysisNo=int ]
    name=string
  [ wuID=int ]
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:om="http://openmalaria.org/schema/scenario_35"
    xsi:schemaLocation="http://openmalaria.org/schema/scenario_35 scenario_35.xsd"
  >
IN ANY ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entomology ... /> 
| [ <parasiteGenetics ... /> ]
| [ <pharmacology ... /> ]
| [ <diagnostics ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Name of intervention

Work unit identifier

wuID=int

Units: Number

Work unit ID. Obselete and no longer required.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Description of demography

Attributes

Name of demography data

name=string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Years Min: 0 Max: 100

Maximum age of simulated humans in years

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

list of age groups included in demography

Documentation (type)

list of age groups included in demography or surveys

Attributes

Lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Units: Percentage Min: 0 Max: 100

Percentage of human population in age group

Upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ startDate=string ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
| [ <cohorts ... /> ]
</monitoring>

Documentation (element)

Description of surveys

Attributes

Name of monitoring settings

name=string

Name of monitoring settings

Start of monitoring

startDate=string

continuous

→ scenario → monitoring → continuous

<continuous
    period=string
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Delay between reports

period=string

Units: User defined (default: steps)

Delay between reports; typically one time step but can be greater. Can be specified in steps (e.g. 1t) or days (e.g. 5d).

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See model/mon/OutputMeasures.h for a list of supported outputs. Should also be on the wiki.

option

→ scenario → monitoring → SurveyOptions → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  [ outputNumber=int ]
  [ byAge=boolean ]
  [ byCohort=boolean ]
  [ bySpecies=boolean ]
  [ byGenotype=boolean ]
  [ byDrugType=boolean ]
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Number identifying measure in output

outputNumber=int

Report by age category

byAge=boolean

Report by cohort

byCohort=boolean

Report by mosquito species

bySpecies=boolean

Report by parasite genotype

byGenotype=boolean

Report by drug type

byDrugType=boolean

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
  [ detectionLimit=double ]
  [ diagnostic=string ]
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/microlitre Min: 0

Deprecated: limit above which a human's infection is reported as patent. Alternative: do not specify this; instead specify "diagnostic".

Name of monitoring diagnostic

diagnostic=string

Name of a parameterised diagnostic to use in surveys (see scenario/diagnostics).

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime
  [ repeatStep=string ]
  [ repeatEnd=string ]
  [ reported=boolean ] DEFAULT VALUE true
  >
    string
</surveyTime>

Documentation (element)

Units: User defined (defaults to steps) Min: 0

The simulation ends immediately after the last survey is taken.

Attributes

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

reported

reported=boolean

Default value: true

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Cohorts

→ scenario → monitoring → cohorts

<cohorts>
IN THIS ORDER:
| ( <subPop ... /> )+
</cohorts>

subPop

Documentation (element)

Allows the configuration of multiple cohorts (output segregated according to membership within specific sub-populations).

If this element is omitted, monitoring surveys cover the entire simulated human population.

It does not affect the "continuous" outputs (these never take cohorts into account).

Sub-population

→ scenario → monitoring → cohorts → subPop

<subPop
    id=string
    number=integer
  />

Documentation (element)

In the output file, the output set is identified by multiplying this number by 1000 then adding it to the age group column.

Attributes

Sub-population identifier

id=string

Textual identifier for the sub-population (i.e. for an intervention component, since sub-populations are defined as the hosts an intervention component is deployed to).

Sub-population number

number=integer

Units: dimensionless Min: 1 Max: 2097152

Number identifying a sub-population; used to define identifiers of output sets. This number must be a power of 2 (i.e. 1, 2, 4, 8, ...). See documentation of subPop element.

Preventative interventions

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfections ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <vectorPop ... /> ]
| [ <human ... /> ]
</interventions>

Documentation (element)

Attributes

Name of intervention set

name=string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeHS>

timedDeployment

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeHS → timedDeployment

<timedDeployment
    time=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timedDeployment>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</uncomplicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

multiple

→ scenario → interventions → human → component → decisionTree → multiple

<multiple
  [ name=string ]
  >
IN THIS ORDER:
| ( <caseType ... /> )*
| ( <diagnostic ... /> )*
| ( <random ... /> )*
| ( <age ... /> )*
| ( <treatPKPD ... /> )*
| [ <treatSimple ... /> ]
| ( <deploy ... /> )*
</multiple>

Documentation (type)

A special node allowing multiple sub-trees to be evaluated.

This is different from an ordinary decision tree node in that:

a) multiple types of child can occur simultaneously (e.g. multiple types of treatment or treatment plus a 'random' sub-tree)

b) the 'noTreatment' and 'treatFailure' nodes are not allowed

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → multiple → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

firstLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → firstLine

<firstLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</firstLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

secondLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → secondLine

<secondLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</secondLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

positive

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

outcome

→ scenario → interventions → human → component → decisionTree → multiple → random → outcome

<outcome
  [ name=string ]
    p=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</outcome>

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Probability

p=double

Units: None Min: 0 Max: 1

Probability of selecting this outcome. The sum of probabilities across all outcomes must be 1.

age

→ scenario → interventions → human → component → decisionTree → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Age range

→ scenario → interventions → human → component → decisionTree → multiple → age → age

<age
  [ name=string ]
    lb=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</age>

Documentation (element)

Describes a branch, selected for patients of a certain age.

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Lower bound (inclusive)

lb=double

Min: 0

noTreatment

→ scenario → interventions → human → component → decisionTree → noTreatment

<noTreatment
  [ name=string ]
  />

Documentation (type)

An end node doing nothing. This exists to explicitly state that no treatment happens and to prevent trees from accidentally being left incomplete.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatFailure

→ scenario → interventions → human → component → decisionTree → treatFailure

<treatFailure
  [ name=string ]
  />

Documentation (type)

An end node which reports treatment but does not change parasitalogical status. This allows correct labelling of second-line cases.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → multiple → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

age

→ scenario → interventions → human → component → decisionTree → multiple → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → multiple → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → multiple → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → multiple → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</complicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: Days Min: 0 Max: unbounded

Maximum number of timesteps (including first day of case) that an individual with an uncomplicated case of malaria will remember he/she was sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial or non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of a complicated or severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
  [ name=string ]
  [ useDiagnosticUC=boolean ] DEFAULT VALUE false
  >
IN ANY ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <treatmentActions ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
</ImmediateOutcomes>

Documentation (type)

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Name of case management parameterisation

name=string

Name of health system

useDiagnosticUC

useDiagnosticUC=boolean

Default value: false

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Description of drug regimen.

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Artemisinine based combination therapy

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Quinine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0 Max: 1name:P(self-treat)

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Effectiveness of treatment for non-compliant patients

treatmentActions

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions

<treatmentActions>
IN ANY ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
</treatmentActions>

CQ
SP
AQ
SPAQ
ACT
QN

CQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ

<CQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</CQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

deploy

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy

<deploy
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ p=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| ( <component ... /> )+
</deploy>

component

Attributes

Maximum age of eligible humans

maxAge=double

Units: Years Min: 0

Maximum age of eligible humans (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible humans

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible humans (defaults to 0). Input is rounded to the nearest time step.

Probability of delivery to eligible humans

p=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Probability of this list of components being deployed, given that other constraints are met.

component

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Prophylactic treatment

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere → clearInfections

<clearInfections
    timesteps=string
    stage=("liver" or "blood" or "both")
  />

Documentation (element)

Attributes

Length of effect

timesteps=string

Units: User defined (defaults to steps)

Target stage

stage=("liver" or "blood" or "both")

SP

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SP

<SP
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SP>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

AQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → AQ

<AQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</AQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

SPAQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SPAQ

<SPAQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SPAQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

ACT

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → ACT

<ACT
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</ACT>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

QN

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → QN

<QN
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</QN>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

Probability that human is incompatible with liver-stage drug treatment

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pHumanCannotReceive

<pHumanCannotReceive
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that a human is determined to be unable to receive liver-stage drug treatment. Treatment is neither reported or given for such humans.

This is sampled once per human at birth.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Ignore liver-stage drug treatment incompatibility

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → ignoreCannotReceive

<ignoreCannotReceive
    value=boolean
  />

Documentation (element)

If true, ignore pHumanCannotReceive and consider all humans eligible for treatment; if false (or not specified), do not treat those demed incompatible with liver-stage drug treatment.

The point of this is that pHumanCannotReceive cannot be altered by changeHS interventions, but this property can be.

Attributes

Input parameter value

value=boolean

A boolean value.

Prob use in UC case

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pUseUncomplicated

<pUseUncomplicated
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

This feature is deprecated; it is suggested to use the "simple treatment" feature configured to clear liver-stage parasites, leaving this option unset or zero.

Chance of liver-stage drug treatment being used for routine treatment of an uncomplicated case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Effectiveness

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → effectivenessOnUse

<effectivenessOnUse
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that liver-stage drug treatment is effective.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

DecisionTree5Day

<DecisionTree5Day
  [ name=string ]
  >
IN ANY ORDER:
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
|   <treeUCOfficial ... /> 
|   <treeUCSelfTreat ... /> 
|   <cureRateSevere ... /> 
|   <treatmentSevere ... /> 
</DecisionTree5Day>

Documentation (type)

Besides greater flexibility, this allows treatment via PK/PD models.

Attributes

Name of case management parameterisation

name=string

Name of health system

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → DecisionTree5Day → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → DecisionTree5Day → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

treeUCOfficial

→ scenario → healthSystem → DecisionTree5Day → treeUCOfficial

<treeUCOfficial
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCOfficial>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treeUCSelfTreat

→ scenario → healthSystem → DecisionTree5Day → treeUCSelfTreat

<treeUCSelfTreat
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCSelfTreat>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Cure rate (severe cases)

→ scenario → healthSystem → DecisionTree5Day → cureRateSevere

<cureRateSevere
    value=double
  />

Documentation (element)

Min: 0 Max: 1

The probability of clearing parasites given access to appropriate (hospital) care, for a severe case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

treatmentSevere

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere

<treatmentSevere
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</treatmentSevere>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Case fatality rate for inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: Dimensionless

List of age-specific probabilities of sequelae in inpatients, during a severe bout of malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeEIR>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeEIR → timedDeployment

<timedDeployment
    eipDuration=int
    time=string
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timedDeployment>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Time

time=string

Units: User defined (defauls to steps) Min: 0

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=string ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=string

Units: User defined (default: steps) Min: 0

Default value: 0

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=string
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time of start

time=string

Units: User defined (defauls to steps) Min: 0

Insert R_0 case

<insertR_0Case
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</insertR_0Case>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → insertR_0Case → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Uninfect vectors

<uninfectVectors
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</uninfectVectors>

timedDeployment

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → uninfectVectors → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Vector population intervention

→ scenario → interventions → vectorPop

<vectorPop>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorPop>

intervention

Documentation (element)

Units: List of elements

A list of parameterisations of generic vector host-inspecific interventions.

intervention

→ scenario → interventions → vectorPop → intervention

<intervention
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

Units: List of elements

An intervention which may have various effects on the vector populations as a whole. (Not host specific.)

Multiple instances of this intervention class are allowed (multiple parameterisations, not just deployments).

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → vectorPop → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → vectorPop → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <seekingDeathRateIncrease ... /> ]
| [ <probDeathOvipositing ... /> ]
| [ <emergenceReduction ... /> ]
</anopheles>

Documentation (type)

Units: dimensionless Min: 0 Max: 1

Descriptions of the effects of vector interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Proportional increase in deaths while host searching

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease

<seekingDeathRateIncrease
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</seekingDeathRateIncrease>

decay

Documentation (element)

Units: dimensionless

Describe an effect on the increase in the death rate while host seeking (mu_vA) due to this intervention.

Enter the rate increase (i.e. if rate increases to 120% of normal, give 0.2). New death rate while seeking is old × (1 + increase) where increase is this factor given. Must have increas ≥ -1.

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Proportion ovipositing mosquitoes killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing

<probDeathOvipositing
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probDeathOvipositing>

decay

Documentation (element)

Units: dimensionless

Describe an effect of increased mortality while ovipositing due to this intervention. Enter the probability of dying due to this intervention.

Attributes

Initial probability of killing

initial=double

Units: dimensionless Min: 0 Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Proportion of emerging pupa killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction

<emergenceReduction
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</emergenceReduction>

decay

Documentation (element)

Units: dimensionless

Describe an effect on emergence of pupa into adults: this value is the proportion of emerging pupa which are killed by this intervention.

Attributes

Initial proportion reduction

initial=double

Units: dimensionless Min: -inf Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Vector population intervention deployment

→ scenario → interventions → vectorPop → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

deploy

→ scenario → interventions → vectorPop → intervention → timed → deploy

<deploy
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Human-specific interventions

→ scenario → interventions → human

<human>
IN THIS ORDER:
| ( <component ... /> )+
| ( <deployment ... /> )*
</human>

Documentation (element)

Encapsulates all interventions whose effects are specific to the human host: any interventions where target humans may be selected via population-coverage, age limits and sub-population membership.

Component

→ scenario → interventions → human → component

<component
    id=string
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <screen ... /> 
| |   <treatSimple ... /> 
| |   <treatPKPD ... /> 
| |   <decisionTree ... /> 
| |   <PEV ... /> 
| |   <BSV ... /> 
| |   <TBV ... /> 
| |   <ITN ... /> 
| |   <IRS ... /> 
| |   <GVI ... /> 
| | [ <recruitmentOnly ... /> ]
| |   <clearImmunity ... /> 
| [ <subPopRemoval ... /> ]
</component>

Documentation (element)

Each element describes one component: its effects, decay of the(se) effect(s), and related stuff (e.g. description of indirect decay and of usage levels).

Attributes

Component identifier

id=string

Name of component

name=string

An informal name/description for the component

screen

→ scenario → interventions → human → component → screen

<screen
    diagnostic=string
  >
IN THIS ORDER:
| ( <positive ... /> )*
| ( <negative ... /> )*
</screen>

Documentation (type)

This can be combined with MDA to achieve mass screen and treat (MSAT) or other types of mass screening intervention.

The use of the screening itself is reported (if enabled), but not the outcome. Deployment of interventions triggered by the screening may be reported, however.

Attributes

Name of diagnostic

diagnostic=string

Name of a parameterised diagnostic (see scenario/diagnostics).

positive

→ scenario → interventions → human → component → screen → positive

<positive
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → screen → negative

<negative
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

treatSimple

→ scenario → interventions → human → component → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

treatPKPD

→ scenario → interventions → human → component → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

decisionTree

→ scenario → interventions → human → component → decisionTree

<decisionTree
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</decisionTree>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Vaccines

→ scenario → interventions → human → component → PEV

<PEV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</PEV>

Documentation (element)

Pre-erythrocytic vaccine (PEV): prevents a proportion of infections from commencing.

Documentation (type)

Description of a vaccine's effect

Decay of effect

→ scenario → interventions → human → component → PEV → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Specification of decay of efficacy. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Variance parameter for vaccine efficacy

→ scenario → interventions → human → component → PEV → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vaccines

→ scenario → interventions → human → component → BSV

<BSV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</BSV>

Documentation (element)

Blood-stage vaccine (BSV): acts as a killing factor on blood-stage parasites. Exact action depends on the within host model.

Documentation (type)

Description of a vaccine's effect

Vaccines

→ scenario → interventions → human → component → TBV

<TBV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</TBV>

Documentation (element)

Transmission-blocking vaccine (TBV): one minus this scales the probability of transmission to mosquitoes

Documentation (type)

Description of a vaccine's effect

Bed nets

→ scenario → interventions → human → component → ITN

<ITN>
IN THIS ORDER:
| [ <usage ... /> ]
|   <holeRate ... /> 
|   <ripRate ... /> 
|   <ripFactor ... /> 
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
|   <attritionOfNets ... /> 
| ( <anophelesParams ... /> )+
</ITN>

Documentation (element)

Description of bed-net interventions (ITNs, LLINs).

Proportion of time nets are used by humans

→ scenario → interventions → human → component → ITN → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of nets by humans, from 0 to 1.

At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing.

See also "propActing" (proportion of bits for which net acts).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Rate at which holes are made

→ scenario → interventions → human → component → ITN → holeRate

<holeRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Holes per annum Min: 0

The rate at which new holes are made in nets.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ ln N( log(mean)-sigma²/2, sigma² ).

Equivalent R sample: rlnorm(n, log(m) - s*s/2, s)

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rate at which holes are enlarged

→ scenario → interventions → human → component → ITN → ripRate

<ripRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Rips per existing hole per annum Min: 0

Each existing hole has a probability of being ripped bigger according to a Poisson process with this rate as (only) parameter.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ ln N( log(mean)-sigma²/2, sigma² ).

Equivalent R sample: rlnorm(n, log(m) - s*s/2, s)

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rip factor

→ scenario → interventions → human → component → ITN → ripFactor

<ripFactor
    value=double
  />

Documentation (element)

Units: none Min: 0

This factor expresses how important rips are in increasing the hole.

The hole index of a net is h + F×x where h and x are the total numbers of holes and rips respectively and F is the rip factor.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → ITN → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: mg/m² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → human → component → ITN → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of nets. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Attrition of nets

→ scenario → interventions → human → component → ITN → attritionOfNets

<attritionOfNets
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: dimensionless

Specifies the rate at which nets are disposed of over time. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Humans are removed from the intervention component's sub-population on disposal (attrition) of their nets. Currently this event is not reported.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → human → component → ITN → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterrency ... /> 
| |   <twoStageDeterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which net acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency

<twoStageDeterrency>
IN ANY ORDER:
|   <entering ... /> 
|   <attacking ... /> 
</twoStageDeterrency>

Documentation (element)

Units: dimensionless

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

This deterrency model multiplies human attractiveness by pEnt×pAtt divided by a base factor to normalise the output to 1 when there are no nets.

RA (entering)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → entering

<entering
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless

pEnt represents the relative probability of entering due to ITNs: pEnt = exp(log(P)×p) where P is the insecticide factor and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

RA (attacking)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attacking

<attacking
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless

pAtt represents the relative probability of attacking a human after entering a house due to ITNs (i.e. of feeding/dying vs. flying off): pAtt = B + H×h + P×p + I×h×p where B is the base (without net) probability; H, P and I are the hole, insecticide and interaction factors respectively, h=exp(-holeIndex×holeScalingFactor) and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Pre-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Indoor residual spraying

→ scenario → interventions → human → component → IRS

<IRS>
IN THIS ORDER:
| [ <usage ... /> ]
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
| ( <anophelesParams ... /> )+
</IRS>

Documentation (element)

Description of indoor residual spraying interventions.

Documentation (type)

Description of effect for the more complex and probably more realistic Briet model: IRS has three effects, whos strength is calculated as a function of surviving insecticide content.

Proportion of Indoor residual spraying (IRS) interventions

→ scenario → interventions → human → component → IRS → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Indoor residual spraying (IRS) interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → IRS → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: μg/cm² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → human → component → IRS → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → IRS → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → IRS → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied by exp(P×log(p)) where P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Generic vector intervention

→ scenario → interventions → human → component → GVI

<GVI>
IN THIS ORDER:
| [ <usage ... /> ]
|   <decay ... /> 
| ( <anophelesParams ... /> )+
</GVI>

Documentation (element)

Note that all actions of this intervention component will decay according to a single decay function. If independant decay is wanted, a separate component can be used for each action.

Proportion of generic vector interventions

→ scenario → interventions → human → component → GVI → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Generic vector interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay

→ scenario → interventions → human → component → GVI → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Description of decay of all intervention effects. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → GVI → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <deterrency ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → GVI → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied this factor times survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Recruitment only

→ scenario → interventions → human → component → recruitmentOnly

<recruitmentOnly/>

Documentation (element)

Recruitment of a host into a sub-population.

Clear Immunity

→ scenario → interventions → human → component → clearImmunity

<clearImmunity/>

Documentation (element)

Removes all exposure-related immunitsy gained over time by hosts without removing infections (or affecting the ability to gain immunity through exposure).

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

subPopRemoval

→ scenario → interventions → human → component → subPopRemoval

<subPopRemoval
  [ onFirstBout=boolean ] DEFAULT VALUE false
  [ onFirstTreatment=boolean ] DEFAULT VALUE false
  [ onFirstInfection=boolean ] DEFAULT VALUE false
  [ afterYears=double ]
  />

Documentation (type)

ITN attrition also removes humans from sub-populations.

Attributes

Time to first episode only

onFirstBout=boolean

Default value: false

Time to first treatment only

onFirstTreatment=boolean

Default value: false

Time to first infection only

onFirstInfection=boolean

Default value: false

Remove from sub-population after

afterYears=double

Units: Years Min: 0

Deployment

→ scenario → interventions → human → deployment

<deployment
  [ name=string ]
  >
IN THIS ORDER:
| ( <component ... /> )+
| ( <condition ... /> )*
| ( <continuous ... /> )*
| ( <timed ... /> )*
</deployment>

Documentation (element)

All components deployed by this intervention are deployed to the same people (each timed or continuous deployment selects recipients and then gives each recipient all components of the intervention).

Attributes

Intervention name

name=string

Name of intervention

component

→ scenario → interventions → human → deployment → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Condition

→ scenario → interventions → human → deployment → condition

<condition
    measure=string
  [ minValue=double ]
  [ maxValue=double ]
    initialState=boolean
  />

Documentation (element)

Conditions are evaluated for the whole population, not for individual age-groups or cohorts.

This affects all types of deployment.

Attributes

Measure

measure=string

The monitoring measure to test. Not all measures are available for use.

Minimum value

minValue=double

Minimum value. If specified, the measured variable must be greater than this value for the condition to be satisfied.

Maximum value

maxValue=double

Maximum value. If specified, the measured variable must be less than this value for the condition to be satisfied.

Initial state

initialState=boolean

Whether this condition is considered true or false before updated by a survey.

Age-based (continuous) deployment

→ scenario → interventions → human → deployment → continuous

<continuous>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| ( <deploy ... /> )+
</continuous>

Documentation (element)

List of ages at which deployment takes place (through EPI, post-natal and school-based programmes, etc.).

A sub-population restriction may be added as a property of the list of continuous deployments.

restrictToSubPop

→ scenario → interventions → human → deployment → continuous → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

deploy

→ scenario → interventions → human → deployment → continuous → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    targetAgeYrs=double
  [ begin=string ]
  [ end=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention. Input is rounded to the nearest time step.

First time active

begin=string

Units: User defined (defauls to steps)

End step

end=string

Units: User defined (defauls to steps)

Mass (timed) deployment

→ scenario → interventions → human → deployment → timed

<timed>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| [ <cumulativeCoverage ... /> ]
| ( <deploy ... /> )+
</timed>

Documentation (element)

List of timed deployments of the intervention (that is, of deployment campaigns).

Cumulative deployment mode can be specified for all deployments in a timed list. To allow multiple cumulative deployment descriptions, the entire timed list may be repeated.

restrictToSubPop

→ scenario → interventions → human → deployment → timed → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

Cumulative coverage

→ scenario → interventions → human → deployment → timed → cumulativeCoverage

<cumulativeCoverage
    component=string
  />

Documentation (element)

Attributes

Component identifier

component=string

The identifier (short name) of the component used when selecting people.

deploy

→ scenario → interventions → human → deployment → timed → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    time=string
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ repeatStep=string ]
  [ repeatEnd=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Time

time=string

Units: User defined (defauls to steps) Min: 0

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0

Maximum age of eligible individuals (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible individuals (defaults to 0). Input is rounded to the nearest time step.

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Description of health system.

Documentation (type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("forced" or "dynamic")
  [ scaledAnnualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Description of entomological data

Attributes

Entomology dataset name

name=string

Name of entomology data

Transmission model mode

mode=("forced" or "dynamic")

Override annual EIR

scaledAnnualEIR=double

Units: Infectious bites per adult per year

If set, the annual EIR (for all species of vector) is scaled to this level; can be omitted if not needed.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters of the transmission model

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <seasonality ... /> 
|   <mosq ... /> 
| [ <lifeCycle ... /> ]
| [ <simpleMPD ... /> ]
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial estimate of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial estimate of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial estimate of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Seasonality of transmission

→ scenario → entomology → vector → anopheles → seasonality

<seasonality
    input=("EIR")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <fourierSeries ... /> 
| |   <monthlyValues ... /> 
| |   <dailyValues ... /> 
</seasonality>

Documentation (element)

Specifies the seasonality of transmission and optionally the level of annual transmission.

Attributes

Seasonality input

input=("EIR")

Annual EIR

annualEIR=double

Units: Inoculations per adult per annum Min: 0

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries

<fourierSeries
    EIRRotateAngle=double
  >
IN THIS ORDER:
| ( <coeffic ... /> )*
</fourierSeries>

coeffic

Documentation (element)

Units: Infectious bites per adult per day

Attributes

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: Radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Pair of Fourier coefficients

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries → coeffic

<coeffic
    a=double
    b=double
  />

Documentation (element)

A pair of Fourier series coefficients. The first element specifies a1 and b1, the second a2 and b2, etc. Any number (from 0 up) of pairs may be given.

Attributes

a_n parameter of Fourier approximation to ln(EIR)

a=double

a_n parameter of Fourier approximation to ln(EIR) for some natural number n.

b_n parameter of Fourier approximation to ln(EIR)

b=double

b_n parameter of Fourier approximation to ln(EIR) for some natural number n.

List of monthly values

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues

<monthlyValues
    smoothing=("none" or "fourier")
  >
IN THIS ORDER:
| ( <value ... /> ){12,12}
</monthlyValues>

value

Documentation (element)

Description of seasonality from monthly values. Multiple smoothing methods are possible (see smoothing attribute).

List should contain twelve entries: January to December.

Attributes

Smoothing function

smoothing=("none" or "fourier")

How the monthly values are converted into a daily sequence of values:

none: no smoothing (step function)
Fourier: a Fourier series (with terms up to a2/b2) is fit to the sequence of monthly values and used to generate a smoothed list of daily values.

Monthly value

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Monthly value

List of daily values

→ scenario → entomology → vector → anopheles → seasonality → dailyValues

<dailyValues>
IN THIS ORDER:
| ( <value ... /> ){365,365}
</dailyValues>

value

Documentation (element)

Description of seasonality from daily values.

List should contain 365 entries: 1st January to 31st December.

Daily value

→ scenario → entomology → vector → anopheles → seasonality → dailyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Daily value

Mosquito feeding cycle parameters

→ scenario → entomology → vector → anopheles → mosq

<mosq
    minInfectedThreshold=double
  >
IN ANY ORDER:
|   <mosqRestDuration ... /> 
|   <extrinsicIncubationPeriod ... /> 
|   <mosqLaidEggsSameDayProportion ... /> 
|   <mosqSeekingDuration ... /> 
|   <mosqSurvivalFeedingCycleProbability ... /> 
|   <availabilityVariance ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <mosqProbOvipositing ... /> 
|   <mosqHumanBloodIndex ... /> 
</mosq>

Documentation (element)

Parameters describing the feeding cycle and human mosquito interaction of a single species of anopheles mosquito.

Attributes

Mininum infected threshold for mosquitos

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

Duration of the resting period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqRestDuration

<mosqRestDuration
    value=int
  />

Documentation (element)

Units: Days

name:Duration of the resting period of the vector (days);

Attributes

Input parameter value

value=int

An integer value.

Extrinsic incubation period

→ scenario → entomology → vector → anopheles → mosq → extrinsicIncubationPeriod

<extrinsicIncubationPeriod
    value=int
  />

Documentation (element)

Units: Days

name:Extrinsic incubation period (days)

Attributes

Input parameter value

value=int

An integer value.

Proportion of mosquitoes host seeking on same day as ovipositing

→ scenario → entomology → vector → anopheles → mosq → mosqLaidEggsSameDayProportion

<mosqLaidEggsSameDayProportion
    value=double
  />

Documentation (element)

Units: Proportion

Proportion of mosquitoes host seeking on same day as ovipositing

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Duration of the host-seeking period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqSeekingDuration

<mosqSeekingDuration
    value=double
  />

Documentation (element)

Units: Days

Duration of the host-seeking period of the vector (days)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito survives the feeding cycle

→ scenario → entomology → vector → anopheles → mosq → mosqSurvivalFeedingCycleProbability

<mosqSurvivalFeedingCycleProbability
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito survives the feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Variance in human availability rate

→ scenario → entomology → vector → anopheles → mosq → availabilityVariance

<availabilityVariance
    value=double
  />

Documentation (element)

Variance in availability rate of humans to mosquitoes. The mean rate is calculated based on other parameters.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito succesfully bites chosen host

→ scenario → entomology → vector → anopheles → mosq → mosqProbBiting

<mosqProbBiting
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito succesfully bites chosen host

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → mosq → mosqProbFindRestSite

<mosqProbFindRestSite
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito escapes host and finds a resting place after biting

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → mosq → mosqProbResting

<mosqProbResting
    mean=double
    variance=double
  />

Documentation (element)

Probability of mosquito successfully resting after finding a resting site

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of a mosquito successfully laying eggs given that it has rested

→ scenario → entomology → vector → anopheles → mosq → mosqProbOvipositing

<mosqProbOvipositing
    value=double
  />

Documentation (element)

Probability of a mosquito successfully laying eggs given that it has rested

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human blood index

→ scenario → entomology → vector → anopheles → mosq → mosqHumanBloodIndex

<mosqHumanBloodIndex
    value=double
  />

Documentation (element)

Units: Proportion

The proportion of resting mosquitoes which fed on human blood during the last feed.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mosquito life cycle parameters

→ scenario → entomology → vector → anopheles → lifeCycle

<lifeCycle
  [ estimatedLarvalResources=double ] DEFAULT VALUE 1e8
  >
IN ANY ORDER:
|   <eggStage ... /> 
|   <larvalStage ... /> 
|   <pupalStage ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</lifeCycle>

Documentation (element)

Parameters describing the life-cycle of this species of mosquito

Attributes

Estimate of larval resources

estimatedLarvalResources=double

Units: X

Default value: 1e8

Egg stage

→ scenario → entomology → vector → anopheles → lifeCycle → eggStage

<eggStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the egg stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

larvalStage

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage

<larvalStage>
</larvalStage>

daily

Documentation (type)

Parameters for the larval stage of development

Documentation (base type)

Parameters associated with a mosquito development stage.

Daily development

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage → daily

<daily
    resourceUsage=double
    effectCompetition=double
  />

Documentation (element)

Attributes

Resource usage

resourceUsage=double

Units: X

Resource usage during larval stage of development. Units are arbitrary.

Effect of competition

effectCompetition=double

Units: none

Effect of competition over resources on development.

Pupal stage

→ scenario → entomology → vector → anopheles → lifeCycle → pupalStage

<pupalStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the pupal stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → lifeCycle → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Simple Mosq-Pop-Dynamics parameters

→ scenario → entomology → vector → anopheles → simpleMPD

<simpleMPD>
IN ANY ORDER:
|   <developmentDuration ... /> 
|   <developmentSurvival ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</simpleMPD>

Documentation (element)

Parameters describing the simple mosquito population dynamics model.

This is a simpler version of the life-cycle model, requiring less parameters and with much simpler initialisation.

Duration

→ scenario → entomology → vector → anopheles → simpleMPD → developmentDuration

<developmentDuration
    value=int
  />

Documentation (element)

Units: Days Min: 1

Duration from egg laying to emergence in days.

Attributes

Input parameter value

value=int

An integer value.

Probability of survival

→ scenario → entomology → vector → anopheles → simpleMPD → developmentSurvival

<developmentSurvival
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that mosquito survives from the egg being laid to emergence, given no resouce limitations (no density constraints).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → simpleMPD → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Alternative (non-human) host paramters

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN ANY ORDER:
|   <mosqRelativeEntoAvailability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
</nonHumanHosts>

Documentation (element)

Min: 0

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of non-human host (ξ_i)

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqRelativeEntoAvailability

<mosqRelativeEntoAvailability
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Name of this species of non human hosts (must match up with those described per anopheles section).

Population size of alternative host species

number=double

Units: Number

Population size of this non-human host.

Parasite genetics

<parasiteGenetics
    samplingMode=("initial" or "tracking")
  >
IN THIS ORDER:
| ( <locus ... /> )+
</parasiteGenetics>

locus

Documentation (element)

A specification of genotypes of infection parasites.

May be omitted; in this case there is no modelling of genetic differences of infections (resistance, fitness).

Attributes

samplingMode

samplingMode=("initial" or "tracking")

Locus

→ scenario → parasiteGenetics → locus

<locus
    name=string
  >
IN THIS ORDER:
| ( <allele ... /> )+
</locus>

allele

Documentation (element)

Alleles at loci can affect fitness and resistance to any number of drugs.

Attributes

Name of locus

name=string

Name of the Locus

Allele

→ scenario → parasiteGenetics → locus → allele

<allele
    name=string
    initialFrequency=double
    fitness=double
  />

Documentation (element)

Describes an allele, or one possible genetic option of multiple at one point of variance.

Attributes

Name

name=string

Name of the allele; used to refer to it elsewhere.

Initial frequency

initialFrequency=double

Fitness factor

fitness=double

Drug parameters (PK, PD and usage)

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
|   <treatments ... /> 
|   <drugs ... /> 
</pharmacology>

Documentation (element)

Drug model parameters and drug usage parameters

Documentation (type)

A library of drug related data for the PK/PD model.

Treatments library

→ scenario → pharmacology → treatments

<treatments>
IN THIS ORDER:
| ( <schedule ... /> )+
| ( <dosages ... /> )+
</treatments>

Documentation (element)

A library of drug deployment schedules and dosages.

schedule

→ scenario → pharmacology → treatments → schedule

<schedule
    name=string
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

A schedule for the administration of drugs in a course of treatment.

Note that dose sizes are multiplied by some multiplier (see dosages) and the times of all doses may be delayed.

Attributes

Name

name=string

Name for referring to this deployment schedule

medicate

→ scenario → pharmacology → treatments → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  />

Attributes

drug

drug=string

Abbreviated name of drug compound

Drug dose (mg with multiplier)

mg=double

Units: mg per something

Quantity of drug compound in mg per something. A separate dosage table must be used when medicating, which may specify multipliers of this number based on patient age or weight.

Time of administration

hour=double

Units: Hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

dosages

→ scenario → pharmacology → treatments → dosages

<dosages
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | ( <age ... /> )+
| | ( <bodymass ... /> )+
| |   <multiply ... /> 
</dosages>

Documentation (type)

A table for selecting a dose size given an age.

Attributes

Name

name=string

Name for referring to this dosage table

age

→ scenario → pharmacology → treatments → dosages → age

<age
    lowerbound=double
    dose_mult=double
  />

Documentation (type)

Gives a dose multiplier for an age or body mass range.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in mg) is multiplied by this value for patients falling into this age range when this dosage table is used.

bodymass

→ scenario → pharmacology → treatments → dosages → bodymass

<bodymass
    lowerbound=double
    dose_mult=double
  />

Documentation (type)

Gives a dose multiplier for an age or body mass range.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in mg) is multiplied by this value for patients falling into this age range when this dosage table is used.

Multiply dose

→ scenario → pharmacology → treatments → dosages → multiply

<multiply
    by=("kg")
  />

Documentation (element)

Multiply the dose by some quantity, such as patient weight.

Attributes

By what?

by=("kg")

Quantity to multiply the dose by. Only option is "kg" (patient weight in kg).

Drug library

→ scenario → pharmacology → drugs

<drugs>
IN THIS ORDER:
| ( <drug ... /> )+
</drugs>

drug

Documentation (element)

A library of drug PK/PD data.

drug

→ scenario → pharmacology → drugs → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (type)

A drug description with PK/PD parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drugs → drug → PD

<PD
  [ locus=string ]
  >
IN THIS ORDER:
| ( <phenotype ... /> )+
</PD>

phenotype

Attributes

Locus

locus=string

PD parameters for some allele / resistance phenotype

→ scenario → pharmacology → drugs → drug → PD → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

Restrict phenotype applicability to certain alleles

→ scenario → pharmacology → drugs → drug → PD → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (element)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Maximal parasite killing rate

→ scenario → pharmacology → drugs → drug → PD → phenotype → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drugs → drug → PD → phenotype → IC50

<IC50
  [ sigma=double ] DEFAULT VALUE 0
  >
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Attributes

Sigma parameter for per-infection variation of IC50

sigma=double

Default value: 0

Distribution parameter describing per-infection variation of IC50. If zero or not specified, the IC50 is not sampled. See documentation of parent element.

Slope of effect curve

→ scenario → pharmacology → drugs → drug → PD → phenotype → slope

<slope>
    double
</slope>

Documentation (element)

Units: dimensionless

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drugs → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
| EXACTLY ONE OF:
| |   <half_life ... /> 
| | IN THIS ORDER:
| | |   <k ... /> 
| | |   <m_exponent ... /> 
| [ <k_a ... /> ]
| [ <conversion ... /> ]
|   <vol_dist ... /> 
| [ <compartment2 ... /> ]
| [ <compartment3 ... /> ]
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drugs → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drugs → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate λ, calculated as λ = ln(2) / half_life. The basic form of decay is C(t) = C0 * exp(-λ*t).

Alternatively, elimination rate can be specified via k and m_exponent.

Constant associated with elimination rate (k)

→ scenario → pharmacology → drugs → drug → PK → k

<k
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

If sigma > 0, k is sampled per-human from the log-normal distribution: ln N( ln(mean) - σ^2 / 2, σ^2).

Alternatively, elimination rate can be specified via half_life.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Constant associated with elimination rate (m_exponent)

→ scenario → pharmacology → drugs → drug → PK → m_exponent

<m_exponent>
    double
</m_exponent>

Documentation (element)

Units: day^-1 Min: 0

Alternatively, elimination rate can be specified via half_life.

Note that in the case of a conversion model, this applies to both the elimination and the conversion rates.

Absorption rate constant (k_a)

→ scenario → pharmacology → drugs → drug → PK → k_a

<k_a
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Min: 0

Absorption rate parameter. Not allowed for one compartment models, but required for two and three compartment models and one compartment with conversion model (for the parent drug only).

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Conversion parameters (parent drug)

→ scenario → pharmacology → drugs → drug → PK → conversion

<conversion>
IN ANY ORDER:
|   <metabolite ... /> 
|   <rate ... /> 
|   <molRatio ... /> 
</conversion>

Documentation (element)

Configures the parent drug in a conversion model.

To use a conversion model, the parent drug should have this section defined as well as half-life or k (direct elimination; this may be zero) and k_a (absorption rate; this may be large).

Metabolite drug (abbreviation)

→ scenario → pharmacology → drugs → drug → PK → conversion → metabolite

<metabolite>
    string
</metabolite>

Documentation (element)

The abbreviation of the metabolite drug (e.g. "DHA" or "DHA_AR").

Rate of conversion

→ scenario → pharmacology → drugs → drug → PK → conversion → rate

<rate
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Rate of conversion of parent drug to metabolite.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Molecular weight ratio

→ scenario → pharmacology → drugs → drug → PK → conversion → molRatio

<molRatio>
    double
</molRatio>

Documentation (element)

Ratio of molecular weights: molecular weight of the metabolite divided by molecular weight of the parent.

Volume of Distribution (Vd)

→ scenario → pharmacology → drugs → drug → PK → vol_dist

<vol_dist
  [ sigma=double ] DEFAULT VALUE 0
  >
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Attributes

Sigma parameter for per-human variation of Vd

sigma=double

Default value: 0

Distribution parameter describing per-human variation of volume of distribution. If zero or not specified, the parameter is not sampled. See documentation of parent element.

Second compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment2

<compartment2>
IN ANY ORDER:
|   <a12 ... /> 
|   <a21 ... /> 
</compartment2>

Documentation (element)

Optional element specifying conversion parameters to- and from- a second compartment.

Absorption rate to compartment 2 (a12)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → a12

<a12
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the first periphery compartment (2). The parameter k12 = a12 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Absorption rate from compartment 2 (a21)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → a21

<a21
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the first periphery compartment (2) to the central compartment. The parameter k21 = a21 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Third compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment3

<compartment3>
IN ANY ORDER:
|   <a13 ... /> 
|   <a31 ... /> 
</compartment3>

Documentation (element)

Optional element specifying conversion parameters to- and from- a third compartment.

Absorption rate to compartment 3 (a13)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → a13

<a13
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the second periphery compartment (3). The parameter k13 = a13 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Absorption rate from compartment 3 (a31)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → a31

<a31
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the second periphery compartment (3) to the central compartment. The parameter k31 = a31 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Diagnostic parameters

→ scenario → diagnostics

<diagnostics>
IN THIS ORDER:
| ( <diagnostic ... /> )*
</diagnostics>

diagnostic

Documentation (element)

Diagnostic model parameters

diagnostic

→ scenario → diagnostics → diagnostic

<diagnostic
    name=string
  [ units=("Other" or "Garki" or "Malariatherapy") ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterministic ... /> 
| |   <stochastic ... /> 
</diagnostic>

Attributes

Name of diagnostic

name=string

Name of this diagnostic (parameterisation). May be used elsewhere in the XML document to refer to this set of diagnostic parameters.

Parasite density units / methodology

units=("Other" or "Garki" or "Malariatherapy")

Deterministic detection

→ scenario → diagnostics → diagnostic → deterministic

<deterministic
    minDensity=double
  />

Documentation (element)

Specify that an artificial deterministic test is used: outcome is positive if parasite density is at least the minimum given.

Attributes

Minimum detectible density

minDensity=double

Units: parasites/microlitre Min: 0

The minimum density at which parasites can be detected. If 0, the test outcome is always positive.

Non-deterministic detection

→ scenario → diagnostics → diagnostic → stochastic

<stochastic
    dens_50=double
    specificity=double
  />

Documentation (element)

An improved model of detection which is non-deterministic, including false positive results as well as false negatives.

Some parameterisations:

Microscopy sensitivity/specificity data in Africa; Source: expert opinion — Allan Schapira dens_50 = 20.0 specificity = .75

RDT sensitivity/specificity for Plasmodium falciparum in Africa Source: Murray et al (Clinical Microbiological Reviews, Jan. 2008) dens_50 = 50.0; specificity = .942;

Attributes

Density 50

dens_50=double

Units: parasites/microlitre Min: 0

The density at which the test outcome has a 50% chance of being positive.

Specificity

specificity=double

Units: Dimensionless Min: 0 Max: 1

The probability of a positive test outcome in the absense of parasites.

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
| [ <vivax ... /> ]
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: model/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=string
  >
IN ANY ORDER:
| [ <NeonatalMortality ... /> ]
| [ <NonMalariaFevers ... /> ]
</clinical>

Documentation (type)

Attributes

Follow-up period during which recurrence is considered a treatment failure

healthSystemMemory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

Neonatal mortality parameters

→ scenario → model → clinical → NeonatalMortality

<NeonatalMortality
    diagnostic=string
  />

Attributes

Diagnostic used to parameterise model

diagnostic=string

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
| [ <prNeedTreatmentNMF ... /> ]
| [ <prNeedTreatmentMF ... /> ]
</NonMalariaFevers>

Documentation (type)

Description of the incidence of non-malaria fever. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a non-malarial fever requires treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

Availability of humans to mosquitoes relative to an adult, categorized by age group

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ]
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

vivax

→ scenario → model → vivax

<vivax>
IN ANY ORDER:
|   <probBloodStageInfectiousToMosq ... /> 
|   <hypnozoiteRelease ... /> 
|   <bloodStageProtectionLatency ... /> 
|   <bloodStageLengthDays ... /> 
|   <clinicalEvents ... /> 
</vivax>

probBloodStageInfectiousToMosq

→ scenario → model → vivax → probBloodStageInfectiousToMosq

<probBloodStageInfectiousToMosq
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

hypnozoiteRelease

→ scenario → model → vivax → hypnozoiteRelease

<hypnozoiteRelease
  [ pSecondRelease=double ] DEFAULT VALUE 0
  >
IN ANY ORDER:
|   <numberHypnozoites ... /> 
|   <firstRelease ... /> 
| [ <secondRelease ... /> ]
</hypnozoiteRelease>

Documentation (type)

This element defines probabilites when and how many hypnozoites are released from the liverstage into the blood.

The gap between the start of a new brood of hypnozoites and its release are defined as follows:

latentP + latentRelapseDays + randomReleaseDelay

randomReleaseDelay is based on one or two lognormal distributions, which are defined in firstRelease and optionally secondRelease.

You can define 2 release distributions, which get added together and represent the probability of hypnozoites which get released before winter (first release) or after (second release).

You can omit the secondRelease element if no release to the blood happens after winter.

Attributes

latent relapse days

pSecondRelease=double

Default value: 0

Probability of a second release. If undefined it is zero.

Number of Hypnozoites

→ scenario → model → vivax → hypnozoiteRelease → numberHypnozoites

<numberHypnozoites
    max=int
    base=double
  />

Documentation (element)

numberHypnozoites calculates the number of hypnozoites in the liver stage based on a base which is between 0 and 1.

This number is random based on the following distribution and normalized:

max ∑ (base ^ n) n = 0

Attributes

max

max=int

base

base=double

firstRelease

→ scenario → model → vivax → hypnozoiteRelease → firstRelease

<firstRelease
    mu=double
    sigma=double
    latentRelapseDays=int
  />

Documentation (base type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

latent relapse days

latentRelapseDays=int

Usually 15 days or 10 days (3 or 2 5-day timesteps).

secondRelease

→ scenario → model → vivax → hypnozoiteRelease → secondRelease

<secondRelease
    mu=double
    sigma=double
    latentRelapseDays=int
  />

Documentation (base type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

latent relapse days

latentRelapseDays=int

Usually 15 days or 10 days (3 or 2 5-day timesteps).

bloodStageProtectionLatency

→ scenario → model → vivax → bloodStageProtectionLatency

<bloodStageProtectionLatency
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

bloodStageLengthDays

→ scenario → model → vivax → bloodStageLengthDays

<bloodStageLengthDays
    weibullScale=double
    weibullShape=double
  />

Attributes

weibullScale

weibullScale=double

weibullShape

weibullShape=double

clinicalEvents

→ scenario → model → vivax → clinicalEvents

<clinicalEvents>
IN THIS ORDER:
|   <pPrimaryInfection ... /> 
|   <pRelapseOne ... /> 
|   <pRelapseTwoPlus ... /> 
|   <pEventIsSevere ... /> 
</clinicalEvents>

Documentation (type)

This elements holds all information about probabilites for clinical events from infections and relapses.

pPrimaryInfection

→ scenario → model → vivax → clinicalEvents → pPrimaryInfection

<pPrimaryInfection
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseOne

→ scenario → model → vivax → clinicalEvents → pRelapseOne

<pRelapseOne
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseTwoPlus

→ scenario → model → vivax → clinicalEvents → pRelapseTwoPlus

<pRelapseTwoPlus
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pEventIsSevere

→ scenario → model → vivax → clinicalEvents → pEventIsSevere

<pEventIsSevere
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=string
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=string

Units: User defined (default: steps) Min: 0 Max: 20

Pre-erythrocytic latent period Can be specified in steps (e.g. 3t) or days (e.g. 15d).

parameter

→ scenario → model → parameters → parameter

<parameter
  [ name=string ]
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 34 documentation

Generated from: scenario_34.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
  [ analysisNo=int ]
    name=string
  [ wuID=int ]
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:om="http://openmalaria.org/schema/scenario_34"
    xsi:schemaLocation="http://openmalaria.org/schema/scenario_34 scenario_34.xsd"
  >
IN ANY ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entomology ... /> 
| [ <parasiteGenetics ... /> ]
| [ <pharmacology ... /> ]
| [ <diagnostics ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Name of intervention

Work unit identifier

wuID=int

Units: Number

Work unit ID. Obselete and no longer required.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Description of demography

Attributes

Name of demography data

name=string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Years Min: 0 Max: 100

Maximum age of simulated humans in years

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

list of age groups included in demography

Documentation (type)

list of age groups included in demography or surveys

Attributes

Lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Units: Percentage Min: 0 Max: 100

Percentage of human population in age group

Upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ startDate=string ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
| [ <cohorts ... /> ]
</monitoring>

Documentation (element)

Description of surveys

Attributes

Name of monitoring settings

name=string

Name of monitoring settings

Start of monitoring

startDate=string

continuous

→ scenario → monitoring → continuous

<continuous
    period=string
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Delay between reports

period=string

Units: User defined (default: steps)

Delay between reports; typically one time step but can be greater. Can be specified in steps (e.g. 1t) or days (e.g. 5d).

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See model/mon/OutputMeasures.h for a list of supported outputs. Should also be on the wiki.

option

→ scenario → monitoring → SurveyOptions → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  [ outputNumber=int ]
  [ byAge=boolean ]
  [ byCohort=boolean ]
  [ bySpecies=boolean ]
  [ byGenotype=boolean ]
  [ byDrugType=boolean ]
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Number identifying measure in output

outputNumber=int

Report by age category

byAge=boolean

Report by cohort

byCohort=boolean

Report by mosquito species

bySpecies=boolean

Report by parasite genotype

byGenotype=boolean

Report by drug type

byDrugType=boolean

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
  [ detectionLimit=double ]
  [ diagnostic=string ]
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/microlitre Min: 0

Deprecated: limit above which a human's infection is reported as patent. Alternative: do not specify this; instead specify "diagnostic".

Name of monitoring diagnostic

diagnostic=string

Name of a parameterised diagnostic to use in surveys (see scenario/diagnostics).

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime
  [ repeatStep=string ]
  [ repeatEnd=string ]
  >
    string
</surveyTime>

Documentation (element)

Units: User defined (defaults to steps) Min: 0

The simulation ends immediately after the last survey is taken.

Attributes

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Cohorts

→ scenario → monitoring → cohorts

<cohorts>
IN THIS ORDER:
| ( <subPop ... /> )+
</cohorts>

subPop

Documentation (element)

Allows the configuration of multiple cohorts (output segregated according to membership within specific sub-populations).

If this element is omitted, monitoring surveys cover the entire simulated human population.

It does not affect the "continuous" outputs (these never take cohorts into account).

Sub-population

→ scenario → monitoring → cohorts → subPop

<subPop
    id=string
    number=integer
  />

Documentation (element)

In the output file, the output set is identified by multiplying this number by 1000 then adding it to the age group column.

Attributes

Sub-population identifier

id=string

Textual identifier for the sub-population (i.e. for an intervention component, since sub-populations are defined as the hosts an intervention component is deployed to).

Sub-population number

number=integer

Units: dimensionless Min: 1 Max: 2097152

Number identifying a sub-population; used to define identifiers of output sets. This number must be a power of 2 (i.e. 1, 2, 4, 8, ...). See documentation of subPop element.

Preventative interventions

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfections ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <vectorPop ... /> ]
| [ <human ... /> ]
</interventions>

Documentation (element)

Attributes

Name of intervention set

name=string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeHS>

timedDeployment

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeHS → timedDeployment

<timedDeployment
    time=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timedDeployment>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</uncomplicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

multiple

→ scenario → interventions → human → component → decisionTree → multiple

<multiple
  [ name=string ]
  >
IN THIS ORDER:
| ( <caseType ... /> )*
| ( <diagnostic ... /> )*
| ( <random ... /> )*
| ( <age ... /> )*
| ( <treatPKPD ... /> )*
| [ <treatSimple ... /> ]
| ( <deploy ... /> )*
</multiple>

Documentation (type)

A special node allowing multiple sub-trees to be evaluated.

This is different from an ordinary decision tree node in that:

a) multiple types of child can occur simultaneously (e.g. multiple types of treatment or treatment plus a 'random' sub-tree)

b) the 'noTreatment' and 'treatFailure' nodes are not allowed

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → multiple → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

firstLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → firstLine

<firstLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</firstLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

secondLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → secondLine

<secondLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</secondLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

positive

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

outcome

→ scenario → interventions → human → component → decisionTree → multiple → random → outcome

<outcome
  [ name=string ]
    p=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</outcome>

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Probability

p=double

Units: None Min: 0 Max: 1

Probability of selecting this outcome. The sum of probabilities across all outcomes must be 1.

age

→ scenario → interventions → human → component → decisionTree → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Age range

→ scenario → interventions → human → component → decisionTree → multiple → age → age

<age
  [ name=string ]
    lb=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</age>

Documentation (element)

Describes a branch, selected for patients of a certain age.

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Lower bound (inclusive)

lb=double

Min: 0

noTreatment

→ scenario → interventions → human → component → decisionTree → noTreatment

<noTreatment
  [ name=string ]
  />

Documentation (type)

An end node doing nothing. This exists to explicitly state that no treatment happens and to prevent trees from accidentally being left incomplete.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatFailure

→ scenario → interventions → human → component → decisionTree → treatFailure

<treatFailure
  [ name=string ]
  />

Documentation (type)

An end node which reports treatment but does not change parasitalogical status. This allows correct labelling of second-line cases.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → multiple → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

age

→ scenario → interventions → human → component → decisionTree → multiple → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → multiple → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → multiple → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → multiple → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</complicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: Days Min: 0 Max: unbounded

Maximum number of timesteps (including first day of case) that an individual with an uncomplicated case of malaria will remember he/she was sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial or non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of a complicated or severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
  [ name=string ]
  [ useDiagnosticUC=boolean ] DEFAULT VALUE false
  >
IN ANY ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <treatmentActions ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
</ImmediateOutcomes>

Documentation (type)

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Name of case management parameterisation

name=string

Name of health system

useDiagnosticUC

useDiagnosticUC=boolean

Default value: false

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Description of drug regimen.

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Artemisinine based combination therapy

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Quinine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0 Max: 1name:P(self-treat)

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Effectiveness of treatment for non-compliant patients

treatmentActions

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions

<treatmentActions>
IN ANY ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
</treatmentActions>

CQ
SP
AQ
SPAQ
ACT
QN

CQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ

<CQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</CQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

deploy

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy

<deploy
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ p=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| ( <component ... /> )+
</deploy>

component

Attributes

Maximum age of eligible humans

maxAge=double

Units: Years Min: 0

Maximum age of eligible humans (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible humans

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible humans (defaults to 0). Input is rounded to the nearest time step.

Probability of delivery to eligible humans

p=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Probability of this list of components being deployed, given that other constraints are met.

component

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Prophylactic treatment

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere → clearInfections

<clearInfections
    timesteps=string
    stage=("liver" or "blood" or "both")
  />

Documentation (element)

Attributes

Length of effect

timesteps=string

Units: User defined (defaults to steps)

Target stage

stage=("liver" or "blood" or "both")

SP

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SP

<SP
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SP>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

AQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → AQ

<AQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</AQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

SPAQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SPAQ

<SPAQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SPAQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

ACT

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → ACT

<ACT
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</ACT>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

QN

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → QN

<QN
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</QN>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

Probability that human is incompatible with liver-stage drug treatment

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pHumanCannotReceive

<pHumanCannotReceive
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that a human is determined to be unable to receive liver-stage drug treatment. Treatment is neither reported or given for such humans.

This is sampled once per human at birth.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Ignore liver-stage drug treatment incompatibility

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → ignoreCannotReceive

<ignoreCannotReceive
    value=boolean
  />

Documentation (element)

If true, ignore pHumanCannotReceive and consider all humans eligible for treatment; if false (or not specified), do not treat those demed incompatible with liver-stage drug treatment.

The point of this is that pHumanCannotReceive cannot be altered by changeHS interventions, but this property can be.

Attributes

Input parameter value

value=boolean

A boolean value.

Prob use in UC case

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → pUseUncomplicated

<pUseUncomplicated
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

This feature is deprecated; it is suggested to use the "simple treatment" feature configured to clear liver-stage parasites, leaving this option unset or zero.

Chance of liver-stage drug treatment being used for routine treatment of an uncomplicated case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Effectiveness

→ scenario → healthSystem → ImmediateOutcomes → liverStageDrug → effectivenessOnUse

<effectivenessOnUse
    value=double
  />

Documentation (element)

Units: Probability Min: 0 Max: 1

Chance that liver-stage drug treatment is effective.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

DecisionTree5Day

<DecisionTree5Day
  [ name=string ]
  >
IN ANY ORDER:
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <liverStageDrug ... /> ]
|   <treeUCOfficial ... /> 
|   <treeUCSelfTreat ... /> 
|   <cureRateSevere ... /> 
|   <treatmentSevere ... /> 
</DecisionTree5Day>

Documentation (type)

Besides greater flexibility, this allows treatment via PK/PD models.

Attributes

Name of case management parameterisation

name=string

Name of health system

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → DecisionTree5Day → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

liverStageDrug

→ scenario → healthSystem → DecisionTree5Day → liverStageDrug

<liverStageDrug>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
| [ <ignoreCannotReceive ... /> ]
| [ <pUseUncomplicated ... /> ]
|   <effectivenessOnUse ... /> 
</liverStageDrug>

Documentation (type)

Parameters for drug treatment which have an effect on the liver-stage of parasites (Primaquine and potentially Tafenoquine); for use with the Vivax model only.

Note: if this section is not listed, the following default values are assumed: pHumanCannotReceive=0, pUseUncomplicated=0, effectivenessOnUse=1.

treeUCOfficial

→ scenario → healthSystem → DecisionTree5Day → treeUCOfficial

<treeUCOfficial
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCOfficial>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treeUCSelfTreat

→ scenario → healthSystem → DecisionTree5Day → treeUCSelfTreat

<treeUCSelfTreat
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCSelfTreat>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Cure rate (severe cases)

→ scenario → healthSystem → DecisionTree5Day → cureRateSevere

<cureRateSevere
    value=double
  />

Documentation (element)

Min: 0 Max: 1

The probability of clearing parasites given access to appropriate (hospital) care, for a severe case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

treatmentSevere

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere

<treatmentSevere
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</treatmentSevere>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Case fatality rate for inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: Dimensionless

List of age-specific probabilities of sequelae in inpatients, during a severe bout of malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeEIR>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeEIR → timedDeployment

<timedDeployment
    eipDuration=int
    time=string
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timedDeployment>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Time

time=string

Units: User defined (defauls to steps) Min: 0

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=string ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=string

Units: User defined (default: steps) Min: 0

Default value: 0

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=string
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time of start

time=string

Units: User defined (defauls to steps) Min: 0

Insert R_0 case

<insertR_0Case
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</insertR_0Case>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → insertR_0Case → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Uninfect vectors

<uninfectVectors
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</uninfectVectors>

timedDeployment

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → uninfectVectors → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Vector population intervention

→ scenario → interventions → vectorPop

<vectorPop>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorPop>

intervention

Documentation (element)

Units: List of elements

A list of parameterisations of generic vector host-inspecific interventions.

intervention

→ scenario → interventions → vectorPop → intervention

<intervention
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

Units: List of elements

An intervention which may have various effects on the vector populations as a whole. (Not host specific.)

Multiple instances of this intervention class are allowed (multiple parameterisations, not just deployments).

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → vectorPop → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → vectorPop → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <seekingDeathRateIncrease ... /> ]
| [ <probDeathOvipositing ... /> ]
| [ <emergenceReduction ... /> ]
</anopheles>

Documentation (type)

Units: dimensionless Min: 0 Max: 1

Descriptions of the effects of vector interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Proportional increase in deaths while host searching

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease

<seekingDeathRateIncrease
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</seekingDeathRateIncrease>

decay

Documentation (element)

Units: dimensionless

Describe an effect on the increase in the death rate while host seeking (mu_vA) due to this intervention.

Enter the rate increase (i.e. if rate increases to 120% of normal, give 0.2). New death rate while seeking is old × (1 + increase) where increase is this factor given. Must have increas ≥ -1.

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Proportion ovipositing mosquitoes killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing

<probDeathOvipositing
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probDeathOvipositing>

decay

Documentation (element)

Units: dimensionless

Describe an effect of increased mortality while ovipositing due to this intervention. Enter the probability of dying due to this intervention.

Attributes

Initial probability of killing

initial=double

Units: dimensionless Min: 0 Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Proportion of emerging pupa killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction

<emergenceReduction
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</emergenceReduction>

decay

Documentation (element)

Units: dimensionless

Describe an effect on emergence of pupa into adults: this value is the proportion of emerging pupa which are killed by this intervention.

Attributes

Initial proportion reduction

initial=double

Units: dimensionless Min: -inf Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Vector population intervention deployment

→ scenario → interventions → vectorPop → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

deploy

→ scenario → interventions → vectorPop → intervention → timed → deploy

<deploy
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Human-specific interventions

→ scenario → interventions → human

<human>
IN THIS ORDER:
| ( <component ... /> )+
| ( <deployment ... /> )*
</human>

Documentation (element)

Encapsulates all interventions whose effects are specific to the human host: any interventions where target humans may be selected via population-coverage, age limits and sub-population membership.

Component

→ scenario → interventions → human → component

<component
    id=string
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <screen ... /> 
| |   <treatSimple ... /> 
| |   <treatPKPD ... /> 
| |   <decisionTree ... /> 
| |   <PEV ... /> 
| |   <BSV ... /> 
| |   <TBV ... /> 
| |   <ITN ... /> 
| |   <IRS ... /> 
| |   <GVI ... /> 
| | [ <recruitmentOnly ... /> ]
| |   <clearImmunity ... /> 
| [ <subPopRemoval ... /> ]
</component>

Documentation (element)

Each element describes one component: its effects, decay of the(se) effect(s), and related stuff (e.g. description of indirect decay and of usage levels).

Attributes

Component identifier

id=string

Name of component

name=string

An informal name/description for the component

screen

→ scenario → interventions → human → component → screen

<screen
    diagnostic=string
  >
IN THIS ORDER:
| ( <positive ... /> )*
| ( <negative ... /> )*
</screen>

Documentation (type)

This can be combined with MDA to achieve mass screen and treat (MSAT) or other types of mass screening intervention.

The use of the screening itself is reported (if enabled), but not the outcome. Deployment of interventions triggered by the screening may be reported, however.

Attributes

Name of diagnostic

diagnostic=string

Name of a parameterised diagnostic (see scenario/diagnostics).

positive

→ scenario → interventions → human → component → screen → positive

<positive
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → screen → negative

<negative
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

treatSimple

→ scenario → interventions → human → component → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

treatPKPD

→ scenario → interventions → human → component → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

decisionTree

→ scenario → interventions → human → component → decisionTree

<decisionTree
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</decisionTree>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Vaccines

→ scenario → interventions → human → component → PEV

<PEV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</PEV>

Documentation (element)

Pre-erythrocytic vaccine (PEV): prevents a proportion of infections from commencing.

Documentation (type)

Description of a vaccine's effect

Decay of effect

→ scenario → interventions → human → component → PEV → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Specification of decay of efficacy. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Variance parameter for vaccine efficacy

→ scenario → interventions → human → component → PEV → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vaccines

→ scenario → interventions → human → component → BSV

<BSV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</BSV>

Documentation (element)

Blood-stage vaccine (BSV): acts as a killing factor on blood-stage parasites. Exact action depends on the within host model.

Documentation (type)

Description of a vaccine's effect

Vaccines

→ scenario → interventions → human → component → TBV

<TBV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</TBV>

Documentation (element)

Transmission-blocking vaccine (TBV): one minus this scales the probability of transmission to mosquitoes

Documentation (type)

Description of a vaccine's effect

Bed nets

→ scenario → interventions → human → component → ITN

<ITN>
IN THIS ORDER:
| [ <usage ... /> ]
|   <holeRate ... /> 
|   <ripRate ... /> 
|   <ripFactor ... /> 
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
|   <attritionOfNets ... /> 
| ( <anophelesParams ... /> )+
</ITN>

Documentation (element)

Description of bed-net interventions (ITNs, LLINs).

Proportion of time nets are used by humans

→ scenario → interventions → human → component → ITN → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of nets by humans, from 0 to 1.

At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing.

See also "propActing" (proportion of bits for which net acts).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Rate at which holes are made

→ scenario → interventions → human → component → ITN → holeRate

<holeRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Holes per annum Min: 0

The rate at which new holes are made in nets.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ ln N( log(mean)-sigma²/2, sigma² ).

Equivalent R sample: rlnorm(n, log(m) - s*s/2, s)

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rate at which holes are enlarged

→ scenario → interventions → human → component → ITN → ripRate

<ripRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Rips per existing hole per annum Min: 0

Each existing hole has a probability of being ripped bigger according to a Poisson process with this rate as (only) parameter.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ ln N( log(mean)-sigma²/2, sigma² ).

Equivalent R sample: rlnorm(n, log(m) - s*s/2, s)

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rip factor

→ scenario → interventions → human → component → ITN → ripFactor

<ripFactor
    value=double
  />

Documentation (element)

Units: none Min: 0

This factor expresses how important rips are in increasing the hole.

The hole index of a net is h + F×x where h and x are the total numbers of holes and rips respectively and F is the rip factor.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → ITN → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: mg/m² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → human → component → ITN → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of nets. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Attrition of nets

→ scenario → interventions → human → component → ITN → attritionOfNets

<attritionOfNets
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: dimensionless

Specifies the rate at which nets are disposed of over time. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Humans are removed from the intervention component's sub-population on disposal (attrition) of their nets. Currently this event is not reported.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → human → component → ITN → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterrency ... /> 
| |   <twoStageDeterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which net acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency

<twoStageDeterrency>
IN ANY ORDER:
|   <entering ... /> 
|   <attacking ... /> 
</twoStageDeterrency>

Documentation (element)

Units: dimensionless

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

This deterrency model multiplies human attractiveness by pEnt×pAtt divided by a base factor to normalise the output to 1 when there are no nets.

RA (entering)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → entering

<entering
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless

pEnt represents the relative probability of entering due to ITNs: pEnt = exp(log(P)×p) where P is the insecticide factor and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

RA (attacking)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attacking

<attacking
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless

pAtt represents the relative probability of attacking a human after entering a house due to ITNs (i.e. of feeding/dying vs. flying off): pAtt = B + H×h + P×p + I×h×p where B is the base (without net) probability; H, P and I are the hole, insecticide and interaction factors respectively, h=exp(-holeIndex×holeScalingFactor) and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Pre-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Indoor residual spraying

→ scenario → interventions → human → component → IRS

<IRS>
IN THIS ORDER:
| [ <usage ... /> ]
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
| ( <anophelesParams ... /> )+
</IRS>

Documentation (element)

Description of indoor residual spraying interventions.

Documentation (type)

Description of effect for the more complex and probably more realistic Briet model: IRS has three effects, whos strength is calculated as a function of surviving insecticide content.

Proportion of Indoor residual spraying (IRS) interventions

→ scenario → interventions → human → component → IRS → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Indoor residual spraying (IRS) interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → IRS → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: μg/cm² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → human → component → IRS → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → IRS → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → IRS → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied by exp(P×log(p)) where P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Generic vector intervention

→ scenario → interventions → human → component → GVI

<GVI>
IN THIS ORDER:
| [ <usage ... /> ]
|   <decay ... /> 
| ( <anophelesParams ... /> )+
</GVI>

Documentation (element)

Note that all actions of this intervention component will decay according to a single decay function. If independant decay is wanted, a separate component can be used for each action.

Proportion of generic vector interventions

→ scenario → interventions → human → component → GVI → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of Generic vector interventions, from 0 to 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Decay

→ scenario → interventions → human → component → GVI → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Description of decay of all intervention effects. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → GVI → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <deterrency ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → GVI → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied this factor times survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Recruitment only

→ scenario → interventions → human → component → recruitmentOnly

<recruitmentOnly/>

Documentation (element)

Recruitment of a host into a sub-population.

Clear Immunity

→ scenario → interventions → human → component → clearImmunity

<clearImmunity/>

Documentation (element)

Removes all exposure-related immunitsy gained over time by hosts without removing infections (or affecting the ability to gain immunity through exposure).

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

subPopRemoval

→ scenario → interventions → human → component → subPopRemoval

<subPopRemoval
  [ onFirstBout=boolean ] DEFAULT VALUE false
  [ onFirstTreatment=boolean ] DEFAULT VALUE false
  [ onFirstInfection=boolean ] DEFAULT VALUE false
  [ afterYears=double ]
  />

Documentation (type)

ITN attrition also removes humans from sub-populations.

Attributes

Time to first episode only

onFirstBout=boolean

Default value: false

Time to first treatment only

onFirstTreatment=boolean

Default value: false

Time to first infection only

onFirstInfection=boolean

Default value: false

Remove from sub-population after

afterYears=double

Units: Years Min: 0

Deployment

→ scenario → interventions → human → deployment

<deployment
  [ name=string ]
  >
IN THIS ORDER:
| ( <component ... /> )+
| ( <continuous ... /> )*
| ( <timed ... /> )*
</deployment>

Documentation (element)

All components deployed by this intervention are deployed to the same people (each timed or continuous deployment selects recipients and then gives each recipient all components of the intervention).

Attributes

Intervention name

name=string

Name of intervention

component

→ scenario → interventions → human → deployment → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Age-based (continuous) deployment

→ scenario → interventions → human → deployment → continuous

<continuous>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| ( <deploy ... /> )+
</continuous>

Documentation (element)

List of ages at which deployment takes place (through EPI, post-natal and school-based programmes, etc.).

A sub-population restriction may be added as a property of the list of continuous deployments.

restrictToSubPop

→ scenario → interventions → human → deployment → continuous → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

deploy

→ scenario → interventions → human → deployment → continuous → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    targetAgeYrs=double
  [ begin=string ]
  [ end=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention. Input is rounded to the nearest time step.

First time active

begin=string

Units: User defined (defauls to steps)

End step

end=string

Units: User defined (defauls to steps)

Mass (timed) deployment

→ scenario → interventions → human → deployment → timed

<timed>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| [ <cumulativeCoverage ... /> ]
| ( <deploy ... /> )+
</timed>

Documentation (element)

List of timed deployments of the intervention (that is, of deployment campaigns).

Cumulative deployment mode can be specified for all deployments in a timed list. To allow multiple cumulative deployment descriptions, the entire timed list may be repeated.

restrictToSubPop

→ scenario → interventions → human → deployment → timed → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

Cumulative coverage

→ scenario → interventions → human → deployment → timed → cumulativeCoverage

<cumulativeCoverage
    component=string
  />

Documentation (element)

Attributes

Component identifier

component=string

The identifier (short name) of the component used when selecting people.

deploy

→ scenario → interventions → human → deployment → timed → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    time=string
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Time

time=string

Units: User defined (defauls to steps) Min: 0

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0

Maximum age of eligible individuals (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible individuals (defaults to 0). Input is rounded to the nearest time step.

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Description of health system.

Documentation (type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("forced" or "dynamic")
  [ scaledAnnualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Description of entomological data

Attributes

Entomology dataset name

name=string

Name of entomology data

Transmission model mode

mode=("forced" or "dynamic")

Override annual EIR

scaledAnnualEIR=double

Units: Infectious bites per adult per year

If set, the annual EIR (for all species of vector) is scaled to this level; can be omitted if not needed.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters of the transmission model

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <seasonality ... /> 
|   <mosq ... /> 
| [ <lifeCycle ... /> ]
| [ <simpleMPD ... /> ]
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial estimate of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial estimate of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial estimate of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Seasonality of transmission

→ scenario → entomology → vector → anopheles → seasonality

<seasonality
    input=("EIR")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <fourierSeries ... /> 
| |   <monthlyValues ... /> 
| |   <dailyValues ... /> 
</seasonality>

Documentation (element)

Specifies the seasonality of transmission and optionally the level of annual transmission.

Attributes

Seasonality input

input=("EIR")

Annual EIR

annualEIR=double

Units: Inoculations per adult per annum Min: 0

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries

<fourierSeries
    EIRRotateAngle=double
  >
IN THIS ORDER:
| ( <coeffic ... /> )*
</fourierSeries>

coeffic

Documentation (element)

Units: Infectious bites per adult per day

Attributes

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: Radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Pair of Fourier coefficients

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries → coeffic

<coeffic
    a=double
    b=double
  />

Documentation (element)

A pair of Fourier series coefficients. The first element specifies a1 and b1, the second a2 and b2, etc. Any number (from 0 up) of pairs may be given.

Attributes

a_n parameter of Fourier approximation to ln(EIR)

a=double

a_n parameter of Fourier approximation to ln(EIR) for some natural number n.

b_n parameter of Fourier approximation to ln(EIR)

b=double

b_n parameter of Fourier approximation to ln(EIR) for some natural number n.

List of monthly values

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues

<monthlyValues
    smoothing=("none" or "fourier")
  >
IN THIS ORDER:
| ( <value ... /> ){12,12}
</monthlyValues>

value

Documentation (element)

Description of seasonality from monthly values. Multiple smoothing methods are possible (see smoothing attribute).

List should contain twelve entries: January to December.

Attributes

Smoothing function

smoothing=("none" or "fourier")

How the monthly values are converted into a daily sequence of values:

none: no smoothing (step function)
Fourier: a Fourier series (with terms up to a2/b2) is fit to the sequence of monthly values and used to generate a smoothed list of daily values.

Monthly value

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Monthly value

List of daily values

→ scenario → entomology → vector → anopheles → seasonality → dailyValues

<dailyValues>
IN THIS ORDER:
| ( <value ... /> ){365,365}
</dailyValues>

value

Documentation (element)

Description of seasonality from daily values.

List should contain 365 entries: 1st January to 31st December.

Daily value

→ scenario → entomology → vector → anopheles → seasonality → dailyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Daily value

Mosquito feeding cycle parameters

→ scenario → entomology → vector → anopheles → mosq

<mosq
    minInfectedThreshold=double
  >
IN ANY ORDER:
|   <mosqRestDuration ... /> 
|   <extrinsicIncubationPeriod ... /> 
|   <mosqLaidEggsSameDayProportion ... /> 
|   <mosqSeekingDuration ... /> 
|   <mosqSurvivalFeedingCycleProbability ... /> 
|   <availabilityVariance ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <mosqProbOvipositing ... /> 
|   <mosqHumanBloodIndex ... /> 
</mosq>

Documentation (element)

Parameters describing the feeding cycle and human mosquito interaction of a single species of anopheles mosquito.

Attributes

Mininum infected threshold for mosquitos

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

Duration of the resting period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqRestDuration

<mosqRestDuration
    value=int
  />

Documentation (element)

Units: Days

name:Duration of the resting period of the vector (days);

Attributes

Input parameter value

value=int

An integer value.

Extrinsic incubation period

→ scenario → entomology → vector → anopheles → mosq → extrinsicIncubationPeriod

<extrinsicIncubationPeriod
    value=int
  />

Documentation (element)

Units: Days

name:Extrinsic incubation period (days)

Attributes

Input parameter value

value=int

An integer value.

Proportion of mosquitoes host seeking on same day as ovipositing

→ scenario → entomology → vector → anopheles → mosq → mosqLaidEggsSameDayProportion

<mosqLaidEggsSameDayProportion
    value=double
  />

Documentation (element)

Units: Proportion

Proportion of mosquitoes host seeking on same day as ovipositing

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Duration of the host-seeking period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqSeekingDuration

<mosqSeekingDuration
    value=double
  />

Documentation (element)

Units: Days

Duration of the host-seeking period of the vector (days)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito survives the feeding cycle

→ scenario → entomology → vector → anopheles → mosq → mosqSurvivalFeedingCycleProbability

<mosqSurvivalFeedingCycleProbability
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito survives the feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Variance in human availability rate

→ scenario → entomology → vector → anopheles → mosq → availabilityVariance

<availabilityVariance
    value=double
  />

Documentation (element)

Variance in availability rate of humans to mosquitoes. The mean rate is calculated based on other parameters.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito succesfully bites chosen host

→ scenario → entomology → vector → anopheles → mosq → mosqProbBiting

<mosqProbBiting
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito succesfully bites chosen host

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → mosq → mosqProbFindRestSite

<mosqProbFindRestSite
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito escapes host and finds a resting place after biting

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → mosq → mosqProbResting

<mosqProbResting
    mean=double
    variance=double
  />

Documentation (element)

Probability of mosquito successfully resting after finding a resting site

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of a mosquito successfully laying eggs given that it has rested

→ scenario → entomology → vector → anopheles → mosq → mosqProbOvipositing

<mosqProbOvipositing
    value=double
  />

Documentation (element)

Probability of a mosquito successfully laying eggs given that it has rested

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human blood index

→ scenario → entomology → vector → anopheles → mosq → mosqHumanBloodIndex

<mosqHumanBloodIndex
    value=double
  />

Documentation (element)

Units: Proportion

The proportion of resting mosquitoes which fed on human blood during the last feed.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mosquito life cycle parameters

→ scenario → entomology → vector → anopheles → lifeCycle

<lifeCycle
  [ estimatedLarvalResources=double ] DEFAULT VALUE 1e8
  >
IN ANY ORDER:
|   <eggStage ... /> 
|   <larvalStage ... /> 
|   <pupalStage ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</lifeCycle>

Documentation (element)

Parameters describing the life-cycle of this species of mosquito

Attributes

Estimate of larval resources

estimatedLarvalResources=double

Units: X

Default value: 1e8

Egg stage

→ scenario → entomology → vector → anopheles → lifeCycle → eggStage

<eggStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the egg stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

larvalStage

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage

<larvalStage>
</larvalStage>

daily

Documentation (type)

Parameters for the larval stage of development

Documentation (base type)

Parameters associated with a mosquito development stage.

Daily development

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage → daily

<daily
    resourceUsage=double
    effectCompetition=double
  />

Documentation (element)

Attributes

Resource usage

resourceUsage=double

Units: X

Resource usage during larval stage of development. Units are arbitrary.

Effect of competition

effectCompetition=double

Units: none

Effect of competition over resources on development.

Pupal stage

→ scenario → entomology → vector → anopheles → lifeCycle → pupalStage

<pupalStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the pupal stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → lifeCycle → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Simple Mosq-Pop-Dynamics parameters

→ scenario → entomology → vector → anopheles → simpleMPD

<simpleMPD>
IN ANY ORDER:
|   <developmentDuration ... /> 
|   <developmentSurvival ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</simpleMPD>

Documentation (element)

Parameters describing the simple mosquito population dynamics model.

This is a simpler version of the life-cycle model, requiring less parameters and with much simpler initialisation.

Duration

→ scenario → entomology → vector → anopheles → simpleMPD → developmentDuration

<developmentDuration
    value=int
  />

Documentation (element)

Units: Days Min: 1

Duration from egg laying to emergence in days.

Attributes

Input parameter value

value=int

An integer value.

Probability of survival

→ scenario → entomology → vector → anopheles → simpleMPD → developmentSurvival

<developmentSurvival
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that mosquito survives from the egg being laid to emergence, given no resouce limitations (no density constraints).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → simpleMPD → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Alternative (non-human) host paramters

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN ANY ORDER:
|   <mosqRelativeEntoAvailability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
</nonHumanHosts>

Documentation (element)

Min: 0

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of non-human host (ξ_i)

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqRelativeEntoAvailability

<mosqRelativeEntoAvailability
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Name of this species of non human hosts (must match up with those described per anopheles section).

Population size of alternative host species

number=double

Units: Number

Population size of this non-human host.

Parasite genetics

<parasiteGenetics
    samplingMode=("initial" or "tracking")
  >
IN THIS ORDER:
| ( <locus ... /> )+
</parasiteGenetics>

locus

Documentation (element)

A specification of genotypes of infection parasites.

May be omitted; in this case there is no modelling of genetic differences of infections (resistance, fitness).

Attributes

samplingMode

samplingMode=("initial" or "tracking")

Locus

→ scenario → parasiteGenetics → locus

<locus
    name=string
  >
IN THIS ORDER:
| ( <allele ... /> )+
</locus>

allele

Documentation (element)

Alleles at loci can affect fitness and resistance to any number of drugs.

Attributes

Name of locus

name=string

Name of the Locus

Allele

→ scenario → parasiteGenetics → locus → allele

<allele
    name=string
    initialFrequency=double
    fitness=double
  />

Documentation (element)

Describes an allele, or one possible genetic option of multiple at one point of variance.

Attributes

Name

name=string

Name of the allele; used to refer to it elsewhere.

Initial frequency

initialFrequency=double

Fitness factor

fitness=double

Drug parameters (PK, PD and usage)

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
|   <treatments ... /> 
|   <drugs ... /> 
</pharmacology>

Documentation (element)

Drug model parameters and drug usage parameters

Documentation (type)

A library of drug related data for the PK/PD model.

Treatments library

→ scenario → pharmacology → treatments

<treatments>
IN THIS ORDER:
| ( <schedule ... /> )+
| ( <dosages ... /> )+
</treatments>

Documentation (element)

A library of drug deployment schedules and dosages.

schedule

→ scenario → pharmacology → treatments → schedule

<schedule
    name=string
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

A schedule for the administration of drugs in a course of treatment.

Note that dose sizes are multiplied by some multiplier (see dosages) and the times of all doses may be delayed.

Attributes

Name

name=string

Name for referring to this deployment schedule

medicate

→ scenario → pharmacology → treatments → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  />

Attributes

drug

drug=string

Abbreviated name of drug compound

Drug dose (mg with multiplier)

mg=double

Units: mg per something

Quantity of drug compound in mg per something. A separate dosage table must be used when medicating, which may specify multipliers of this number based on patient age or weight.

Time of administration

hour=double

Units: Hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

dosages

→ scenario → pharmacology → treatments → dosages

<dosages
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | ( <age ... /> )+
| | ( <bodymass ... /> )+
| |   <multiply ... /> 
</dosages>

Documentation (type)

A table for selecting a dose size given an age.

Attributes

Name

name=string

Name for referring to this dosage table

age

→ scenario → pharmacology → treatments → dosages → age

<age
    lowerbound=double
    dose_mult=double
  />

Documentation (type)

Gives a dose multiplier for an age or body mass range.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in mg) is multiplied by this value for patients falling into this age range when this dosage table is used.

bodymass

→ scenario → pharmacology → treatments → dosages → bodymass

<bodymass
    lowerbound=double
    dose_mult=double
  />

Documentation (type)

Gives a dose multiplier for an age or body mass range.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in mg) is multiplied by this value for patients falling into this age range when this dosage table is used.

Multiply dose

→ scenario → pharmacology → treatments → dosages → multiply

<multiply
    by=("kg")
  />

Documentation (element)

Multiply the dose by some quantity, such as patient weight.

Attributes

By what?

by=("kg")

Quantity to multiply the dose by. Only option is "kg" (patient weight in kg).

Drug library

→ scenario → pharmacology → drugs

<drugs>
IN THIS ORDER:
| ( <drug ... /> )+
</drugs>

drug

Documentation (element)

A library of drug PK/PD data.

drug

→ scenario → pharmacology → drugs → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (type)

A drug description with PK/PD parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drugs → drug → PD

<PD
  [ locus=string ]
  >
IN THIS ORDER:
| ( <phenotype ... /> )+
</PD>

phenotype

Attributes

Locus

locus=string

PD parameters for some allele / resistance phenotype

→ scenario → pharmacology → drugs → drug → PD → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

Restrict phenotype applicability to certain alleles

→ scenario → pharmacology → drugs → drug → PD → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (element)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Maximal parasite killing rate

→ scenario → pharmacology → drugs → drug → PD → phenotype → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drugs → drug → PD → phenotype → IC50

<IC50
  [ sigma=double ] DEFAULT VALUE 0
  >
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Attributes

Sigma parameter for per-infection variation of IC50

sigma=double

Default value: 0

Distribution parameter describing per-infection variation of IC50. If zero or not specified, the IC50 is not sampled. See documentation of parent element.

Slope of effect curve

→ scenario → pharmacology → drugs → drug → PD → phenotype → slope

<slope>
    double
</slope>

Documentation (element)

Units: dimensionless

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drugs → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
| EXACTLY ONE OF:
| |   <half_life ... /> 
| | IN THIS ORDER:
| | |   <k ... /> 
| | |   <m_exponent ... /> 
| [ <k_a ... /> ]
| [ <conversion ... /> ]
|   <vol_dist ... /> 
| [ <compartment2 ... /> ]
| [ <compartment3 ... /> ]
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drugs → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drugs → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate λ, calculated as λ = ln(2) / half_life. The basic form of decay is C(t) = C0 * exp(-λ*t).

Alternatively, elimination rate can be specified via k and m_exponent.

Constant associated with elimination rate (k)

→ scenario → pharmacology → drugs → drug → PK → k

<k
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

If sigma > 0, k is sampled per-human from the log-normal distribution: ln N( ln(mean) - σ^2 / 2, σ^2).

Alternatively, elimination rate can be specified via half_life.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Constant associated with elimination rate (m_exponent)

→ scenario → pharmacology → drugs → drug → PK → m_exponent

<m_exponent>
    double
</m_exponent>

Documentation (element)

Units: day^-1 Min: 0

Alternatively, elimination rate can be specified via half_life.

Note that in the case of a conversion model, this applies to both the elimination and the conversion rates.

Absorption rate constant (k_a)

→ scenario → pharmacology → drugs → drug → PK → k_a

<k_a
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Min: 0

Absorption rate parameter. Not allowed for one compartment models, but required for two and three compartment models and one compartment with conversion model (for the parent drug only).

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Conversion parameters (parent drug)

→ scenario → pharmacology → drugs → drug → PK → conversion

<conversion>
IN ANY ORDER:
|   <metabolite ... /> 
|   <rate ... /> 
|   <molRatio ... /> 
</conversion>

Documentation (element)

Configures the parent drug in a conversion model.

To use a conversion model, the parent drug should have this section defined as well as half-life or k (direct elimination; this may be zero) and k_a (absorption rate; this may be large).

Metabolite drug (abbreviation)

→ scenario → pharmacology → drugs → drug → PK → conversion → metabolite

<metabolite>
    string
</metabolite>

Documentation (element)

The abbreviation of the metabolite drug (e.g. "DHA" or "DHA_AR").

Rate of conversion

→ scenario → pharmacology → drugs → drug → PK → conversion → rate

<rate
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Rate of conversion of parent drug to metabolite.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Molecular weight ratio

→ scenario → pharmacology → drugs → drug → PK → conversion → molRatio

<molRatio>
    double
</molRatio>

Documentation (element)

Ratio of molecular weights: molecular weight of the metabolite divided by molecular weight of the parent.

Volume of Distribution (Vd)

→ scenario → pharmacology → drugs → drug → PK → vol_dist

<vol_dist
  [ sigma=double ] DEFAULT VALUE 0
  >
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Attributes

Sigma parameter for per-human variation of Vd

sigma=double

Default value: 0

Distribution parameter describing per-human variation of volume of distribution. If zero or not specified, the parameter is not sampled. See documentation of parent element.

Second compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment2

<compartment2>
IN ANY ORDER:
|   <a12 ... /> 
|   <a21 ... /> 
</compartment2>

Documentation (element)

Optional element specifying conversion parameters to- and from- a second compartment.

Absorption rate to compartment 2 (a12)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → a12

<a12
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the first periphery compartment (2). The parameter k12 = a12 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Absorption rate from compartment 2 (a21)

→ scenario → pharmacology → drugs → drug → PK → compartment2 → a21

<a21
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the first periphery compartment (2) to the central compartment. The parameter k21 = a21 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Third compartment parameters

→ scenario → pharmacology → drugs → drug → PK → compartment3

<compartment3>
IN ANY ORDER:
|   <a13 ... /> 
|   <a31 ... /> 
</compartment3>

Documentation (element)

Optional element specifying conversion parameters to- and from- a third compartment.

Absorption rate to compartment 3 (a13)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → a13

<a13
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the central compartment to the second periphery compartment (3). The parameter k13 = a13 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Absorption rate from compartment 3 (a31)

→ scenario → pharmacology → drugs → drug → PK → compartment3 → a31

<a31
    mean=double
  [ cv=double ]
    distr=("lnorm" or "const")
  />

Documentation (element)

Units: day^-1 Min: 0

Absorption rate from the second periphery compartment (3) to the central compartment. The parameter k31 = a31 / m where m is the body mass (kg).

It is sampled per-patient when sigma > 0.

Documentation (type)

Parameters of some distribution. The mean is that provided and the standard deviation is cv*mean.

Log-normal: σ = cv * mean ; μ = ln(mean) - σ² / 2 ; X ~ ln N( μ, σ² ) ; equivalent R sample: rlnorm(1, log(mean) - ((cv * mean)^2) / 2, cv * mean).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the distribution.

Coefficient of variance

cv=double

Units: unitless

Coefficient of variance (mean * cv gives standard deviation). Must be specified when distribution is not constant.

Distribution

distr=("lnorm" or "const")

Selects the distribution to use. const: constant (no distribution). Setting cv=0 has the same behaviour. lnorm: log-normal distribution

Diagnostic parameters

→ scenario → diagnostics

<diagnostics>
IN THIS ORDER:
| ( <diagnostic ... /> )*
</diagnostics>

diagnostic

Documentation (element)

Diagnostic model parameters

diagnostic

→ scenario → diagnostics → diagnostic

<diagnostic
    name=string
  [ units=("Other" or "Garki" or "Malariatherapy") ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterministic ... /> 
| |   <stochastic ... /> 
</diagnostic>

Attributes

Name of diagnostic

name=string

Name of this diagnostic (parameterisation). May be used elsewhere in the XML document to refer to this set of diagnostic parameters.

Parasite density units / methodology

units=("Other" or "Garki" or "Malariatherapy")

Deterministic detection

→ scenario → diagnostics → diagnostic → deterministic

<deterministic
    minDensity=double
  />

Documentation (element)

Specify that an artificial deterministic test is used: outcome is positive if parasite density is at least the minimum given.

Attributes

Minimum detectible density

minDensity=double

Units: parasites/microlitre Min: 0

The minimum density at which parasites can be detected. If 0, the test outcome is always positive.

Non-deterministic detection

→ scenario → diagnostics → diagnostic → stochastic

<stochastic
    dens_50=double
    specificity=double
  />

Documentation (element)

An improved model of detection which is non-deterministic, including false positive results as well as false negatives.

Some parameterisations:

Microscopy sensitivity/specificity data in Africa; Source: expert opinion — Allan Schapira dens_50 = 20.0 specificity = .75

RDT sensitivity/specificity for Plasmodium falciparum in Africa Source: Murray et al (Clinical Microbiological Reviews, Jan. 2008) dens_50 = 50.0; specificity = .942;

Attributes

Density 50

dens_50=double

Units: parasites/microlitre Min: 0

The density at which the test outcome has a 50% chance of being positive.

Specificity

specificity=double

Units: Dimensionless Min: 0 Max: 1

The probability of a positive test outcome in the absense of parasites.

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
| [ <vivax ... /> ]
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: model/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=string
  >
IN ANY ORDER:
| [ <NeonatalMortality ... /> ]
| [ <NonMalariaFevers ... /> ]
</clinical>

Documentation (type)

Attributes

Follow-up period during which recurrence is considered a treatment failure

healthSystemMemory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

Neonatal mortality parameters

→ scenario → model → clinical → NeonatalMortality

<NeonatalMortality
    diagnostic=string
  />

Attributes

Diagnostic used to parameterise model

diagnostic=string

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
| [ <prNeedTreatmentNMF ... /> ]
| [ <prNeedTreatmentMF ... /> ]
</NonMalariaFevers>

Documentation (type)

Description of the incidence of non-malaria fever. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a non-malarial fever requires treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

Availability of humans to mosquitoes relative to an adult, categorized by age group

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ]
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

vivax

→ scenario → model → vivax

<vivax>
IN ANY ORDER:
|   <probBloodStageInfectiousToMosq ... /> 
|   <hypnozoiteRelease ... /> 
|   <bloodStageProtectionLatency ... /> 
|   <bloodStageLengthDays ... /> 
|   <clinicalEvents ... /> 
</vivax>

probBloodStageInfectiousToMosq

→ scenario → model → vivax → probBloodStageInfectiousToMosq

<probBloodStageInfectiousToMosq
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

hypnozoiteRelease

→ scenario → model → vivax → hypnozoiteRelease

<hypnozoiteRelease
  [ pSecondRelease=double ] DEFAULT VALUE 0
  >
IN ANY ORDER:
|   <numberHypnozoites ... /> 
|   <firstRelease ... /> 
| [ <secondRelease ... /> ]
</hypnozoiteRelease>

Documentation (type)

This element defines probabilites when and how many hypnozoites are released from the liverstage into the blood.

The gap between the start of a new brood of hypnozoites and its release are defined as follows:

latentP + latentRelapseDays + randomReleaseDelay

randomReleaseDelay is based on one or two lognormal distributions, which are defined in firstRelease and optionally secondRelease.

You can define 2 release distributions, which get added together and represent the probability of hypnozoites which get released before winter (first release) or after (second release).

You can omit the secondRelease element if no release to the blood happens after winter.

Attributes

latent relapse days

pSecondRelease=double

Default value: 0

Probability of a second release. If undefined it is zero.

Number of Hypnozoites

→ scenario → model → vivax → hypnozoiteRelease → numberHypnozoites

<numberHypnozoites
    max=int
    base=double
  />

Documentation (element)

numberHypnozoites calculates the number of hypnozoites in the liver stage based on a base which is between 0 and 1.

This number is random based on the following distribution and normalized:

max ∑ (base ^ n) n = 0

Attributes

max

max=int

base

base=double

firstRelease

→ scenario → model → vivax → hypnozoiteRelease → firstRelease

<firstRelease
    mu=double
    sigma=double
    latentRelapseDays=int
  />

Documentation (base type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

latent relapse days

latentRelapseDays=int

Usually 15 days or 10 days (3 or 2 5-day timesteps).

secondRelease

→ scenario → model → vivax → hypnozoiteRelease → secondRelease

<secondRelease
    mu=double
    sigma=double
    latentRelapseDays=int
  />

Documentation (base type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

latent relapse days

latentRelapseDays=int

Usually 15 days or 10 days (3 or 2 5-day timesteps).

bloodStageProtectionLatency

→ scenario → model → vivax → bloodStageProtectionLatency

<bloodStageProtectionLatency
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

bloodStageLengthDays

→ scenario → model → vivax → bloodStageLengthDays

<bloodStageLengthDays
    weibullScale=double
    weibullShape=double
  />

Attributes

weibullScale

weibullScale=double

weibullShape

weibullShape=double

clinicalEvents

→ scenario → model → vivax → clinicalEvents

<clinicalEvents>
IN THIS ORDER:
|   <pPrimaryInfection ... /> 
|   <pRelapseOne ... /> 
|   <pRelapseTwoPlus ... /> 
|   <pEventIsSevere ... /> 
</clinicalEvents>

Documentation (type)

This elements holds all information about probabilites for clinical events from infections and relapses.

pPrimaryInfection

→ scenario → model → vivax → clinicalEvents → pPrimaryInfection

<pPrimaryInfection
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseOne

→ scenario → model → vivax → clinicalEvents → pRelapseOne

<pRelapseOne
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pRelapseTwoPlus

→ scenario → model → vivax → clinicalEvents → pRelapseTwoPlus

<pRelapseTwoPlus
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pEventIsSevere

→ scenario → model → vivax → clinicalEvents → pEventIsSevere

<pEventIsSevere
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=string
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=string

Units: User defined (default: steps) Min: 0 Max: 20

Pre-erythrocytic latent period Can be specified in steps (e.g. 3t) or days (e.g. 15d).

parameter

→ scenario → model → parameters → parameter

<parameter
  [ name=string ]
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 33 documentation

Generated from: scenario_33.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
  [ analysisNo=int ]
    name=string
  [ wuID=int ]
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:om="http://openmalaria.org/schema/scenario_33"
    xsi:schemaLocation="http://openmalaria.org/schema/scenario_33 scenario_33.xsd"
  >
IN ANY ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entomology ... /> 
| [ <parasiteGenetics ... /> ]
| [ <pharmacology ... /> ]
| [ <diagnostics ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Name of intervention

Work unit identifier

wuID=int

Units: Number

Work unit ID. Obselete and no longer required.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Description of demography

Attributes

Name of demography data

name=string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Years Min: 0 Max: 100

Maximum age of simulated humans in years

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

list of age groups included in demography

Documentation (type)

list of age groups included in demography or surveys

Attributes

Lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Units: Percentage Min: 0 Max: 100

Percentage of human population in age group

Upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ startDate=string ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
| [ <cohorts ... /> ]
</monitoring>

Documentation (element)

Description of surveys

Attributes

Name of monitoring settings

name=string

Name of monitoring settings

Start of monitoring

startDate=string

continuous

→ scenario → monitoring → continuous

<continuous
    period=string
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Delay between reports

period=string

Units: User defined (default: steps)

Delay between reports; typically one time step but can be greater. Can be specified in steps (e.g. 1t) or days (e.g. 5d).

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

option

→ scenario → monitoring → SurveyOptions → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  [ outputNumber=int ]
  [ byAge=boolean ]
  [ byCohort=boolean ]
  [ bySpecies=boolean ]
  [ byGenotype=boolean ]
  [ byDrugType=boolean ]
  />

Attributes

Option name

name=string

Name of an option (monitoring measure or model option).

Indicator of whether option is required

value=boolean

Default value: true

Number identifying measure in output

outputNumber=int

Report by age category

byAge=boolean

Report by cohort

byCohort=boolean

Report by mosquito species

bySpecies=boolean

Report by parasite genotype

byGenotype=boolean

Report by drug type

byDrugType=boolean

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
  [ detectionLimit=double ]
  [ diagnostic=string ]
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

Units: list of elements

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/microlitre Min: 0

Deprecated: limit above which a human's infection is reported as patent. Alternative: do not specify this; instead specify "diagnostic".

Name of monitoring diagnostic

diagnostic=string

Name of a parameterised diagnostic to use in surveys (see scenario/diagnostics).

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime
  [ repeatStep=string ]
  [ repeatEnd=string ]
  >
    string
</surveyTime>

Documentation (element)

Units: User defined (defaults to steps) Min: 0

The simulation ends immediately after the last survey is taken.

Attributes

Step of repetition

repeatStep=string

Units: User defined

See repeatEnd's documentation.

End of repetition (exclusive)

repeatEnd=string

Units: User defined

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Cohorts

→ scenario → monitoring → cohorts

<cohorts>
IN THIS ORDER:
| ( <subPop ... /> )+
</cohorts>

subPop

Documentation (element)

Allows the configuration of multiple cohorts (output segregated according to membership within specific sub-populations).

If this element is omitted, monitoring surveys cover the entire simulated human population.

It does not affect the "continuous" outputs (these never take cohorts into account).

Sub-population

→ scenario → monitoring → cohorts → subPop

<subPop
    id=string
    number=integer
  />

Documentation (element)

In the output file, the output set is identified by multiplying this number by 1000 then adding it to the age group column.

Attributes

Sub-population identifier

id=string

Textual identifier for the sub-population (i.e. for an intervention component, since sub-populations are defined as the hosts an intervention component is deployed to).

Sub-population number

number=integer

Units: dimensionless Min: 1 Max: 2097152

Number identifying a sub-population; used to define identifiers of output sets. This number must be a power of 2 (i.e. 1, 2, 4, 8, ...). See documentation of subPop element.

Preventative interventions

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfections ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <vectorPop ... /> ]
| [ <human ... /> ]
</interventions>

Documentation (element)

Attributes

Name of intervention set

name=string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeHS>

timedDeployment

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeHS → timedDeployment

<timedDeployment
    time=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timedDeployment>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</uncomplicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

multiple

→ scenario → interventions → human → component → decisionTree → multiple

<multiple
  [ name=string ]
  >
IN THIS ORDER:
| ( <caseType ... /> )*
| ( <diagnostic ... /> )*
| ( <random ... /> )*
| ( <age ... /> )*
| ( <treatPKPD ... /> )*
| [ <treatSimple ... /> ]
| ( <deploy ... /> )*
</multiple>

Documentation (type)

A special node allowing multiple sub-trees to be evaluated.

This is different from an ordinary decision tree node in that:

a) multiple types of child can occur simultaneously (e.g. multiple types of treatment or treatment plus a 'random' sub-tree)

b) the 'noTreatment' and 'treatFailure' nodes are not allowed

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → multiple → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

firstLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → firstLine

<firstLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</firstLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

caseType

→ scenario → interventions → human → component → decisionTree → caseType

<caseType
  [ name=string ]
  >
IN ANY ORDER:
|   <firstLine ... /> 
|   <secondLine ... /> 
</caseType>

Documentation (type)

A switch which choses a branch deterministically, based on whether the patient was treated recently (second line) or not (first line).

For uncomplicated cases only.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

secondLine

→ scenario → interventions → human → component → decisionTree → multiple → caseType → secondLine

<secondLine
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</secondLine>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

positive

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → positive

<positive
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</positive>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

outcome

→ scenario → interventions → human → component → decisionTree → multiple → random → outcome

<outcome
  [ name=string ]
    p=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</outcome>

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Probability

p=double

Units: None Min: 0 Max: 1

Probability of selecting this outcome. The sum of probabilities across all outcomes must be 1.

age

→ scenario → interventions → human → component → decisionTree → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Age range

→ scenario → interventions → human → component → decisionTree → multiple → age → age

<age
  [ name=string ]
    lb=double
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</age>

Documentation (element)

Describes a branch, selected for patients of a certain age.

Documentation (base type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Lower bound (inclusive)

lb=double

Min: 0

noTreatment

→ scenario → interventions → human → component → decisionTree → noTreatment

<noTreatment
  [ name=string ]
  />

Documentation (type)

An end node doing nothing. This exists to explicitly state that no treatment happens and to prevent trees from accidentally being left incomplete.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatFailure

→ scenario → interventions → human → component → decisionTree → treatFailure

<treatFailure
  [ name=string ]
  />

Documentation (type)

An end node which reports treatment but does not change parasitalogical status. This allows correct labelling of second-line cases.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic → negative

<negative
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</negative>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

diagnostic

→ scenario → interventions → human → component → decisionTree → multiple → diagnostic

<diagnostic
    diagnostic=string
  [ name=string ]
  >
IN ANY ORDER:
|   <positive ... /> 
|   <negative ... /> 
</diagnostic>

Documentation (type)

A switch which choses a branch deterministically, based on the outcome of some type of diagnostic.

Attributes

Name of diagnostic

diagnostic=string

Should match the name of some parameterised diagnostic (see scenario/diagnostics).

Name

name=string

An optional piece of documentation attached to this node.

random

→ scenario → interventions → human → component → decisionTree → multiple → random

<random
  [ name=string ]
  >
IN THIS ORDER:
| ( <outcome ... /> )+
</random>

outcome

Documentation (type)

A switch which choses a branch randomly.

Each branch must be listed with a probability; the sum of all these probabilities must equal 1.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

age

→ scenario → interventions → human → component → decisionTree → multiple → age

<age
  [ name=string ]
  >
IN THIS ORDER:
| ( <age ... /> )+
</age>

Documentation (type)

A switch which choses a branch deterministically, based on the patient's age (in years).

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treatPKPD

→ scenario → interventions → human → component → decisionTree → multiple → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

treatSimple

→ scenario → interventions → human → component → decisionTree → multiple → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

deploy

→ scenario → interventions → human → component → decisionTree → multiple → deploy

<deploy
    component=string
  />

Documentation (type)

Deploy one or more intervention components.

Attributes

Component identifier

component=string

The identifier (short name) of a component.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</complicated>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: Days Min: 0 Max: unbounded

Maximum number of timesteps (including first day of case) that an individual with an uncomplicated case of malaria will remember he/she was sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial or non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of a complicated or severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
  [ name=string ]
  [ useDiagnosticUC=boolean ] DEFAULT VALUE false
  >
IN ANY ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <treatmentActions ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <primaquine ... /> ]
</ImmediateOutcomes>

Documentation (type)

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Name of case management parameterisation

name=string

Name of health system

useDiagnosticUC

useDiagnosticUC=boolean

Default value: false

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Description of drug regimen.

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Artemisinine based combination therapy

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Quinine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0 Max: 1name:P(self-treat)

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Effectiveness of treatment for non-compliant patients

treatmentActions

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions

<treatmentActions>
IN ANY ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
</treatmentActions>

CQ
SP
AQ
SPAQ
ACT
QN

CQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ

<CQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</CQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

deploy

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy

<deploy
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ p=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| ( <component ... /> )+
</deploy>

component

Attributes

Maximum age of eligible humans

maxAge=double

Units: Years Min: 0

Maximum age of eligible humans (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible humans

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible humans (defaults to 0). Input is rounded to the nearest time step.

Probability of delivery to eligible humans

p=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Probability of this list of components being deployed, given that other constraints are met.

component

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → deploy → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Prophylactic treatment

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere → clearInfections

<clearInfections
    timesteps=string
    stage=("liver" or "blood" or "both")
  />

Documentation (element)

Attributes

Length of effect

timesteps=string

Units: User defined (defaults to steps)

Target stage

stage=("liver" or "blood" or "both")

SP

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SP

<SP
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SP>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

AQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → AQ

<AQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</AQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

SPAQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SPAQ

<SPAQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SPAQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

ACT

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → ACT

<ACT
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</ACT>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

QN

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → QN

<QN
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</QN>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

primaquine

→ scenario → healthSystem → ImmediateOutcomes → primaquine

<primaquine>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
|   <pUseUncomplicated ... /> 
|   <effectivenessOnUse ... /> 
</primaquine>

pHumanCannotReceive

→ scenario → healthSystem → ImmediateOutcomes → primaquine → pHumanCannotReceive

<pHumanCannotReceive
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

pUseUncomplicated

→ scenario → healthSystem → ImmediateOutcomes → primaquine → pUseUncomplicated

<pUseUncomplicated
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

effectivenessOnUse

→ scenario → healthSystem → ImmediateOutcomes → primaquine → effectivenessOnUse

<effectivenessOnUse
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

DecisionTree5Day

<DecisionTree5Day
  [ name=string ]
  >
IN ANY ORDER:
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <primaquine ... /> ]
|   <treeUCOfficial ... /> 
|   <treeUCSelfTreat ... /> 
|   <cureRateSevere ... /> 
|   <treatmentSevere ... /> 
</DecisionTree5Day>

Documentation (type)

Besides greater flexibility, this allows treatment via PK/PD models.

Attributes

Name of case management parameterisation

name=string

Name of health system

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → DecisionTree5Day → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease without recent history of disease (i.e. first line) will self-treat.

Note that in second line cases there is no probability of self-treatment.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → DecisionTree5Day → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

primaquine

→ scenario → healthSystem → DecisionTree5Day → primaquine

<primaquine>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
|   <pUseUncomplicated ... /> 
|   <effectivenessOnUse ... /> 
</primaquine>

treeUCOfficial

→ scenario → healthSystem → DecisionTree5Day → treeUCOfficial

<treeUCOfficial
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCOfficial>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

treeUCSelfTreat

→ scenario → healthSystem → DecisionTree5Day → treeUCSelfTreat

<treeUCSelfTreat
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</treeUCSelfTreat>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Cure rate (severe cases)

→ scenario → healthSystem → DecisionTree5Day → cureRateSevere

<cureRateSevere
    value=double
  />

Documentation (element)

Min: 0 Max: 1

The probability of clearing parasites given access to appropriate (hospital) care, for a severe case.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

treatmentSevere

→ scenario → healthSystem → DecisionTree5Day → treatmentSevere

<treatmentSevere
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</treatmentSevere>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Case fatality rate for inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: Dimensionless

List of age-specific probabilities of sequelae in inpatients, during a severe bout of malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeEIR>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeEIR → timedDeployment

<timedDeployment
    eipDuration=int
    time=string
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timedDeployment>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Time

time=string

Units: User defined (defauls to steps) Min: 0

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=string ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=string

Units: User defined (default: steps) Min: 0

Default value: 0

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=string
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time of start

time=string

Units: User defined (defauls to steps) Min: 0

Insert R_0 case

<insertR_0Case
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</insertR_0Case>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → insertR_0Case → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Uninfect vectors

<uninfectVectors
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</uninfectVectors>

timedDeployment

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → uninfectVectors → timedDeployment

<timedDeployment
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Vector population intervention

→ scenario → interventions → vectorPop

<vectorPop>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorPop>

intervention

Documentation (element)

Units: List of elements

A list of parameterisations of generic vector host-inspecific interventions.

intervention

→ scenario → interventions → vectorPop → intervention

<intervention
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

Units: List of elements

An intervention which may have various effects on the vector populations as a whole. (Not host specific.)

Multiple instances of this intervention class are allowed (multiple parameterisations, not just deployments).

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → vectorPop → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → vectorPop → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <seekingDeathRateIncrease ... /> ]
| [ <probDeathOvipositing ... /> ]
| [ <emergenceReduction ... /> ]
</anopheles>

Documentation (type)

Units: dimensionless Min: 0 Max: 1

Descriptions of the effects of vector interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Proportional increase in deaths while host searching

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease

<seekingDeathRateIncrease
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</seekingDeathRateIncrease>

decay

Documentation (element)

Units: dimensionless

Describe an effect on the increase in the death rate while host seeking (mu_vA) due to this intervention.

Enter the rate increase (i.e. if rate increases to 120% of normal, give 0.2). New death rate while seeking is old × (1 + increase) where increase is this factor given. Must have increas ≥ -1.

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Proportion ovipositing mosquitoes killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing

<probDeathOvipositing
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probDeathOvipositing>

decay

Documentation (element)

Units: dimensionless

Describe an effect of increased mortality while ovipositing due to this intervention. Enter the probability of dying due to this intervention.

Attributes

Initial probability of killing

initial=double

Units: dimensionless Min: 0 Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Proportion of emerging pupa killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction

<emergenceReduction
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</emergenceReduction>

decay

Documentation (element)

Units: dimensionless

Describe an effect on emergence of pupa into adults: this value is the proportion of emerging pupa which are killed by this intervention.

Attributes

Initial proportion reduction

initial=double

Units: dimensionless Min: -inf Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Vector population intervention deployment

→ scenario → interventions → vectorPop → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

deploy

→ scenario → interventions → vectorPop → intervention → timed → deploy

<deploy
    time=string
  />

Attributes

Time

time=string

Units: User defined (defauls to steps) Min: 0

Human-specific interventions

→ scenario → interventions → human

<human>
IN THIS ORDER:
| ( <component ... /> )+
| ( <deployment ... /> )*
</human>

Documentation (element)

Encapsulates all interventions whose effects are specific to the human host: any interventions where target humans may be selected via population-coverage, age limits and sub-population membership.

Component

→ scenario → interventions → human → component

<component
    id=string
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <screen ... /> 
| |   <treatSimple ... /> 
| |   <treatPKPD ... /> 
| |   <decisionTree ... /> 
| |   <PEV ... /> 
| |   <BSV ... /> 
| |   <TBV ... /> 
| |   <ITN ... /> 
| |   <IRS ... /> 
| |   <GVI ... /> 
| | [ <recruitmentOnly ... /> ]
| |   <clearImmunity ... /> 
| [ <subPopRemoval ... /> ]
</component>

Documentation (element)

Each element describes one component: its effects, decay of the(se) effect(s), and related stuff (e.g. description of indirect decay and of usage levels).

Attributes

Component identifier

id=string

Name of component

name=string

An informal name/description for the component

screen

→ scenario → interventions → human → component → screen

<screen
    diagnostic=string
  >
IN THIS ORDER:
| ( <positive ... /> )*
| ( <negative ... /> )*
</screen>

Documentation (type)

This can be combined with MDA to achieve mass screen and treat (MSAT) or other types of mass screening intervention.

The use of the screening itself is reported (if enabled), but not the outcome. Deployment of interventions triggered by the screening may be reported, however.

Attributes

Name of diagnostic

diagnostic=string

Name of a parameterised diagnostic (see scenario/diagnostics).

positive

→ scenario → interventions → human → component → screen → positive

<positive
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

negative

→ scenario → interventions → human → component → screen → negative

<negative
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

treatSimple

→ scenario → interventions → human → component → treatSimple

<treatSimple
    durationLiver=string
    durationBlood=string
  />

Documentation (type)

Infections are considered liver-stage when less than five days old and blood-stage after that. Effects are described independently for the two stages.

Attributes

Length of liver-stage effect

durationLiver=string

Units: User defined

Length of blood-stage effect

durationBlood=string

Units: User defined

treatPKPD

→ scenario → interventions → human → component → treatPKPD

<treatPKPD
    schedule=string
    dosage=string
  [ delay_h=double ] DEFAULT VALUE 0
  />

Documentation (type)

A command to administer drugs according to a given schedule and dosage table, optionally with a delay.

Attributes

Name of treatment schedule

schedule=string

The name of a schedule to use for treatment.

Name of dosage table

dosage=string

The name of a dosage table to use for treatment.

Delay (hours)

delay_h=double

Default value: 0

decisionTree

→ scenario → interventions → human → component → decisionTree

<decisionTree
  [ name=string ]
  >
EXACTLY ONE OF:
|   <multiple ... /> 
|   <caseType ... /> 
|   <diagnostic ... /> 
|   <random ... /> 
|   <age ... /> 
|   <noTreatment ... /> 
|   <treatFailure ... /> 
| ( <treatPKPD ... /> )+
|   <treatSimple ... /> 
| ( <deploy ... /> )+
</decisionTree>

Documentation (type)

Describes how "decisions" are made, both probabilistically and deterministically, and what actions are carried out.

Quantities may also be reported as a side effect of decisions made in the tree, for example the number of diagnostics used.

Attributes

Name

name=string

An optional piece of documentation attached to this node.

Vaccines

→ scenario → interventions → human → component → PEV

<PEV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</PEV>

Documentation (element)

Pre-erythrocytic vaccine (PEV): prevents a proportion of infections from commencing.

Documentation (type)

Description of a vaccine's effect

Decay of effect

→ scenario → interventions → human → component → PEV → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Specification of decay of efficacy. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Variance parameter for vaccine efficacy

→ scenario → interventions → human → component → PEV → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vaccines

→ scenario → interventions → human → component → BSV

<BSV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</BSV>

Documentation (element)

Blood-stage vaccine (BSV): acts as a killing factor on blood-stage parasites. Exact action depends on the within host model.

Documentation (type)

Description of a vaccine's effect

Vaccines

→ scenario → interventions → human → component → TBV

<TBV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</TBV>

Documentation (element)

Transmission-blocking vaccine (TBV): one minus this scales the probability of transmission to mosquitoes

Documentation (type)

Description of a vaccine's effect

Bed nets

→ scenario → interventions → human → component → ITN

<ITN>
IN THIS ORDER:
|   <usage ... /> 
|   <holeRate ... /> 
|   <ripRate ... /> 
|   <ripFactor ... /> 
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
|   <attritionOfNets ... /> 
| ( <anophelesParams ... /> )+
</ITN>

Documentation (element)

Description of bed-net interventions (ITNs, LLINs).

Proportion of time nets are used by humans

→ scenario → interventions → human → component → ITN → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of nets by humans, from 0 to 1.

At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing.

See also "propActing" (proportion of bits for which net acts).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Rate at which holes are made

→ scenario → interventions → human → component → ITN → holeRate

<holeRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Holes per annum Min: 0

The rate at which new holes are made in nets.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ log N( log(mean)-sigma²/2, sigma² ).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rate at which holes are enlarged

→ scenario → interventions → human → component → ITN → ripRate

<ripRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Rips per existing hole per annum Min: 0

Each existing hole has a probability of being ripped bigger according to a Poisson process with this rate as (only) parameter.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ log N( log(mean)-sigma²/2, sigma² ).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rip factor

→ scenario → interventions → human → component → ITN → ripFactor

<ripFactor
    value=double
  />

Documentation (element)

Units: none Min: 0

This factor expresses how important rips are in increasing the hole.

The hole index of a net is h + F×x where h and x are the total numbers of holes and rips respectively and F is the rip factor.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → ITN → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: mg/m² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → human → component → ITN → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of nets. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Attrition of nets

→ scenario → interventions → human → component → ITN → attritionOfNets

<attritionOfNets
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: dimensionless

Specifies the rate at which nets are disposed of over time. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Humans are removed from the intervention component's sub-population on disposal (attrition) of their nets. Currently this event is not reported.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → human → component → ITN → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterrency ... /> 
| |   <twoStageDeterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which net acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency

<twoStageDeterrency>
IN ANY ORDER:
|   <entering ... /> 
|   <attacking ... /> 
</twoStageDeterrency>

Documentation (element)

Units: dimensionless

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

This deterrency model multiplies human attractiveness by pEnt×pAtt divided by a base factor to normalise the output to 1 when there are no nets.

RA (entering)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → entering

<entering
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless

pEnt represents the relative probability of entering due to ITNs: pEnt = exp(log(P)×p) where P is the insecticide factor and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

RA (attacking)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attacking

<attacking
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless

pAtt represents the relative probability of attacking a human after entering a house due to ITNs (i.e. of feeding/dying vs. flying off): pAtt = B + H×h + P×p + I×h×p where B is the base (without net) probability; H, P and I are the hole, insecticide and interaction factors respectively, h=exp(-holeIndex×holeScalingFactor) and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Pre-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Indoor residual spraying

→ scenario → interventions → human → component → IRS

<IRS>
IN THIS ORDER:
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
| ( <anophelesParams ... /> )+
</IRS>

Documentation (element)

Description of indoor residual spraying interventions.

Documentation (type)

Description of effect for the more complex and probably more realistic Briet model: IRS has three effects, whos strength is calculated as a function of surviving insecticide content.

Initial insecticide

→ scenario → interventions → human → component → IRS → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: μg/cm² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → human → component → IRS → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → IRS → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → IRS → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied by exp(P×log(p)) where P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Generic vector intervention

→ scenario → interventions → human → component → GVI

<GVI>
IN THIS ORDER:
|   <decay ... /> 
| ( <anophelesParams ... /> )+
</GVI>

Documentation (element)

Note that all actions of this intervention component will decay according to a single decay function. If independant decay is wanted, a separate component can be used for each action.

Decay

→ scenario → interventions → human → component → GVI → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
  [ L=string ]
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Description of decay of all intervention effects. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=string

Units: User-defined (defaults to years) Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → GVI → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <deterrency ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → GVI → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied this factor times survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Recruitment only

→ scenario → interventions → human → component → recruitmentOnly

<recruitmentOnly/>

Documentation (element)

Recruitment of a host into a sub-population.

Clear Immunity

→ scenario → interventions → human → component → clearImmunity

<clearImmunity/>

Documentation (element)

Removes all exposure-related immunitsy gained over time by hosts without removing infections (or affecting the ability to gain immunity through exposure).

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

subPopRemoval

→ scenario → interventions → human → component → subPopRemoval

<subPopRemoval
  [ onFirstBout=boolean ] DEFAULT VALUE false
  [ onFirstTreatment=boolean ] DEFAULT VALUE false
  [ onFirstInfection=boolean ] DEFAULT VALUE false
  [ afterYears=double ]
  />

Documentation (type)

ITN attrition also removes humans from sub-populations.

Attributes

Time to first episode only

onFirstBout=boolean

Default value: false

Time to first treatment only

onFirstTreatment=boolean

Default value: false

Time to first infection only

onFirstInfection=boolean

Default value: false

Remove from sub-population after

afterYears=double

Units: Years Min: 0

Deployment

→ scenario → interventions → human → deployment

<deployment
  [ name=string ]
  >
IN THIS ORDER:
| ( <component ... /> )+
| ( <continuous ... /> )*
| ( <timed ... /> )*
</deployment>

Documentation (element)

All components deployed by this intervention are deployed to the same people (each timed or continuous deployment selects recipients and then gives each recipient all components of the intervention).

Attributes

Intervention name

name=string

Name of intervention

component

→ scenario → interventions → human → deployment → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Age-based (continuous) deployment

→ scenario → interventions → human → deployment → continuous

<continuous>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| ( <deploy ... /> )+
</continuous>

Documentation (element)

List of ages at which deployment takes place (through EPI, post-natal and school-based programmes, etc.).

A sub-population restriction may be added as a property of the list of continuous deployments.

restrictToSubPop

→ scenario → interventions → human → deployment → continuous → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

deploy

→ scenario → interventions → human → deployment → continuous → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    targetAgeYrs=double
  [ begin=string ]
  [ end=string ]
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention. Input is rounded to the nearest time step.

First time active

begin=string

Units: User defined (defauls to steps)

End step

end=string

Units: User defined (defauls to steps)

Mass (timed) deployment

→ scenario → interventions → human → deployment → timed

<timed>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| [ <cumulativeCoverage ... /> ]
| ( <deploy ... /> )+
</timed>

Documentation (element)

List of timed deployments of the intervention (that is, of deployment campaigns).

Cumulative deployment mode can be specified for all deployments in a timed list. To allow multiple cumulative deployment descriptions, the entire timed list may be repeated.

restrictToSubPop

→ scenario → interventions → human → deployment → timed → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

Cumulative coverage

→ scenario → interventions → human → deployment → timed → cumulativeCoverage

<cumulativeCoverage
    component=string
  />

Documentation (element)

Attributes

Component identifier

component=string

The identifier (short name) of the component used when selecting people.

deploy

→ scenario → interventions → human → deployment → timed → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    time=string
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Time

time=string

Units: User defined (defauls to steps) Min: 0

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0

Maximum age of eligible individuals (defaults to no limit). Input is rounded to the nearest time step.

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible individuals (defaults to 0). Input is rounded to the nearest time step.

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
| |   <DecisionTree5Day ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Description of health system.

Documentation (type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("forced" or "dynamic")
  [ scaledAnnualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Description of entomological data

Attributes

Entomology dataset name

name=string

Name of entomology data

Transmission model mode

mode=("forced" or "dynamic")

Override annual EIR

scaledAnnualEIR=double

Units: Infectious bites per adult per year

If set, the annual EIR (for all species of vector) is scaled to this level; can be omitted if not needed.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters of the transmission model

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <seasonality ... /> 
|   <mosq ... /> 
| [ <lifeCycle ... /> ]
| [ <simpleMPD ... /> ]
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial estimate of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial estimate of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial estimate of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Seasonality of transmission

→ scenario → entomology → vector → anopheles → seasonality

<seasonality
    input=("EIR")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <fourierSeries ... /> 
| |   <monthlyValues ... /> 
| |   <dailyValues ... /> 
</seasonality>

Documentation (element)

Specifies the seasonality of transmission and optionally the level of annual transmission.

Attributes

Seasonality input

input=("EIR")

Annual EIR

annualEIR=double

Units: Inoculations per adult per annum Min: 0

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries

<fourierSeries
    EIRRotateAngle=double
  >
IN THIS ORDER:
| ( <coeffic ... /> )*
</fourierSeries>

coeffic

Documentation (element)

Units: Infectious bites per adult per day

Attributes

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: Radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Pair of Fourier coefficients

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries → coeffic

<coeffic
    a=double
    b=double
  />

Documentation (element)

A pair of Fourier series coefficients. The first element specifies a1 and b1, the second a2 and b2, etc. Any number (from 0 up) of pairs may be given.

Attributes

a_n parameter of Fourier approximation to ln(EIR)

a=double

a_n parameter of Fourier approximation to ln(EIR) for some natural number n.

b_n parameter of Fourier approximation to ln(EIR)

b=double

b_n parameter of Fourier approximation to ln(EIR) for some natural number n.

List of monthly values

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues

<monthlyValues
    smoothing=("none" or "fourier")
  >
IN THIS ORDER:
| ( <value ... /> ){12,12}
</monthlyValues>

value

Documentation (element)

Description of seasonality from monthly values. Multiple smoothing methods are possible (see smoothing attribute).

List should contain twelve entries: January to December.

Attributes

Smoothing function

smoothing=("none" or "fourier")

How the monthly values are converted into a daily sequence of values:

none: no smoothing (step function)
Fourier: a Fourier series (with terms up to a2/b2) is fit to the sequence of monthly values and used to generate a smoothed list of daily values.

Monthly value

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Monthly value

List of daily values

→ scenario → entomology → vector → anopheles → seasonality → dailyValues

<dailyValues>
IN THIS ORDER:
| ( <value ... /> ){365,365}
</dailyValues>

value

Documentation (element)

Description of seasonality from daily values.

List should contain 365 entries: 1st January to 31st December.

Daily value

→ scenario → entomology → vector → anopheles → seasonality → dailyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Daily value

Mosquito feeding cycle parameters

→ scenario → entomology → vector → anopheles → mosq

<mosq
    minInfectedThreshold=double
  >
IN ANY ORDER:
|   <mosqRestDuration ... /> 
|   <extrinsicIncubationPeriod ... /> 
|   <mosqLaidEggsSameDayProportion ... /> 
|   <mosqSeekingDuration ... /> 
|   <mosqSurvivalFeedingCycleProbability ... /> 
|   <availabilityVariance ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <mosqProbOvipositing ... /> 
|   <mosqHumanBloodIndex ... /> 
</mosq>

Documentation (element)

Parameters describing the feeding cycle and human mosquito interaction of a single species of anopheles mosquito.

Attributes

Mininum infected threshold for mosquitos

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

Duration of the resting period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqRestDuration

<mosqRestDuration
    value=int
  />

Documentation (element)

Units: Days

name:Duration of the resting period of the vector (days);

Attributes

Input parameter value

value=int

An integer value.

Extrinsic incubation period

→ scenario → entomology → vector → anopheles → mosq → extrinsicIncubationPeriod

<extrinsicIncubationPeriod
    value=int
  />

Documentation (element)

Units: Days

name:Extrinsic incubation period (days)

Attributes

Input parameter value

value=int

An integer value.

Proportion of mosquitoes host seeking on same day as ovipositing

→ scenario → entomology → vector → anopheles → mosq → mosqLaidEggsSameDayProportion

<mosqLaidEggsSameDayProportion
    value=double
  />

Documentation (element)

Units: Proportion

Proportion of mosquitoes host seeking on same day as ovipositing

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Duration of the host-seeking period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqSeekingDuration

<mosqSeekingDuration
    value=double
  />

Documentation (element)

Units: Days

Duration of the host-seeking period of the vector (days)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito survives the feeding cycle

→ scenario → entomology → vector → anopheles → mosq → mosqSurvivalFeedingCycleProbability

<mosqSurvivalFeedingCycleProbability
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito survives the feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Variance in human availability rate

→ scenario → entomology → vector → anopheles → mosq → availabilityVariance

<availabilityVariance
    value=double
  />

Documentation (element)

Variance in availability rate of humans to mosquitoes. The mean rate is calculated based on other parameters.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito succesfully bites chosen host

→ scenario → entomology → vector → anopheles → mosq → mosqProbBiting

<mosqProbBiting
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito succesfully bites chosen host

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → mosq → mosqProbFindRestSite

<mosqProbFindRestSite
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito escapes host and finds a resting place after biting

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → mosq → mosqProbResting

<mosqProbResting
    mean=double
    variance=double
  />

Documentation (element)

Probability of mosquito successfully resting after finding a resting site

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of a mosquito successfully laying eggs given that it has rested

→ scenario → entomology → vector → anopheles → mosq → mosqProbOvipositing

<mosqProbOvipositing
    value=double
  />

Documentation (element)

Probability of a mosquito successfully laying eggs given that it has rested

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human blood index

→ scenario → entomology → vector → anopheles → mosq → mosqHumanBloodIndex

<mosqHumanBloodIndex
    value=double
  />

Documentation (element)

Units: Proportion

The proportion of resting mosquitoes which fed on human blood during the last feed.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mosquito life cycle parameters

→ scenario → entomology → vector → anopheles → lifeCycle

<lifeCycle
  [ estimatedLarvalResources=double ] DEFAULT VALUE 1e8
  >
IN ANY ORDER:
|   <eggStage ... /> 
|   <larvalStage ... /> 
|   <pupalStage ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</lifeCycle>

Documentation (element)

Parameters describing the life-cycle of this species of mosquito

Attributes

Estimate of larval resources

estimatedLarvalResources=double

Units: X

Default value: 1e8

Egg stage

→ scenario → entomology → vector → anopheles → lifeCycle → eggStage

<eggStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the egg stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

larvalStage

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage

<larvalStage>
</larvalStage>

daily

Documentation (type)

Parameters for the larval stage of development

Documentation (base type)

Parameters associated with a mosquito development stage.

Daily development

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage → daily

<daily
    resourceUsage=double
    effectCompetition=double
  />

Documentation (element)

Attributes

Resource usage

resourceUsage=double

Units: X

Resource usage during larval stage of development. Units are arbitrary.

Effect of competition

effectCompetition=double

Units: none

Effect of competition over resources on development.

Pupal stage

→ scenario → entomology → vector → anopheles → lifeCycle → pupalStage

<pupalStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the pupal stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → lifeCycle → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Simple Mosq-Pop-Dynamics parameters

→ scenario → entomology → vector → anopheles → simpleMPD

<simpleMPD>
IN ANY ORDER:
|   <developmentDuration ... /> 
|   <developmentSurvival ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</simpleMPD>

Documentation (element)

Parameters describing the simple mosquito population dynamics model.

This is a simpler version of the life-cycle model, requiring less parameters and with much simpler initialisation.

Duration

→ scenario → entomology → vector → anopheles → simpleMPD → developmentDuration

<developmentDuration
    value=int
  />

Documentation (element)

Units: Days Min: 1

Duration from egg laying to emergence in days.

Attributes

Input parameter value

value=int

An integer value.

Probability of survival

→ scenario → entomology → vector → anopheles → simpleMPD → developmentSurvival

<developmentSurvival
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that mosquito survives from the egg being laid to emergence, given no resouce limitations (no density constraints).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → simpleMPD → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Alternative (non-human) host paramters

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN ANY ORDER:
|   <mosqRelativeEntoAvailability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
</nonHumanHosts>

Documentation (element)

Min: 0

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of non-human host (ξ_i)

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqRelativeEntoAvailability

<mosqRelativeEntoAvailability
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Name of this species of non human hosts (must match up with those described per anopheles section).

Population size of alternative host species

number=double

Units: Number

Population size of this non-human host.

Parasite genetics

<parasiteGenetics
    samplingMode=("initial" or "tracking")
  >
IN THIS ORDER:
| ( <locus ... /> )+
</parasiteGenetics>

locus

Documentation (element)

A specification of genotypes of infection parasites.

May be omitted; in this case there is no modelling of genetic differences of infections (resistance, fitness).

Attributes

samplingMode

samplingMode=("initial" or "tracking")

Locus

→ scenario → parasiteGenetics → locus

<locus
    name=string
  >
IN THIS ORDER:
| ( <allele ... /> )+
</locus>

allele

Documentation (element)

Alleles at loci can affect fitness and resistance to any number of drugs.

Attributes

Name of locus

name=string

Name of the Locus

Allele

→ scenario → parasiteGenetics → locus → allele

<allele
    name=string
    initialFrequency=double
    fitness=double
  />

Documentation (element)

Describes an allele, or one possible genetic option of multiple at one point of variance.

Attributes

Name

name=string

Name of the allele; used to refer to it elsewhere.

Initial frequency

initialFrequency=double

Fitness factor

fitness=double

Drug parameters (PK, PD and usage)

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
|   <treatments ... /> 
|   <drugs ... /> 
</pharmacology>

Documentation (element)

Drug model parameters and drug usage parameters

Documentation (type)

A library of drug related data for the PK/PD model.

Treatments library

→ scenario → pharmacology → treatments

<treatments>
IN THIS ORDER:
| ( <schedule ... /> )+
| ( <dosages ... /> )+
</treatments>

Documentation (element)

A library of drug deployment schedules and dosages.

schedule

→ scenario → pharmacology → treatments → schedule

<schedule
    name=string
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

A schedule for the administration of drugs in a course of treatment.

Note that dose sizes are multiplied by some multiplier (see dosages) and the times of all doses may be delayed.

Attributes

Name

name=string

Name for referring to this deployment schedule

medicate

→ scenario → pharmacology → treatments → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  [ duration=double ]
  />

Attributes

drug

drug=string

Abbreviated name of drug compound

Drug dose

mg=double

Units: mg or mg/kg

Quantity of drug compound. For oral doses, this should be given in mg, using a separate dosage table to adjust for age/weight. For IV treatment, this should be given in mg/kg without a dosage table.

Time of administration

hour=double

Units: Hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

Duration of administration

duration=double

Units: Hours Min: 0

If this attribute is given, use IV administration instead of orally. Specifies the number of hours during which the dose is administered.

dosages

→ scenario → pharmacology → treatments → dosages

<dosages
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | ( <age ... /> )+
| | ( <bodymass ... /> )+
</dosages>

age
bodymass

Documentation (type)

A table for selecting a dose size given an age.

Attributes

Name

name=string

Name for referring to this dosage table

age

→ scenario → pharmacology → treatments → dosages → age

<age
    lowerbound=double
    dose_mult=double
  />

Documentation (type)

Gives a dose multiplier for an age or body mass range.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in mg) is multiplied by this value for patients falling into this age range when this dosage table is used.

bodymass

→ scenario → pharmacology → treatments → dosages → bodymass

<bodymass
    lowerbound=double
    dose_mult=double
  />

Documentation (type)

Gives a dose multiplier for an age or body mass range.

Attributes

Lower bound (inclusive)

lowerbound=double

Units: years Min: 0

Dose multiplier

dose_mult=double

Min: 0

The dose size given in the schedule (in mg) is multiplied by this value for patients falling into this age range when this dosage table is used.

Drug library

→ scenario → pharmacology → drugs

<drugs>
IN THIS ORDER:
| ( <drug ... /> )+
</drugs>

drug

Documentation (element)

A library of drug PK/PD data.

drug

→ scenario → pharmacology → drugs → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (type)

A drug description with PK/PD parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drugs → drug → PD

<PD
  [ locus=string ]
  >
IN THIS ORDER:
| ( <phenotype ... /> )+
</PD>

phenotype

Attributes

Locus

locus=string

PD parameters for some allele / resistance phenotype

→ scenario → pharmacology → drugs → drug → PD → phenotype

<phenotype
  [ name=string ]
  >
IN THIS ORDER:
| ( <restriction ... /> )*
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</phenotype>

Documentation (element)

Pharmaco-Dynamic parameters for some resistance phenotype.

To model resistance to this drug, describe multiple infection phenotypes (with respect to these PD parameters) and list one or more "restrict" elements for each phenotype.

Loci are specified elsewhere. Multiple loci may influence the action of a single drug and each locus may influence multiple drugs.

Attributes

Name of phenotype

name=string

Name of the phenotype; for documentation use only.

Restrict phenotype applicability to certain alleles

→ scenario → pharmacology → drugs → drug → PD → phenotype → restriction

<restriction
    onLocus=string
    toAllele=string
  />

Documentation (element)

Specifies the mapping from genotype to phenotype. For each drug type, if only one phenotype is present, restrictions need not be specified, but otherwise restrictions must be specified.

The set of loci affecting phenotypes of this drug's action must be fixed for any drug type. Each phenotype must list, for each of these loci, a restriction to one or more alleles under the locus.

Attributes

Locus relevant to the mapping of alleles to this phenotype

onLocus=string

A locus under which only a restricted set of alleles map to this phenotype.

Alleles mapping to this phenotype

toAllele=string

One allele of a locus upon which phenotype choice depends. If multiple alleles under this locus should map to the same phenotype, repeat the whole "restriction onLocus..." element.

Maximal parasite killing rate

→ scenario → pharmacology → drugs → drug → PD → phenotype → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drugs → drug → PD → phenotype → IC50

<IC50>
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

Slope of effect curve

→ scenario → pharmacology → drugs → drug → PD → phenotype → slope

<slope>
    double
</slope>

Documentation (element)

Units: dimensionless

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drugs → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
|   <half_life ... /> 
|   <vol_dist ... /> 
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drugs → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drugs → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate (which is: ln(2) / half_life).

Volume of Distribution

→ scenario → pharmacology → drugs → drug → PK → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Diagnostic parameters

→ scenario → diagnostics

<diagnostics>
IN THIS ORDER:
| ( <diagnostic ... /> )*
</diagnostics>

diagnostic

Documentation (element)

Diagnostic model parameters

diagnostic

→ scenario → diagnostics → diagnostic

<diagnostic
    name=string
  [ units=("Other" or "Garki" or "Malariatherapy") ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterministic ... /> 
| |   <stochastic ... /> 
</diagnostic>

Attributes

Name of diagnostic

name=string

Name of this diagnostic (parameterisation). May be used elsewhere in the XML document to refer to this set of diagnostic parameters.

Parasite density units / methodology

units=("Other" or "Garki" or "Malariatherapy")

Deterministic detection

→ scenario → diagnostics → diagnostic → deterministic

<deterministic
    minDensity=double
  />

Documentation (element)

Specify that an artificial deterministic test is used: outcome is positive if parasite density is at least the minimum given.

Attributes

Minimum detectible density

minDensity=double

Units: parasites/microlitre Min: 0

The minimum density at which parasites can be detected. If 0, the test outcome is always positive.

Non-deterministic detection

→ scenario → diagnostics → diagnostic → stochastic

<stochastic
    dens_50=double
    specificity=double
  />

Documentation (element)

An improved model of detection which is non-deterministic, including false positive results as well as false negatives.

Some parameterisations:

Microscopy sensitivity/specificity data in Africa; Source: expert opinion — Allan Schapira dens_50 = 20.0 specificity = .75

RDT sensitivity/specificity for Plasmodium falciparum in Africa Source: Murray et al (Clinical Microbiological Reviews, Jan. 2008) dens_50 = 50.0; specificity = .942;

Attributes

Density 50

dens_50=double

Units: parasites/microlitre Min: 0

The density at which the test outcome has a 50% chance of being positive.

Specificity

specificity=double

Units: Dimensionless Min: 0 Max: 1

The probability of a positive test outcome in the absense of parasites.

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
| [ <vivax ... /> ]
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: include/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=string
  >
IN ANY ORDER:
| [ <NeonatalMortality ... /> ]
| [ <NonMalariaFevers ... /> ]
</clinical>

Documentation (type)

Attributes

Follow-up period during which recurrence is considered a treatment failure

healthSystemMemory=string

Units: User-defined (defaults to steps)

Follow-up period during which a recurrence is considered to be a treatment failure Can be specified in steps (e.g. 6t) or days (e.g. 28d).

Neonatal mortality parameters

→ scenario → model → clinical → NeonatalMortality

<NeonatalMortality
    diagnostic=string
  />

Attributes

Diagnostic used to parameterise model

diagnostic=string

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
| [ <prNeedTreatmentNMF ... /> ]
| [ <prNeedTreatmentMF ... /> ]
</NonMalariaFevers>

Documentation (type)

Description of the incidence of non-malaria fever. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a non-malarial fever requires treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

Availability of humans to mosquitoes relative to an adult, categorized by age group

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ]
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

vivax

→ scenario → model → vivax

<vivax>
IN ANY ORDER:
|   <probBloodStageInfectiousToMosq ... /> 
|   <numberHypnozoites ... /> 
|   <hypnozoiteReleaseDelayDays ... /> 
|   <bloodStageProtectionLatency ... /> 
|   <bloodStageLengthDays ... /> 
|   <pEventPrimary ... /> 
|   <pEventSecondary ... /> 
|   <pEventIsSevere ... /> 
</vivax>

probBloodStageInfectiousToMosq

→ scenario → model → vivax → probBloodStageInfectiousToMosq

<probBloodStageInfectiousToMosq
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

numberHypnozoites

→ scenario → model → vivax → numberHypnozoites

<numberHypnozoites
    max=int
    base=double
  />

Attributes

max

max=int

base

base=double

hypnozoiteReleaseDelayDays

→ scenario → model → vivax → hypnozoiteReleaseDelayDays

<hypnozoiteReleaseDelayDays
    min=double
    mu=double
    sigma=double
  />

Attributes

min

min=double

mu

mu=double

sigma

sigma=double

bloodStageProtectionLatency

→ scenario → model → vivax → bloodStageProtectionLatency

<bloodStageProtectionLatency
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

bloodStageLengthDays

→ scenario → model → vivax → bloodStageLengthDays

<bloodStageLengthDays
    weibullScale=double
    weibullShape=double
  />

Attributes

weibullScale

weibullScale=double

weibullShape

weibullShape=double

pEventPrimary

→ scenario → model → vivax → pEventPrimary

<pEventPrimary
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pEventSecondary

→ scenario → model → vivax → pEventSecondary

<pEventSecondary
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pEventIsSevere

→ scenario → model → vivax → pEventIsSevere

<pEventIsSevere
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=string
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=string

Units: User defined (default: steps) Min: 0 Max: 20

Pre-erythrocytic latent period Can be specified in steps (e.g. 3t) or days (e.g. 15d).

parameter

→ scenario → model → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 32 documentation

Generated from: scenario_32.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
  [ analysisNo=int ]
    name=string
  [ wuID=int ]
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:om="http://openmalaria.org/schema/scenario_32"
    xsi:schemaLocation="http://openmalaria.org/schema/scenario_32 scenario_32.xsd"
  >
IN ANY ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entomology ... /> 
| [ <pharmacology ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Name of intervention

Work unit identifier

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Description of demography

Attributes

Name of demography data

name=string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Years Min: 0 Max: 100

Maximum age of simulated humans in years

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

list of age groups included in demography

Documentation (type)

list of age groups included in demography or surveys

Attributes

Lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Units: Percentage Min: 0 Max: 100

Percentage of human population in age group

Upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
| [ <cohorts ... /> ]
</monitoring>

Documentation (element)

Description of surveys

Attributes

Name of monitoring information

name=string

Name of monitoring data

continuous

→ scenario → monitoring → continuous

<continuous
    period=int
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Days between reports

period=int

Units: Days Min: 1 Max: unbounded

Number of timesteps between reports.

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Model options required

name=string

Options define different model structures. Option name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.

Indicator of whether option is required

value=boolean

Default value: true

Option value (true/false). Each option has a default value used if the option is not listed (usually false but sometimes true).

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

Units: list of elements

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/microlitre Min: 0

Limit above which a human's infection is reported as patent.

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time; 0 means just before start of main sim and is a valid survey-point. Reported data is either from a point-time survey (immediate data) or is collected over the previous year(data from previous timesteps-per-year period). Simulation will end immediately after last survey is taken.

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Cohorts

→ scenario → monitoring → cohorts

<cohorts>
IN THIS ORDER:
| ( <subPop ... /> )+
</cohorts>

subPop

Documentation (element)

Allows the configuration of multiple cohorts (output segregated according to membership within specific sub-populations).

If this element is omitted, monitoring surveys cover the entire simulated human population.

It does not affect the "continuous" outputs (these never take cohorts into account).

Sub-population

→ scenario → monitoring → cohorts → subPop

<subPop
    id=string
    number=integer
  />

Documentation (element)

In the output file, the output set is identified by multiplying this number by 1000 then adding it to the age group column.

Attributes

Sub-population identifier

id=string

Textual identifier for the sub-population (i.e. for an intervention component, since sub-populations are defined as the hosts an intervention component is deployed to).

Sub-population number

number=integer

Units: dimensionless Min: 1 Max: 2097152

Number identifying a sub-population; used to define identifiers of output sets. This number must be a power of 2 (i.e. 1, 2, 4, 8, ...). See documentation of subPop element.

Preventative interventions

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfections ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <vectorPop ... /> ]
| [ <human ... /> ]
</interventions>

Documentation (element)

Attributes

Name of intervention set

name=string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeHS>

timedDeployment

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeHS → timedDeployment

<timedDeployment
    time=int
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timedDeployment>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this replacement occurs, starting from 0, the first intervention-period time-step.

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</uncomplicated>

Documentation (type)

A set of decisions and a set of treatments.

decisions

→ scenario → interventions → human → component → MDA1D → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )*
</decisions>

decision

Documentation (type)

Description of decisions for a case management tree. A generic view of this tree would be that each decision is deterministic, or based on probabilities which may depend on other decisions. Probabilistic decisions are described here.

In general, each decision has a name, a defined set of outcome values, and a set of dependent decisions mentioned by name. The following decisions, with their associated outcomes, are provided by the code (and may not be included here):

case (uncomplicated only): Returns "UC1" if there is no recent history of a malarial case, or "UC2" if there is.
result: Dependent on decision "test", this performs a parasite density test. Output is one of "none" (no test performed), "positive", "negative".

The following decisions must be described here:

test (uncomplicated only): Outputs must be "none", "microscopy" or "RDT" to describe which test the "result" decision uses.
treatment: Describes which treatment to use. Values aren't restricted but must match up with a treatment described in the corresponding "treatments" section.
hospitalisation (complicated only): none, immediate or delayed.

decision

→ scenario → interventions → human → component → MDA1D → decisions → decision

<decision
    name=string
    depends=string
    values=string
  >
    string
</decision>

Documentation (type)

A decision describes rules for choosing between a set of values.

Lexically, it can contain symbols matching "[_.a-zA-Z0-9]+", round brackets: (), braces: {} and colons. Whitespace is ignored except to separate symbols.

Syntactically, it must match one TREE, where SYMBOL is a symbol described above. (Here, "x|y" means x or y, "x+" means x occurs once or more, brackets show grouping.) TREE := BRANCH_SET | OUTCOME BRANCH_SET := BRANCH+ BRANCH := DECISION '(' VALUE ')' ( ':' OUTCOME | '{' TREE '}' ) OUTCOME, DECISION, VALUE := SYMBOL

For each BRANCH_SET each BRANCH must result in the same DECISION. The DECISION must be one of the dependencies mentioned in "depends". This may be:

another decision, in which case the VALUE immediately following in brackets must correspond to one of its output values. The BRANCH_SET immediately containing this BRANCH must represent each output value of the same decision exactly once, and no parent BRANCH_SET may be for the same DECISION.
"p": this entry indicates a probabilistic decision. Where the value is a probability, the sum of all values for the BRANCH_SET must be 1 and the decision must be associated directly with OUTCOMEs (not sub-TREEs).
"age": this entry indicates an age-test. The VALUE must have the form "a-b", indicating that this branch will be taken for individuals aged such that a <= age < b, where a,b are non-negative real numbers or the special value "inf", and a <= b. All VALUEs in the BRANCH_SET must cover all possible (non-negative real) ages, with no overlap (hence, smallest a must be 0 and greatest b must be inf).

Semantically, each OUTCOME must be one of the values associated with this decision.

Attributes

Name of decision

name=string

The name of this decision. The name must match the regular expression "[_a-zA-Z0-9]+"; that is it can only contain letters, digits and _ characters (no spaces, punctuation, etc.).

Preceding decisions

depends=string

A comma-separated list of decisions that must have already been evaluated before the current decision can be evaluated. May be empty. Each decision must be hard-coded or described here. Can include the special decisions "p" and "age", though "age" cannot be combined with any other dependency.

Outcome values

values=string

A comma-separated list of outcome values this decision may have. The name of each value must be of the same form as decision names (i.e. only contain letters, digits and _ characters).

treatments

→ scenario → interventions → human → component → MDA1D → treatments

<treatments>
IN THIS ORDER:
| ( <treatment ... /> )*
</treatments>

treatment

Documentation (type)

A list of drug treatment tables. Each should have a name corresponding to one of the "drug" decision's values.

treatment

→ scenario → interventions → human → component → MDA1D → treatments → treatment

<treatment
    name=string
  >
IN THIS ORDER:
|   <schedule ... /> 
| ( <modifier ... /> )*
</treatment>

Documentation (type)

A description of a base treatment schedule that includes modifiers to handle delays, quality variations, etc.

Attributes

Treatment administered

name=string

Units: string

Name corresponding to one of the drug decision's output values.

schedule

→ scenario → interventions → human → component → MDA1D → treatments → treatment → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

The base (unmodified)schedule of drugs administered for this treatment.

medicate

→ scenario → interventions → human → component → MDA1D → treatments → treatment → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  [ duration=double ]
  />

Attributes

drug

drug=string

Abbreviated name of drug compound

drug dose

mg=double

Units: mg

Quantity of drug compound

Time of administration

hour=double

Units: Hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

Duration of administration

duration=double

Units: Hours Min: 0

If this attribute is given, use IV administration instead of orally. Specifies the number of hours during which the dose is administered.

modifier

→ scenario → interventions → human → component → MDA1D → treatments → treatment → modifier

<modifier
    decision=string
  >
EXACTLY ONE OF:
| ( <multiplyQty ... /> )*
| ( <delay ... /> )*
| ( <selectTimeRange ... /> )*
</modifier>

Documentation (type)

Units: Choice of elements

A modifier for this treatment, according to the outputs of a decision.

The "decision" attribute must be the name of a known decision. Then, there must be a set of multipyQty, delay or selectTimeRange sub-elements, each of which corresponds to one value output of the decision.

Attributes

Decision

decision=string

Units: string

Specifies the decision that this modifier acts on.

Active ingredient multipliers

→ scenario → interventions → human → component → MDA1D → treatments → treatment → modifier → multiplyQty

<multiplyQty
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Units: Comma-separated list of values

Multiplies the quantity of active ingredients of drugs administered.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of multipliers for each active ingredient, listed in the same order as in the "drugs" attribute. For example, with drugs="A,B" and content="0.5,1" the quantity of drug A is halved while that of B is unchanged.

Attributes

Value of decision

value=string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: None

Does this affect the cost? If false, the effective drug usage (w.r.t. cost)is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

Active ingredient delays

→ scenario → interventions → human → component → MDA1D → treatments → treatment → modifier → delay

<delay
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Units: Comma-separated list of values

Delays administration of drugs listed in the base schedule by so many hours.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of delays (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0,6", drug A is administered as in the base schedule while drug B is administered 6 hours later than specified.

Attributes

Value of decision

value=string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: None

Does this affect the cost? If false, the effective drug usage (w.r.t. cost)is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

Active ingredient time-ranges

→ scenario → interventions → human → component → MDA1D → treatments → treatment → modifier → selectTimeRange

<selectTimeRange
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Selects which drug doses to administer according to time of administration (before times are modified by delays). Half-open interval: [x,y)

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of time-ranges (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. The time-ranges should be of the form x-y and are interpreted as the half-open interval [x,y); that is a drug listed with time t will only be administered if x <= t < y.

Attributes

Value of decision

value=string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: None

Does this affect the cost? If false, the effective drug usage (w.r.t. cost)is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</complicated>

Documentation (type)

A set of decisions and a set of treatments.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: Days Min: 0 Max: unbounded

Maximum number of timesteps (including first day of case) that an individual with an uncomplicated case of malaria will remember he/she was sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial or non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of a complicated or severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
    name=string
  [ useDiagnosticUC=boolean ] DEFAULT VALUE false
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <treatmentActions ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
| [ <primaquine ... /> ]
</ImmediateOutcomes>

Documentation (type)

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Case Management model

name=string

Name of health system

useDiagnosticUC

useDiagnosticUC=boolean

Default value: false

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Description of drug regimen.

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Artemisinine combination therapy

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

QN

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0 Max: 1name:P(self-treat)

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Effectiveness of treatment for non-compliant patients

treatmentActions

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions

<treatmentActions>
IN ANY ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
</treatmentActions>

CQ
SP
AQ
SPAQ
ACT
QN

CQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ

<CQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</CQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

deploy

→ scenario → interventions → human → component → screen → positive → deploy

<deploy
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  [ p=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| ( <component ... /> )+
</deploy>

component

Attributes

Maximum age of eligible humans

maxAge=double

Units: Years Min: 0

Maximum age of eligible humans (defaults to no limit)

Minimum age of eligible humans

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible humans (defaults to 0)

Probability of delivery to eligible humans

p=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Probability of this list of components being deployed, given that other constraints are met.

component

→ scenario → interventions → human → component → screen → positive → deploy → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Prophylactic treatment

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → CQ → clearInfections

<clearInfections
    timesteps=int
    stage=("liver" or "blood" or "both")
  />

Documentation (element)

Attributes

Length of effect

timesteps=int

Units: Timesteps Min: -1

Target stage

stage=("liver" or "blood" or "both")

SP

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SP

<SP
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SP>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

AQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → AQ

<AQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</AQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

SPAQ

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → SPAQ

<SPAQ
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</SPAQ>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

ACT

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → ACT

<ACT
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</ACT>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

QN

→ scenario → healthSystem → ImmediateOutcomes → treatmentActions → QN

<QN
  [ name=string ]
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</QN>

Documentation (type)

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease will self-treat

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

primaquine

→ scenario → healthSystem → ImmediateOutcomes → primaquine

<primaquine>
IN ANY ORDER:
|   <pHumanCannotReceive ... /> 
|   <pUseUncomplicated ... /> 
|   <effectivenessOnUse ... /> 
</primaquine>

pHumanCannotReceive

→ scenario → healthSystem → ImmediateOutcomes → primaquine → pHumanCannotReceive

<pHumanCannotReceive
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

pUseUncomplicated

→ scenario → healthSystem → ImmediateOutcomes → primaquine → pUseUncomplicated

<pUseUncomplicated
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

effectivenessOnUse

→ scenario → healthSystem → ImmediateOutcomes → primaquine → effectivenessOnUse

<effectivenessOnUse
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Case fatality rate for inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: Dimensionless

List of age-specific probabilities of sequelae in inpatients, during a severe bout of malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeEIR>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeEIR → timedDeployment

<timedDeployment
    eipDuration=int
    time=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timedDeployment>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Time

time=int

Units: time-steps Min: 0

Time-step at which this replacement occurs, starting from 0, the first intervention-period time-step.

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=int ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=int

Units: time-steps Min: 0

Default value: 0

If period is 0 (or effectively infinite), the last specified value remains indefinitely in effect, otherwise the times of all values specified must be less than the period, and values are repeated modulo period (timestep period+2 has same value as timestep 2, etc.).

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=int
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time

time=int

Units: time-steps Min: 0

Insert R_0 case

<insertR_0Case
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</insertR_0Case>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → insertR_0Case → timedDeployment

<timedDeployment
    time=int
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Uninfect vectors

<uninfectVectors
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</uninfectVectors>

timedDeployment

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → uninfectVectors → timedDeployment

<timedDeployment
    time=int
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Vector population intervention

→ scenario → interventions → vectorPop

<vectorPop>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorPop>

intervention

Documentation (element)

Units: List of elements

A list of parameterisations of generic vector host-inspecific interventions.

intervention

→ scenario → interventions → vectorPop → intervention

<intervention
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

Units: List of elements

An intervention which may have various effects on the vector populations as a whole. (Not host specific.)

Multiple instances of this intervention class are allowed (multiple parameterisations, not just deployments).

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → vectorPop → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → vectorPop → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <seekingDeathRateIncrease ... /> ]
| [ <probDeathOvipositing ... /> ]
| [ <emergenceReduction ... /> ]
</anopheles>

Documentation (type)

Units: dimensionless Min: 0 Max: 1

Descriptions of the effects of vector interventions with per-species effects.

Attributes

Species/subspecies/variant name

mosquito=string

Name of the species/subspecies/variant.

Proportional increase in deaths while host searching

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease

<seekingDeathRateIncrease
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</seekingDeathRateIncrease>

decay

Documentation (element)

Units: dimensionless

Describe an effect on the increase in the death rate while host seeking (mu_vA) due to this intervention.

Enter the rate increase (i.e. if rate increases to 120% of normal, give 0.2). New death rate while seeking is old × (1 + increase) where increase is this factor given. Must have increas ≥ -1.

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: -1 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

Scale parameter of distribution. With the smooth-compact (smooth function with compact support), step and linear functions, this is the age at which the parameter has decayed to 0; with the other three functions, this is the age at which the parameter has decayed to half its original value. Not used for constant decay (though must be specified anyway).

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Proportion ovipositing mosquitoes killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing

<probDeathOvipositing
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probDeathOvipositing>

decay

Documentation (element)

Units: dimensionless

Describe an effect of increased mortality while ovipositing due to this intervention. Enter the probability of dying due to this intervention.

Attributes

Initial probability of killing

initial=double

Units: dimensionless Min: 0 Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Proportion of emerging pupa killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction

<emergenceReduction
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</emergenceReduction>

decay

Documentation (element)

Units: dimensionless

Describe an effect on emergence of pupa into adults: this value is the proportion of emerging pupa which are killed by this intervention.

Attributes

Initial proportion reduction

initial=double

Units: dimensionless Min: -inf Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Vector population intervention deployment

→ scenario → interventions → vectorPop → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

deploy

→ scenario → interventions → vectorPop → intervention → timed → deploy

<deploy
    time=int
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Human-specific interventions

→ scenario → interventions → human

<human>
IN THIS ORDER:
| ( <component ... /> )+
| ( <deployment ... /> )*
</human>

Documentation (element)

Encapsulates all interventions whose effects are specific to the human host: any interventions where target humans may be selected via population-coverage, age limits and sub-population membership.

Component

→ scenario → interventions → human → component

<component
    id=string
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <screen ... /> 
| |   <MDA ... /> 
| |   <MDA1D ... /> 
| |   <PEV ... /> 
| |   <BSV ... /> 
| |   <TBV ... /> 
| |   <ITN ... /> 
| |   <IRS ... /> 
| |   <GVI ... /> 
| | [ <recruitmentOnly ... /> ]
| |   <clearImmunity ... /> 
| [ <subPopRemoval ... /> ]
</component>

Documentation (element)

Each element describes one component: its effects, decay of the(se) effect(s), and related stuff (e.g. description of indirect decay and of usage levels).

Attributes

Component identifier

id=string

Name of component

name=string

An informal name/description for the component

screen

→ scenario → interventions → human → component → screen

<screen>
IN THIS ORDER:
|   <diagnostic ... /> 
|   <positive ... /> 
|   <negative ... /> 
</screen>

Documentation (type)

This can be combined with MDA to achieve mass screen and treat (MSAT) or other types of mass screening intervention.

The use of the screening itself is reported (if enabled), but not the outcome. Deployment of interventions triggered by the screening may be reported, however.

Diagnostic

→ scenario → interventions → human → component → screen → diagnostic

<diagnostic>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterministic ... /> 
| |   <stochastic ... /> 
</diagnostic>

Documentation (element)

Description of the diagnostic test used by the screening.

Deterministic detection

→ scenario → interventions → human → component → screen → diagnostic → deterministic

<deterministic
    minDensity=double
  />

Documentation (element)

Specify that an artificial deterministic test is used: drugs are administered if parasite density is at least the minimum given.

Attributes

Minimum detectible density

minDensity=double

Units: parasites/microlitre Min: 0

The minimum density at which parasites can be detected. If 0, the test outcome is always positive.

Non-deterministic detection

→ scenario → interventions → human → component → screen → diagnostic → stochastic

<stochastic
    dens_50=double
    specificity=double
  />

Documentation (element)

An improved model of detection which is non-deterministic, including false positive results as well as false negatives.

Some parameterisations:

Microscopy sensitivity/specificity data in Africa; Source: expert opinion — Allan Schapira dens_50 = 20.0 specificity = .75

RDT sensitivity/specificity for Plasmodium falciparum in Africa Source: Murray et al (Clinical Microbiological Reviews, Jan. 2008) dens_50 = 50.0; specificity = .942;

Attributes

Density 50

dens_50=double

Units: parasites/microlitre Min: 0

The density at which the test outcome has a 50% chance of being positive.

Specificity

specificity=double

Units: Dimensionless Min: 0 Max: 1

The probability of a positive test outcome in the absense of parasites.

positive

→ scenario → interventions → human → component → screen → positive

<positive>
IN THIS ORDER:
| ( <deploy ... /> )*
</positive>

deploy

Documentation (type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

negative

→ scenario → interventions → human → component → screen → negative

<negative>
IN THIS ORDER:
| ( <deploy ... /> )*
</negative>

deploy

Documentation (type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

MDA

→ scenario → interventions → human → component → MDA

<MDA>
IN THIS ORDER:
|   <effects ... /> 
</MDA>

effects

Documentation (type)

Description of treatment deployed as an intervention (treatment is usually a simple model of a drug's action, thus when deployed on mass or via screening this becomes part of a mass drug administration (MDA) or mass screen-and-treat (MSAT) intervention. For historical reasons this is called "MDA" in the XML, not "treatment".

For the 1-day timestep models, a more detailed model of drug action and more flexible model of deployment decisions are available; see MDA1D.

The model of action of this intervention is to select one option from a list of treatment options (randomly when multiple are available) then carry out the treatment option's actions (which may be to do nothing).

Treatment options

→ scenario → interventions → human → component → MDA → effects

<effects>
IN THIS ORDER:
| ( <option ... /> )+
</effects>

option

Documentation (element)

A list of treatment options. When treatment is to be given, one option will be selected randomly (according to the "pSelection" probability of selection parameters given), and the actions of that option enacted.

Multiple options are intended to allow simulation of drug failure and varying patient adherence. An option may do nothing.

option

→ scenario → interventions → human → component → MDA → effects → option

<option
  [ name=string ]
    pSelection=double
  >
IN THIS ORDER:
| ( <deploy ... /> )*
</option>

Documentation (base type)

Lists intervention components which are deployed according to some external trigger (for example, screening with a negative patency outcome or health-system treatment).

Attributes

Name

name=string

Describes what this compliance option represents (e.g. "good compliance", "poor compliance with good drugs", ...).

Probability of selection

pSelection=double

Units: dimensionless Min: 0 Max: 1

The probability of selection of this treatment option. The sum of probabilities of all options in the list should be 1.

Mass drug administration (with decision tree and drug PK/PD model)

→ scenario → interventions → human → component → MDA1D

<MDA1D>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</MDA1D>

Documentation (element)

Description of a MDA/MSAT intervention (Mass Screen and Treat is just Mass Drug Administration with a diagnostic).

This MDA/MSAT model piggy-backs the 1-day timestep case management and drug models, and thus is only available when using a 1-day timestep.

Description of treatment type used by mass treatment option of one-day case management model. Can be used to describe one-size-fits-all mass drug dosing, age-based mass drug dosing and screen-and-treat. Number of treatments given can be reported by the nMDAs option.

Documentation (type)

A set of decisions and a set of treatments.

Vaccines

→ scenario → interventions → human → component → PEV

<PEV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</PEV>

Documentation (element)

Pre-erythrocytic vaccine (PEV): prevents a proportion of infections from commencing.

Documentation (type)

Description of a vaccine's effect

Decay of effect

→ scenario → interventions → human → component → PEV → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Specification of decay of efficacy. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Variance parameter for vaccine efficacy

→ scenario → interventions → human → component → PEV → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial mean efficacy

→ scenario → interventions → human → component → PEV → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Vaccines

→ scenario → interventions → human → component → BSV

<BSV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</BSV>

Documentation (element)

Blood-stage vaccine (BSV): acts as a killing factor on blood-stage parasites. Exact action depends on the within host model.

Documentation (type)

Description of a vaccine's effect

Vaccines

→ scenario → interventions → human → component → TBV

<TBV>
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</TBV>

Documentation (element)

Transmission-blocking vaccine (TBV): one minus this scales the probability of transmission to mosquitoes

Documentation (type)

Description of a vaccine's effect

Bed nets

→ scenario → interventions → human → component → ITN

<ITN>
IN THIS ORDER:
|   <usage ... /> 
|   <holeRate ... /> 
|   <ripRate ... /> 
|   <ripFactor ... /> 
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
|   <attritionOfNets ... /> 
| ( <anophelesParams ... /> )+
</ITN>

Documentation (element)

Description of bed-net interventions (ITNs, LLINs).

Proportion of time nets are used by humans

→ scenario → interventions → human → component → ITN → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of nets by humans, from 0 to 1.

At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing.

See also "propActing" (proportion of bits for which net acts).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Rate at which holes are made

→ scenario → interventions → human → component → ITN → holeRate

<holeRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Holes per annum Min: 0

The rate at which new holes are made in nets.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ log N( log(mean)-sigma²/2, sigma² ).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rate at which holes are enlarged

→ scenario → interventions → human → component → ITN → ripRate

<ripRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Rips per existing hole per annum Min: 0

Each existing hole has a probability of being ripped bigger according to a Poisson process with this rate as (only) parameter.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ log N( log(mean)-sigma²/2, sigma² ).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rip factor

→ scenario → interventions → human → component → ITN → ripFactor

<ripFactor
    value=double
  />

Documentation (element)

Units: none Min: 0

This factor expresses how important rips are in increasing the hole.

The hole index of a net is h + F×x where h and x are the total numbers of holes and rips respectively and F is the rip factor.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → human → component → ITN → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: mg/m² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → human → component → ITN → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of nets. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Attrition of nets

→ scenario → interventions → human → component → ITN → attritionOfNets

<attritionOfNets
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: dimensionless

Specifies the rate at which nets are disposed of over time. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Humans are removed from the intervention component's sub-population on disposal (attrition) of their nets. Currently this event is not reported.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → human → component → ITN → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterrency ... /> 
| |   <twoStageDeterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which net acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Relative attractiveness

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency

<twoStageDeterrency>
IN ANY ORDER:
|   <entering ... /> 
|   <attacking ... /> 
</twoStageDeterrency>

Documentation (element)

Units: dimensionless

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

This deterrency model multiplies human attractiveness by pEnt×pAtt divided by a base factor to normalise the output to 1 when there are no nets.

RA (entering)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → entering

<entering
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless

pEnt represents the relative probability of entering due to ITNs: pEnt = exp(log(P)×p) where P is the insecticide factor and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

RA (attacking)

→ scenario → interventions → human → component → ITN → anophelesParams → twoStageDeterrency → attacking

<attacking
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless

pAtt represents the relative probability of attacking a human after entering a house due to ITNs (i.e. of feeding/dying vs. flying off): pAtt = B + H×h + P×p + I×h×p where B is the base (without net) probability; H, P and I are the hole, insecticide and interaction factors respectively, h=exp(-holeIndex×holeScalingFactor) and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Pre-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → ITN → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Indoor residual spraying

→ scenario → interventions → human → component → IRS

<IRS>
IN THIS ORDER:
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
| ( <anophelesParams ... /> )+
</IRS>

Documentation (element)

Description of indoor residual spraying interventions.

Documentation (type)

Description of effect for the more complex and probably more realistic Briet model: IRS has three effects, whos strength is calculated as a function of surviving insecticide content.

Initial insecticide

→ scenario → interventions → human → component → IRS → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: μg/cm² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → human → component → IRS → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → IRS → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → IRS → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied by exp(P×log(p)) where P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → human → component → IRS → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Generic vector intervention

→ scenario → interventions → human → component → GVI

<GVI>
IN THIS ORDER:
|   <decay ... /> 
| ( <anophelesParams ... /> )+
</GVI>

Documentation (element)

Note that all actions of this intervention component will decay according to a single decay function. If independant decay is wanted, a separate component can be used for each action.

Decay

→ scenario → interventions → human → component → GVI → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Description of decay of all intervention effects. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → human → component → GVI → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| [ <deterrency ... /> ]
| [ <preprandialKillingEffect ... /> ]
| [ <postprandialKillingEffect ... /> ]
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → human → component → GVI → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied this factor times survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → human → component → GVI → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Recruitment only

→ scenario → interventions → human → component → recruitmentOnly

<recruitmentOnly/>

Documentation (element)

Recruitment of a host into a sub-population.

Clear Immunity

→ scenario → interventions → human → component → clearImmunity

<clearImmunity/>

Documentation (element)

Removes all exposure-related immunitsy gained over time by hosts without removing infections (or affecting the ability to gain immunity through exposure).

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

subPopRemoval

→ scenario → interventions → human → component → subPopRemoval

<subPopRemoval
  [ onFirstBout=boolean ] DEFAULT VALUE false
  [ onFirstTreatment=boolean ] DEFAULT VALUE false
  [ onFirstInfection=boolean ] DEFAULT VALUE false
  [ afterYears=double ]
  />

Documentation (type)

ITN attrition also removes humans from sub-populations.

Attributes

Time to first episode only

onFirstBout=boolean

Default value: false

Time to first treatment only

onFirstTreatment=boolean

Default value: false

Time to first infection only

onFirstInfection=boolean

Default value: false

Remove from sub-population after

afterYears=double

Units: Years Min: 0

Deployment

→ scenario → interventions → human → deployment

<deployment
  [ name=string ]
  >
IN THIS ORDER:
| ( <component ... /> )+
| ( <continuous ... /> )*
| ( <timed ... /> )*
</deployment>

Documentation (element)

All components deployed by this intervention are deployed to the same people (each timed or continuous deployment selects recipients and then gives each recipient all components of the intervention).

Attributes

Intervention name

name=string

Name of intervention

component

→ scenario → interventions → human → deployment → component

<component
    id=string
  />

Documentation (type)

The list of components deployed to eligible humans.

Attributes

Identifier

id=string

The identifier (short name) of a component.

Age-based (continuous) deployment

→ scenario → interventions → human → deployment → continuous

<continuous>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| ( <deploy ... /> )+
</continuous>

Documentation (element)

List of ages at which deployment takes place (through EPI, post-natal and school-based programmes, etc.).

A sub-population restriction may be added as a property of the list of continuous deployments.

restrictToSubPop

→ scenario → interventions → human → deployment → continuous → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

deploy

→ scenario → interventions → human → deployment → continuous → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    targetAgeYrs=double
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Mass (timed) deployment

→ scenario → interventions → human → deployment → timed

<timed>
IN THIS ORDER:
| [ <restrictToSubPop ... /> ]
| [ <cumulativeCoverage ... /> ]
| ( <deploy ... /> )+
</timed>

Documentation (element)

List of timed deployments of the intervention (that is, of deployment campaigns).

Cumulative deployment mode can be specified for all deployments in a timed list. To allow multiple cumulative deployment descriptions, the entire timed list may be repeated.

restrictToSubPop

→ scenario → interventions → human → deployment → timed → restrictToSubPop

<restrictToSubPop
    id=string
  [ complement=boolean ] DEFAULT VALUE false
  />

Documentation (type)

Attributes

Sub-population identifier

id=string

The identifier (short name) of the sub-population (i.e. the "id" of some intervention component). Also see the "complement" attribute.

Complement

complement=boolean

Default value: false

Cumulative coverage

→ scenario → interventions → human → deployment → timed → cumulativeCoverage

<cumulativeCoverage
    component=string
  />

Documentation (element)

Attributes

Component identifier

component=string

The identifier (short name) of the component used when selecting people.

deploy

→ scenario → interventions → human → deployment → timed → deploy

<deploy
    coverage=double
  [ vaccMinPrevDoses=int ]
  [ vaccMaxCumDoses=int ]
    time=int
  [ maxAge=double ]
  [ minAge=double ] DEFAULT VALUE 0
  />

Attributes

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Proportion of otherwise eligible individuals who will receive this deployment.

Vaccine min previous doses

vaccMinPrevDoses=int

Units: inoculations Min: 0

Vaccine max cumulative doses

vaccMaxCumDoses=int

Units: inoculations Min: 0

Applies to vaccines only: vaccine doses are only deployed by this deployment if the previous number of doses (for the component deployed) is less than this number.

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0

Maximum age of eligible individuals (defaults to no limit)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Description of health system.

Documentation (type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("forced" or "dynamic")
  [ scaledAnnualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Description of entomological data

Attributes

Entomology dataset name

name=string

Name of entomology data

Transmission model mode

mode=("forced" or "dynamic")

Override annual EIR

scaledAnnualEIR=double

Units: Infectious bites per adult per year

If set, the annual EIR (for all species of vector) is scaled to this level; can be omitted if not needed.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters of the transmission model

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <seasonality ... /> 
|   <mosq ... /> 
| [ <lifeCycle ... /> ]
| [ <simpleMPD ... /> ]
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial estimate of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial estimate of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial estimate of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Seasonality of transmission

→ scenario → entomology → vector → anopheles → seasonality

<seasonality
    input=("EIR")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <fourierSeries ... /> 
| |   <monthlyValues ... /> 
| |   <dailyValues ... /> 
</seasonality>

Documentation (element)

Specifies the seasonality of transmission and optionally the level of annual transmission.

Attributes

Seasonality input

input=("EIR")

Annual EIR

annualEIR=double

Units: Inoculations per adult per annum Min: 0

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries

<fourierSeries
    EIRRotateAngle=double
  >
IN THIS ORDER:
| ( <coeffic ... /> )*
</fourierSeries>

coeffic

Documentation (element)

Units: Infectious bites per adult per day

Attributes

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: Radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Pair of Fourier coefficients

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries → coeffic

<coeffic
    a=double
    b=double
  />

Documentation (element)

A pair of Fourier series coefficients. The first element specifies a1 and b1, the second a2 and b2, etc. Any number (from 0 up) of pairs may be given.

Attributes

a_n parameter of Fourier approximation to ln(EIR)

a=double

a_n parameter of Fourier approximation to ln(EIR) for some natural number n.

b_n parameter of Fourier approximation to ln(EIR)

b=double

b_n parameter of Fourier approximation to ln(EIR) for some natural number n.

List of monthly values

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues

<monthlyValues
    smoothing=("none" or "fourier")
  >
IN THIS ORDER:
| ( <value ... /> ){12,12}
</monthlyValues>

value

Documentation (element)

Description of seasonality from monthly values. Multiple smoothing methods are possible (see smoothing attribute).

List should contain twelve entries: January to December.

Attributes

Smoothing function

smoothing=("none" or "fourier")

How the monthly values are converted into a daily sequence of values:

none: no smoothing (step function)
Fourier: a Fourier series (with terms up to a2/b2) is fit to the sequence of monthly values and used to generate a smoothed list of daily values.

Monthly value

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Monthly value

List of daily values

→ scenario → entomology → vector → anopheles → seasonality → dailyValues

<dailyValues>
IN THIS ORDER:
| ( <value ... /> ){365,365}
</dailyValues>

value

Documentation (element)

Description of seasonality from daily values.

List should contain 365 entries: 1st January to 31st December.

Daily value

→ scenario → entomology → vector → anopheles → seasonality → dailyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Daily value

Mosquito feeding cycle parameters

→ scenario → entomology → vector → anopheles → mosq

<mosq
    minInfectedThreshold=double
  >
IN ANY ORDER:
|   <mosqRestDuration ... /> 
|   <extrinsicIncubationPeriod ... /> 
|   <mosqLaidEggsSameDayProportion ... /> 
|   <mosqSeekingDuration ... /> 
|   <mosqSurvivalFeedingCycleProbability ... /> 
|   <availabilityVariance ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <mosqProbOvipositing ... /> 
|   <mosqHumanBloodIndex ... /> 
</mosq>

Documentation (element)

Parameters describing the feeding cycle and human mosquito interaction of a single species of anopheles mosquito.

Attributes

Mininum infected threshold for mosquitos

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

Duration of the resting period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqRestDuration

<mosqRestDuration
    value=int
  />

Documentation (element)

Units: Days

name:Duration of the resting period of the vector (days);

Attributes

Input parameter value

value=int

An integer value.

Extrinsic incubation period

→ scenario → entomology → vector → anopheles → mosq → extrinsicIncubationPeriod

<extrinsicIncubationPeriod
    value=int
  />

Documentation (element)

Units: Days

name:Extrinsic incubation period (days)

Attributes

Input parameter value

value=int

An integer value.

Proportion of mosquitoes host seeking on same day as ovipositing

→ scenario → entomology → vector → anopheles → mosq → mosqLaidEggsSameDayProportion

<mosqLaidEggsSameDayProportion
    value=double
  />

Documentation (element)

Units: Proportion

Proportion of mosquitoes host seeking on same day as ovipositing

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Duration of the host-seeking period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqSeekingDuration

<mosqSeekingDuration
    value=double
  />

Documentation (element)

Units: Days

Duration of the host-seeking period of the vector (days)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito survives the feeding cycle

→ scenario → entomology → vector → anopheles → mosq → mosqSurvivalFeedingCycleProbability

<mosqSurvivalFeedingCycleProbability
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito survives the feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Variance in human availability rate

→ scenario → entomology → vector → anopheles → mosq → availabilityVariance

<availabilityVariance
    value=double
  />

Documentation (element)

Variance in availability rate of humans to mosquitoes. The mean rate is calculated based on other parameters.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito succesfully bites chosen host

→ scenario → entomology → vector → anopheles → mosq → mosqProbBiting

<mosqProbBiting
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito succesfully bites chosen host

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → mosq → mosqProbFindRestSite

<mosqProbFindRestSite
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito escapes host and finds a resting place after biting

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → mosq → mosqProbResting

<mosqProbResting
    mean=double
    variance=double
  />

Documentation (element)

Probability of mosquito successfully resting after finding a resting site

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of a mosquito successfully laying eggs given that it has rested

→ scenario → entomology → vector → anopheles → mosq → mosqProbOvipositing

<mosqProbOvipositing
    value=double
  />

Documentation (element)

Probability of a mosquito successfully laying eggs given that it has rested

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human blood index

→ scenario → entomology → vector → anopheles → mosq → mosqHumanBloodIndex

<mosqHumanBloodIndex
    value=double
  />

Documentation (element)

Units: Proportion

The proportion of resting mosquitoes which fed on human blood during the last feed.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mosquito life cycle parameters

→ scenario → entomology → vector → anopheles → lifeCycle

<lifeCycle
  [ estimatedLarvalResources=double ] DEFAULT VALUE 1e8
  >
IN ANY ORDER:
|   <eggStage ... /> 
|   <larvalStage ... /> 
|   <pupalStage ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</lifeCycle>

Documentation (element)

Parameters describing the life-cycle of this species of mosquito

Attributes

Estimate of larval resources

estimatedLarvalResources=double

Units: X

Default value: 1e8

Egg stage

→ scenario → entomology → vector → anopheles → lifeCycle → eggStage

<eggStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the egg stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

larvalStage

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage

<larvalStage>
</larvalStage>

daily

Documentation (type)

Parameters for the larval stage of development

Documentation (base type)

Parameters associated with a mosquito development stage.

Daily development

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage → daily

<daily
    resourceUsage=double
    effectCompetition=double
  />

Documentation (element)

Attributes

Resource usage

resourceUsage=double

Units: X

Resource usage during larval stage of development. Units are arbitrary.

Effect of competition

effectCompetition=double

Units: none

Effect of competition over resources on development.

Pupal stage

→ scenario → entomology → vector → anopheles → lifeCycle → pupalStage

<pupalStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the pupal stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → lifeCycle → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Simple Mosq-Pop-Dynamics parameters

→ scenario → entomology → vector → anopheles → simpleMPD

<simpleMPD>
IN ANY ORDER:
|   <developmentDuration ... /> 
|   <developmentSurvival ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</simpleMPD>

Documentation (element)

Parameters describing the simple mosquito population dynamics model.

This is a simpler version of the life-cycle model, requiring less parameters and with much simpler initialisation.

Duration

→ scenario → entomology → vector → anopheles → simpleMPD → developmentDuration

<developmentDuration
    value=int
  />

Documentation (element)

Units: Days Min: 1

Duration from egg laying to emergence in days.

Attributes

Input parameter value

value=int

An integer value.

Probability of survival

→ scenario → entomology → vector → anopheles → simpleMPD → developmentSurvival

<developmentSurvival
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that mosquito survives from the egg being laid to emergence, given no resouce limitations (no density constraints).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → simpleMPD → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Alternative (non-human) host paramters

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN ANY ORDER:
|   <mosqRelativeEntoAvailability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
</nonHumanHosts>

Documentation (element)

Min: 0

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of non-human host (ξ_i)

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqRelativeEntoAvailability

<mosqRelativeEntoAvailability
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Name of this species of non human hosts (must match up with those described per anopheles section).

Population size of alternative host species

number=double

Units: Number

Population size of this non-human host.

Pharmacokinetics and pharmacodynamics

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
| ( <drug ... /> )+
</pharmacology>

drug

Documentation (element)

Drug model parameters

Library of drug parameters

→ scenario → pharmacology → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (element)

Sequence of drug descriptions forming a library of drug parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drug → PD

<PD>
IN THIS ORDER:
| ( <allele ... /> )+
</PD>

allele

PD parameters per allele

→ scenario → pharmacology → drug → PD → allele

<allele
    name=string
  >
IN THIS ORDER:
|   <initial_frequency ... /> 
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</allele>

Documentation (element)

PD parameters per allele, plus initial frequency of each allele.

Note: we assume a one-to-one correspondance of drugs to loci, hence each drug has an independent set of alleles here.

Attributes

name

name=string

Relative frequency

→ scenario → pharmacology → drug → PD → allele → initial_frequency

<initial_frequency>
    double
</initial_frequency>

Documentation (element)

Units: dimensionless Min: 0

Frequency, relative to the total frequency of all alleles for this drug/locus.

Maximal parasite killing rate

→ scenario → pharmacology → drug → PD → allele → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drug → PD → allele → IC50

<IC50>
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

Slope of effect curve

→ scenario → pharmacology → drug → PD → allele → slope

<slope>
    double
</slope>

Documentation (element)

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
|   <half_life ... /> 
|   <vol_dist ... /> 
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate (which is: ln(2) / half_life).

Volume of Distribution

→ scenario → pharmacology → drug → PK → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
| [ <vivax ... /> ]
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: include/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=int
  >
IN THIS ORDER:
| [ <NonMalariaFevers ... /> ]
</clinical>

NonMalariaFevers

Documentation (type)

Attributes

Follow-up period during which recurrence is treated as a failure

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
| [ <prNeedTreatmentNMF ... /> ]
| [ <prNeedTreatmentMF ... /> ]
</NonMalariaFevers>

Documentation (type)

Description of the incidence of non-malaria fever. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a non-malarial fever requires treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

Availability of humans to mosquitoes relative to an adult, categorized by age group

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ]
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

vivax

→ scenario → model → vivax

<vivax>
IN ANY ORDER:
|   <probBloodStageInfectiousToMosq ... /> 
|   <numberHypnozoites ... /> 
|   <hypnozoiteReleaseDelayDays ... /> 
|   <bloodStageProtectionLatency ... /> 
|   <bloodStageLengthDays ... /> 
|   <pEventPrimary ... /> 
|   <pEventSecondary ... /> 
|   <pEventIsSevere ... /> 
</vivax>

probBloodStageInfectiousToMosq

→ scenario → model → vivax → probBloodStageInfectiousToMosq

<probBloodStageInfectiousToMosq
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

numberHypnozoites

→ scenario → model → vivax → numberHypnozoites

<numberHypnozoites
    max=int
    base=double
  />

Attributes

max

max=int

base

base=double

hypnozoiteReleaseDelayDays

→ scenario → model → vivax → hypnozoiteReleaseDelayDays

<hypnozoiteReleaseDelayDays
    min=double
    mu=double
    sigma=double
  />

Attributes

min

min=double

mu

mu=double

sigma

sigma=double

bloodStageProtectionLatency

→ scenario → model → vivax → bloodStageProtectionLatency

<bloodStageProtectionLatency
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

bloodStageLengthDays

→ scenario → model → vivax → bloodStageLengthDays

<bloodStageLengthDays
    weibullScale=double
    weibullShape=double
  />

Attributes

weibullScale

weibullScale=double

weibullShape

weibullShape=double

pEventPrimary

→ scenario → model → vivax → pEventPrimary

<pEventPrimary
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pEventSecondary

→ scenario → model → vivax → pEventSecondary

<pEventSecondary
    a=double
    b=double
  />

Attributes

a

a=double

b

b=double

pEventIsSevere

→ scenario → model → vivax → pEventIsSevere

<pEventIsSevere
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → model → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 31 documentation

Generated from: scenario_31.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    name=string
    wuID=int
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_31.xsd"
  >
IN ANY ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entomology ... /> 
| [ <pharmacology ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Name of intervention

Work unit identifier

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Description of demography

Attributes

Name of demography data

name=string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Years Min: 0 Max: 100

Maximum age of simulated humans in years

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

list of age groups included in demography

Documentation (type)

list of age groups included in demography or surveys

Attributes

Lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Units: Percentage Min: 0 Max: 100

Percentage of human population in age group

Upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ cohortOnly=boolean ]
  [ firstBoutOnly=boolean ]
  [ firstTreatmentOnly=boolean ]
  [ firstInfectionOnly=boolean ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Description of surveys

Attributes

Name of monitoring information

name=string

Name of monitoring data

Survey only cohort

cohortOnly=boolean

If true, for many output measures, the output comes only from individuals in the cohort; otherwise output is from the entire population. Does not need to be specified if no cohort-selecting "interventions" are present.

Time to first episode only

firstBoutOnly=boolean

If true, remove individuals from the cohort at the start of the first episode (start of a clinical bout) since they were recruited into the cohort. This is intended for cohort studies that intend to measure time to first episode, using active case detection.

Time to first treatment only

firstTreatmentOnly=boolean

If true, remove individuals from the cohort when they first seek treatment since they were recruited into the cohort. This is intended for cohort studies that intend to measure time to first episode, using passive case detection.

Time to first infection only

firstInfectionOnly=boolean

If true, remove individuals from the cohort at completion of the first survey in which they present with a patent infection since they were recruited into the cohort. This intended for cohort studies that intend to measure time to first infection, using active case detection.

continuous

→ scenario → monitoring → continuous

<continuous
    period=int
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Days between reports

period=int

Units: Days Min: 1 Max: unbounded

Number of timesteps between reports.

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Model options required

name=string

Options define different model structures. Option name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.

Indicator of whether option is required

value=boolean

Default value: true

Option value (true/false). Each option has a default value used if the option is not listed (usually false but sometimes true).

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

Units: list of elements

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/microlitre Min: 0

Limit above which a human's infection is reported as patent.

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

List of age groups included in demography or surveys

Documentation (type)

List of age groups included in surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Preventative interventions

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <vaccine ... /> ]
| [ <IPT ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <vectorDeterrent ... /> ]
| [ <cohort ... /> ]
| [ <importedInfections ... /> ]
| [ <immuneSuppression ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <vectorPop ... /> ]
</interventions>

Documentation (element)

Attributes

Intervention

name=string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeHS>

timedDeployment

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeHS → timedDeployment

<timedDeployment
    time=int
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timedDeployment>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this replacement occurs, starting from 0, the first intervention-period time-step.

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</uncomplicated>

Documentation (type)

A set of decisions and a set of treatments.

decisions

→ scenario → interventions → MDA → description → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )*
</decisions>

decision

Documentation (type)

case (uncomplicated only): Returns "UC1" if there is no recent history of a malarial case, or "UC2" if there is.
result: Dependent on decision "test", this performs a parasite density test. Output is one of "none" (no test performed), "positive", "negative".

The following decisions must be described here:

test (uncomplicated only): Outputs must be "none", "microscopy" or "RDT" to describe which test the "result" decision uses.
treatment: Describes which treatment to use. Values aren't restricted but must match up with a treatment described in the corresponding "treatments" section.
hospitalisation (complicated only): none, immediate or delayed.

decision

→ scenario → interventions → MDA → description → decisions → decision

<decision
    name=string
    depends=string
    values=string
  >
    string
</decision>

Documentation (type)

A decision describes rules for choosing between a set of values.

Lexically, it can contain symbols matching "[_.a-zA-Z0-9]+", round brackets: (), braces: {} and colons. Whitespace is ignored except to separate symbols.

For each BRANCH_SET each BRANCH must result in the same DECISION. The DECISION must be one of the dependencies mentioned in "depends". This may be:

another decision, in which case the VALUE immediately following in brackets must correspond to one of its output values. The BRANCH_SET immediately containing this BRANCH must represent each output value of the same decision exactly once, and no parent BRANCH_SET may be for the same DECISION.
"p": this entry indicates a probabilistic decision. Where the value is a probability, the sum of all values for the BRANCH_SET must be 1 and the decision must be associated directly with OUTCOMEs (not sub-TREEs).
"age": this entry indicates an age-test. The VALUE must have the form "a-b", indicating that this branch will be taken for individuals aged such that a <= age < b, where a,b are non-negative real numbers or the special value "inf", and a <= b. All VALUEs in the BRANCH_SET must cover all possible (non-negative real) ages, with no overlap (hence, smallest a must be 0 and greatest b must be inf).

Semantically, each OUTCOME must be one of the values associated with this decision.

Attributes

Name of decision

name=string

The name of this decision. The name must match the regular expression "[_a-zA-Z0-9]+"; that is it can only contain letters, digits and _ characters (no spaces, punctuation, etc.).

Preceding decisions

depends=string

Outcome values

values=string

A comma-separated list of outcome values this decision may have. The name of each value must be of the same form as decision names (i.e. only contain letters, digits and _ characters).

treatments

→ scenario → interventions → MDA → description → treatments

<treatments>
IN THIS ORDER:
| ( <treatment ... /> )*
</treatments>

treatment

Documentation (type)

A list of drug treatment tables. Each should have a name corresponding to one of the "drug" decision's values.

treatment

→ scenario → interventions → MDA → description → treatments → treatment

<treatment
    name=string
  >
IN THIS ORDER:
|   <schedule ... /> 
| ( <modifier ... /> )*
</treatment>

Documentation (type)

A description of a base treatment schedule that includes modifiers to handle delays, quality variations, etc.

Attributes

Treatment administered

name=string

Units: string

Name corresponding to one of the drug decision's output values.

schedule

→ scenario → interventions → MDA → description → treatments → treatment → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

The base (unmodified)schedule of drugs administered for this treatment.

medicate

→ scenario → interventions → MDA → description → treatments → treatment → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  [ duration=double ]
  />

Attributes

drug

drug=string

Abbreviated name of drug compound

drug dose

mg=double

Units: mg

Quantity of drug compound

Time of administration

hour=double

Units: Hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

Duration of administration

duration=double

Units: Hours Min: 0

If this attribute is given, use IV administration instead of orally. Specifies the number of hours during which the dose is administered.

modifier

→ scenario → interventions → MDA → description → treatments → treatment → modifier

<modifier
    decision=string
  >
EXACTLY ONE OF:
| ( <multiplyQty ... /> )*
| ( <delay ... /> )*
| ( <selectTimeRange ... /> )*
</modifier>

Documentation (type)

Units: Choice of elements

A modifier for this treatment, according to the outputs of a decision.

Attributes

Decision

decision=string

Units: string

Specifies the decision that this modifier acts on.

Active ingredient multipliers

→ scenario → interventions → MDA → description → treatments → treatment → modifier → multiplyQty

<multiplyQty
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Units: Comma-separated list of values

Multiplies the quantity of active ingredients of drugs administered.

Attributes

Value of decision

value=string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: None

Does this affect the cost? If false, the effective drug usage (w.r.t. cost)is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

Active ingredient delays

→ scenario → interventions → MDA → description → treatments → treatment → modifier → delay

<delay
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Units: Comma-separated list of values

Delays administration of drugs listed in the base schedule by so many hours.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of delays (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0,6", drug A is administered as in the base schedule while drug B is administered 6 hours later than specified.

Attributes

Value of decision

value=string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: None

Does this affect the cost? If false, the effective drug usage (w.r.t. cost)is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

Active ingredient time-ranges

→ scenario → interventions → MDA → description → treatments → treatment → modifier → selectTimeRange

<selectTimeRange
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Selects which drug doses to administer according to time of administration (before times are modified by delays). Half-open interval: [x,y)

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of time-ranges (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. The time-ranges should be of the form x-y and are interpreted as the half-open interval [x,y); that is a drug listed with time t will only be administered if x <= t < y.

Attributes

Value of decision

value=string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: None

Does this affect the cost? If false, the effective drug usage (w.r.t. cost)is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</complicated>

Documentation (type)

A set of decisions and a set of treatments.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: Days Min: 0 Max: unbounded

Maximum number of timesteps (including first day of case) that an individual with an uncomplicated case of malaria will remember he/she was sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial or non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of a complicated or severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
    name=string
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
</ImmediateOutcomes>

Documentation (type)

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Case Management model

name=string

Name of health system

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Description of drug regimen.

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Artemisinine combination therapy

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

QN

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0 Max: 1name:P(self-treat)

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Effectiveness of treatment for non-compliant patients

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease will self-treat

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Case fatality rate for inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: Dimensionless

List of age-specific probabilities of sequelae in inpatients, during a severe bout of malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeEIR>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeEIR → timedDeployment

<timedDeployment
    eipDuration=int
    time=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timedDeployment>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Time

time=int

Units: time-steps Min: 0

Time-step at which this replacement occurs, starting from 0, the first intervention-period time-step.

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Mass drug administration

→ scenario → interventions → MDA

<MDA
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | [ <diagnostic ... /> ]
| | [ <description ... /> ]
| [ <timed ... /> ]
</MDA>

Documentation (element)

Description and deployment of MDA interventions (can also be configured as screen and treat or intermittent preventative treatment with 1-day time-step models).

Currently neither diagnostic nor description need be provided for 5-day timestep model; this may change in the future.

Attributes

Name of intervention

name=string

Name of intervention

Diagnostic (5-day)

→ scenario → interventions → MDA → diagnostic

<diagnostic>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterministic ... /> 
| |   <stochastic ... /> 
</diagnostic>

Documentation (element)

Description of diagnostic used by mass treatment option of five-day case management model — may be used to model MDA without diagnostic or MSAT.

Drugs are administered whenever the test outcome is positive.

Deterministic detection

→ scenario → interventions → MDA → diagnostic → deterministic

<deterministic
    minDensity=double
  />

Documentation (element)

Specify that an artificial deterministic test is used: drugs are administered if parasite density is at least the minimum given.

Attributes

Minimum detectible density

minDensity=double

Units: parasites/microlitre Min: 0

The minimum density at which parasites can be detected. If 0, the test outcome is always positive.

Non-deterministic detection

→ scenario → interventions → MDA → diagnostic → stochastic

<stochastic
    dens_50=double
    specificity=double
  />

Documentation (element)

An improved model of detection which is non-deterministic, including false positive results as well as false negatives.

Some parameterisations:

Microscopy sensitivity/specificity data in Africa; Source: expert opinion — Allan Schapira dens_50 = 20.0 specificity = .75

RDT sensitivity/specificity for Plasmodium falciparum in Africa Source: Murray et al (Clinical Microbiological Reviews, Jan. 2008) dens_50 = 50.0; specificity = .942;

Attributes

Density 50

dens_50=double

Units: parasites/microlitre Min: 0

The density at which the test outcome has a 50% chance of being positive.

Specificity

specificity=double

Units: Dimensionless Min: 0 Max: 1

The probability of a positive test outcome in the absense of parasites.

Diagnostic and treatment (1-day)

→ scenario → interventions → MDA → description

<description
  [ name=string ]
  >
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</description>

Documentation (element)

Documentation (base type)

A set of decisions and a set of treatments.

Attributes

Intervention

name=string

Name of set of interventions

Mass administration

→ scenario → interventions → MDA → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed deployments of mass-drug-administration.

deploy

→ scenario → interventions → MDA → timed → deploy

<deploy
    time=int
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: dimensionless Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Vaccines

→ scenario → interventions → vaccine

<vaccine
  [ name=string ]
  >
IN THIS ORDER:
| ( <description ... /> ){0,3}
| [ <continuous ... /> ]
| [ <timed ... /> ]
</vaccine>

Documentation (element)

Description and deployment of vaccine interventions.

Attributes

Name of intervention

name=string

Name of intervention

description

→ scenario → interventions → vaccine → description

<description
    vaccineType=("PEV" or "BSV" or "TBV")
  [ name=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</description>

Documentation (type)

List of vaccine descriptions

Attributes

Type of vaccine

vaccineType=("PEV" or "BSV" or "TBV")

Units: Code

Type of vaccine

Vaccine

name=string

Name of vaccine

Decay of effect

→ scenario → interventions → vaccine → description → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Specification of decay of efficacy. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Variance parameter for vaccine efficacy

→ scenario → interventions → vaccine → description → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial mean efficacy

→ scenario → interventions → vaccine → description → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Age-based vaccination

→ scenario → interventions → vaccine → continuous

<continuous>
IN THIS ORDER:
| ( <deploy ... /> )+
</continuous>

deploy

Documentation (element)

List of ages at which vaccination takes place (through EPI, post-natal and school-based programmes, etc.).

deploy

→ scenario → interventions → vaccine → continuous → deploy

<deploy
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: dimensionless Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: dimensionless Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Mass vaccination

→ scenario → interventions → vaccine → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed mass vaccinations in the communitsy

deploy

→ scenario → interventions → vaccine → timed → deploy

<deploy
    time=int
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: dimensionless Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

If present, activate cumulate deployment mode where intervention is only deployed to individuals not already considered protected in sufficient quantity to bring the total proportion of people covered up to level described by "coverage". Individuals are considered already protected by this intervention when the age of the last net/dose/etc. received is less than "maximum age" (this attribute) years old (i.e. when timeLastDeployment+maximumAge>currentTimeStep).

Intermittent preventative treatment

→ scenario → interventions → IPT

<IPT
  [ name=string ]
  >
IN THIS ORDER:
|   <description ... /> 
| [ <continuous ... /> ]
| [ <timed ... /> ]
</IPT>

Documentation (element)

Description and deployment of IPT interventions.

Attributes

Name of intervention

name=string

Name of intervention

description

→ scenario → interventions → IPT → description

<description
    iptiEffect=int
  [ name=string ]
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</description>

infGenotype

Attributes

Description of ipti effect

iptiEffect=int

Description of ipti effect

IPT name

name=string

Name of IPT intervention

infGenotype

→ scenario → interventions → IPT → description → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

Age specific intervention

name=string

Name of age specific intervention

Frequency

freq=double

Units: dimensionless Min: 0 Max: 1

Frequency of parasite genotype as a proportion (total of all genotypes must add to 1).

ACR

ACR=double

Units: dimensionless Min: 0 Max: 1

Adequate clinical response (probability of effective cure)

Prophylactic period

proph=int

Units: time-step

Prophylactic period

Tolerance period

tolPeriod=int

Units: time steps

Tolerance period

atten=double

Units: dimensionless Min: 1 Max: inf

Attenuation factor (i.e. divisor for density during period of effect)

Age-based IPT deployment

→ scenario → interventions → IPT → continuous

<continuous>
IN THIS ORDER:
| ( <deploy ... /> )+
</continuous>

deploy

Documentation (element)

List of ages at which IPTi/IPTc deployment takes place (through EPI, post-natal and school-based programmes, etc.).

Mass IPT administration

→ scenario → interventions → IPT → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed IPTi/IPTc distribution

Bed nets

→ scenario → interventions → ITN

<ITN
  [ name=string ]
  >
IN THIS ORDER:
|   <description ... /> 
| [ <continuous ... /> ]
| [ <timed ... /> ]
</ITN>

Documentation (element)

Description and deployment of bed-net interventions (ITNs, LLINs).

Attributes

Name of intervention

name=string

Name of intervention

description

→ scenario → interventions → ITN → description

<description>
IN THIS ORDER:
|   <usage ... /> 
|   <holeRate ... /> 
|   <ripRate ... /> 
|   <ripFactor ... /> 
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
|   <attritionOfNets ... /> 
| ( <anophelesParams ... /> )+
</description>

Proportion of time nets are used by humans

→ scenario → interventions → ITN → description → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of nets by humans, from 0 to 1.

At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing.

See also "propActing" (proportion of bits for which net acts).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Rate at which holes are made

→ scenario → interventions → ITN → description → holeRate

<holeRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Holes per annum Min: 0

The rate at which new holes are made in nets.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ log N( log(mean)-sigma²/2, sigma² ).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rate at which holes are enlarged

→ scenario → interventions → ITN → description → ripRate

<ripRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Rips per existing hole per annum Min: 0

Each existing hole has a probability of being ripped bigger according to a Poisson process with this rate as (only) parameter.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ log N( log(mean)-sigma²/2, sigma² ).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rip factor

→ scenario → interventions → ITN → description → ripFactor

<ripFactor
    value=double
  />

Documentation (element)

Units: none Min: 0

This factor expresses how important rips are in increasing the hole.

The hole index of a net is h + F×x where h and x are the total numbers of holes and rips respectively and F is the rip factor.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → ITN → description → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: mg/m² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → ITN → description → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of nets. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Attrition of nets

→ scenario → interventions → ITN → description → attritionOfNets

<attritionOfNets
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: dimensionless

Specifies the rate at which nets are disposed of over time. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → ITN → description → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterrency ... /> 
| |   <twoStageDeterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which net acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → ITN → description → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Relative attractiveness

→ scenario → interventions → ITN → description → anophelesParams → twoStageDeterrency

<twoStageDeterrency>
IN ANY ORDER:
|   <entering ... /> 
|   <attacking ... /> 
</twoStageDeterrency>

Documentation (element)

Units: dimensionless

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

This deterrency model multiplies human attractiveness by pEnt×pAtt divided by a base factor to normalise the output to 1 when there are no nets.

RA (entering)

→ scenario → interventions → ITN → description → anophelesParams → twoStageDeterrency → entering

<entering
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless

pEnt represents the relative probability of entering due to ITNs: pEnt = exp(log(P)×p) where P is the insecticide factor and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

RA (attacking)

→ scenario → interventions → ITN → description → anophelesParams → twoStageDeterrency → attacking

<attacking
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless

pAtt represents the relative probability of attacking a human after entering a house due to ITNs (i.e. of feeding/dying vs. flying off): pAtt = B + H×h + P×p + I×h×p where B is the base (without net) probability; H, P and I are the hole, insecticide and interaction factors respectively, h=exp(-holeIndex×holeScalingFactor) and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Pre-prandial killing effect

→ scenario → interventions → ITN → description → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → ITN → description → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Age-based bed-net deployment

→ scenario → interventions → ITN → continuous

<continuous>
IN THIS ORDER:
| ( <deploy ... /> )+
</continuous>

deploy

Documentation (element)

List of ages at which bed-net deployment takes place (through EPI, post-natal and school-based programmes, etc.).

Mass ITN deployment

→ scenario → interventions → ITN → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed ITN deployment in the communitsy

Indoor residual spraying

→ scenario → interventions → IRS

<IRS
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <description ... /> 
| |   <description_v2 ... /> 
| [ <timed ... /> ]
</IRS>

Documentation (element)

Description and deployment of indoor insecticide interventions (IRS, durable wall linings, insecticide-treated-paint, etc.)

User must choose between using (the old model, where effect decays directly) and <description_v2> (the new model where effect decays indirectly based on decay of insecticide).

Attributes

Name of intervention

name=string

Name of intervention

description

→ scenario → interventions → IRS → description

<description>
IN THIS ORDER:
|   <decay ... /> 
| ( <anophelesParams ... /> )+
</description>

Documentation (type)

Description of effect for the simple model: IRS has three effects, whos strength is calculated as the product of an input parameter and "survival of effect", which is given by a decay function.

Decay

→ scenario → interventions → IRS → description → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Description of decay of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → IRS → description → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → IRS → description → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied this factor times survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → IRS → description → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → IRS → description → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

description_v2

→ scenario → interventions → IRS → description_v2

<description_v2>
IN THIS ORDER:
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
| ( <anophelesParams ... /> )+
</description_v2>

Documentation (type)

Description of effect for the more complex and probably more realistic Briet model: IRS has three effects, whos strength is calculated as a function of surviving insecticide content.

Initial insecticide

→ scenario → interventions → IRS → description_v2 → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: μg/cm² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → IRS → description_v2 → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → IRS → description_v2 → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → IRS → description_v2 → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied by exp(P×log(p)) where P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → IRS → description_v2 → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → IRS → description_v2 → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Mass IRS deployment

→ scenario → interventions → IRS → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed IRS deployment in the communitsy

Vector deterrents

<vectorDeterrent
  [ name=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
| ( <anophelesParams ... /> )+
| [ <timed ... /> ]
</vectorDeterrent>

Documentation (element)

Description and deployment of interventions affecting only human-mosquito availability (deterrents).

Attributes

Name of intervention

name=string

Name of intervention

Decay

→ scenario → interventions → vectorDeterrent → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Description of decay of vector deterrent. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → vectorDeterrent → anophelesParams

<anophelesParams
    mosquito=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</anophelesParams>

deterrency

Documentation (type)

Units: dimensionless Min: 0 Max: 1

Descriptions of initial effectiveness of each of the effects of interventions. Decay is specified by a separate element (ITNDecay etc.)

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Deterrency

→ scenario → interventions → vectorDeterrent → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

One minus this multiplies the host's availability.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mass deployment

→ scenario → interventions → vectorDeterrent → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed mosquito deterrent deployment in the communitsy

Cohort recruitment

→ scenario → interventions → cohort

<cohort
  [ name=string ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
| [ <timed ... /> ]
</cohort>

Documentation (element)

Recruitment of cohort as a pseudo-intervention.

Attributes

Name of intervention

name=string

Name of intervention

Age-based cohort recruitment

→ scenario → interventions → cohort → continuous

<continuous>
IN THIS ORDER:
| ( <deploy ... /> )+
</continuous>

deploy

Documentation (element)

List of ages at which cohort recruitment takes place.

Mass cohort selection

→ scenario → interventions → cohort → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of times of mass cohort selection.

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=int ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=int

Units: time-steps Min: 0

Default value: 0

If period is 0 (or effectively infinite), the last specified value remains indefinitely in effect, otherwise the times of all values specified must be less than the period, and values are repeated modulo period (timestep period+2 has same value as timestep 2, etc.).

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=int
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time

time=int

Units: time-steps Min: 0

Immune suppression

<immuneSuppression>
IN THIS ORDER:
| [ <timed ... /> ]
</immuneSuppression>

timed

Documentation (element)

Removes all exposure-related immunitsy gained over time by hosts without removing infections.

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

timed

→ scenario → interventions → immuneSuppression → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Insert R_0 case

<insertR_0Case>
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</insertR_0Case>

timedDeployment

Documentation (element)

Used to simulate R_0. First, infections should be eliminated, immunitsy removed, and the population given an effective transmission- blocking vaccine (not done by this intervention). Then this intervention may be used to: pick one human, infect him, administer a fully effective Preerythrocytic vaccine and remove transmission-blocking vaccine effect on this human. Thus only this one human will be a source of infections in an unprotected population, and will not reinfected himself.

timedDeployment

→ scenario → interventions → insertR_0Case → timedDeployment

<timedDeployment
    time=int
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Uninfect vectors

<uninfectVectors>
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</uninfectVectors>

timedDeployment

Documentation (element)

Units: List of elements

Removes all infections from mosquitoes -- resulting in zero EIR to humans, until such time that mosquitoes are re-infected and become infectious. Only effectious in dynamic EIR mode (when changeEIR was not used).

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

timedDeployment

→ scenario → interventions → uninfectVectors → timedDeployment

<timedDeployment
    time=int
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Vector population intervention

→ scenario → interventions → vectorPop

<vectorPop>
IN THIS ORDER:
| ( <intervention ... /> )+
</vectorPop>

intervention

Documentation (element)

Units: List of elements

A list of parameterisations of generic vector host-inspecific interventions.

intervention

→ scenario → interventions → vectorPop → intervention

<intervention
    name=string
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</intervention>

Documentation (type)

Units: List of elements

An intervention which may have various effects on the vector populations as a whole. (Not host specific.)

Multiple instances of this intervention class are allowed (multiple parameterisations, not just deployments).

Attributes

Name of intervention

name=string

Name of intervention (e.g. larviciding, sugar bait).

description

→ scenario → interventions → vectorPop → intervention → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → vectorPop → intervention → description → anopheles

<anopheles
    mosquito=string
  >
IN ANY ORDER:
| [ <seekingDeathRateIncrease ... /> ]
| [ <probDeathOvipositing ... /> ]
| [ <emergenceReduction ... /> ]
</anopheles>

Documentation (type)

Units: dimensionless Min: 0 Max: 1

Descriptions of initial effectiveness of the effects of vector population interventions.

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportional increase in deaths while host searching

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease

<seekingDeathRateIncrease
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</seekingDeathRateIncrease>

decay

Documentation (element)

Units: dimensionless

Describe an effect on the increase in the death rate while host seeking (mu_vA) due to this intervention.

Enter the rate increase (i.e. if rate increases to 120% of normal, give 0.2).

Attributes

Initial proportion increase

initial=double

Units: dimensionless Min: 0 Max: inf

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → seekingDeathRateIncrease → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Proportion ovipositing mosquitoes killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing

<probDeathOvipositing
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</probDeathOvipositing>

decay

Documentation (element)

Units: dimensionless

Describe an effect of increased mortality while ovipositing due to this intervention. Enter the probability of dying due to this intervention.

Attributes

Initial probability of killing

initial=double

Units: dimensionless Min: 0 Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → probDeathOvipositing → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Proportion of emerging pupa killed

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction

<emergenceReduction
    initial=double
  >
IN THIS ORDER:
|   <decay ... /> 
</emergenceReduction>

decay

Documentation (element)

Units: dimensionless

Describe an effect on emergence of pupa into adults: this value is the proportion of emerging pupa which are killed by this intervention.

This can be used as a crude way of modelling larviciding.

Attributes

Initial proportion reduction

initial=double

Units: dimensionless Min: 0 Max: 1

decay

→ scenario → interventions → vectorPop → intervention → description → anopheles → emergenceReduction → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Vector population intervention deployment

→ scenario → interventions → vectorPop → intervention → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed vector population intervention deployment

deploy

→ scenario → interventions → vectorPop → intervention → timed → deploy

<deploy
    time=int
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Description of health system.

Documentation (type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("forced" or "dynamic")
  [ scaledAnnualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Description of entomological data

Attributes

Entomology dataset name

name=string

Name of entomology data

Transmission model mode

mode=("forced" or "dynamic")

Override annual EIR

scaledAnnualEIR=double

Units: Infectious bites per adult per year

If set, the annual EIR (for all species of vector) is scaled to this level; can be omitted if not needed.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters of the transmission model

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <seasonality ... /> 
|   <mosq ... /> 
| [ <lifeCycle ... /> ]
| [ <simpleMPD ... /> ]
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial estimate of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial estimate of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial estimate of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Seasonality of transmission

→ scenario → entomology → vector → anopheles → seasonality

<seasonality
    input=("EIR")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <fourierSeries ... /> 
| |   <monthlyValues ... /> 
| |   <dailyValues ... /> 
</seasonality>

Documentation (element)

Specifies the seasonality of transmission and optionally the level of annual transmission.

Attributes

Seasonality input

input=("EIR")

Annual EIR

annualEIR=double

Units: Inoculations per adult per annum Min: 0

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries

<fourierSeries
    EIRRotateAngle=double
  >
IN THIS ORDER:
| ( <coeffic ... /> )*
</fourierSeries>

coeffic

Documentation (element)

Units: Infectious bites per adult per day

Attributes

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: Radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Pair of Fourier coefficients

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries → coeffic

<coeffic
    a=double
    b=double
  />

Documentation (element)

A pair of Fourier series coefficients. The first element specifies a1 and b1, the second a2 and b2, etc. Any number (from 0 up) of pairs may be given.

Attributes

a_n parameter of Fourier approximation to ln(EIR)

a=double

a_n parameter of Fourier approximation to ln(EIR) for some natural number n.

b_n parameter of Fourier approximation to ln(EIR)

b=double

b_n parameter of Fourier approximation to ln(EIR) for some natural number n.

List of monthly values

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues

<monthlyValues
    smoothing=("none" or "fourier")
  >
IN THIS ORDER:
| ( <value ... /> ){12,12}
</monthlyValues>

value

Documentation (element)

Description of seasonality from monthly values. Multiple smoothing methods are possible (see smoothing attribute).

List should contain twelve entries: January to December.

Attributes

Smoothing function

smoothing=("none" or "fourier")

How the monthly values are converted into a daily sequence of values:

none: no smoothing (step function)
Fourier: a Fourier series (with terms up to a2/b2) is fit to the sequence of monthly values and used to generate a smoothed list of daily values.

Monthly value

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Monthly value

List of daily values

→ scenario → entomology → vector → anopheles → seasonality → dailyValues

<dailyValues>
IN THIS ORDER:
| ( <value ... /> ){365,365}
</dailyValues>

value

Documentation (element)

Description of seasonality from daily values.

List should contain 365 entries: 1st January to 31st December.

Daily value

→ scenario → entomology → vector → anopheles → seasonality → dailyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Daily value

Mosquito feeding cycle parameters

→ scenario → entomology → vector → anopheles → mosq

<mosq
    minInfectedThreshold=double
  >
IN ANY ORDER:
|   <mosqRestDuration ... /> 
|   <extrinsicIncubationPeriod ... /> 
|   <mosqLaidEggsSameDayProportion ... /> 
|   <mosqSeekingDuration ... /> 
|   <mosqSurvivalFeedingCycleProbability ... /> 
|   <availabilityVariance ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <mosqProbOvipositing ... /> 
|   <mosqHumanBloodIndex ... /> 
</mosq>

Documentation (element)

Parameters describing the feeding cycle and human mosquito interaction of a single species of anopheles mosquito.

Attributes

Mininum infected threshold for mosquitos

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

Duration of the resting period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqRestDuration

<mosqRestDuration
    value=int
  />

Documentation (element)

Units: Days

name:Duration of the resting period of the vector (days);

Attributes

Input parameter value

value=int

An integer value.

Extrinsic incubation period

→ scenario → entomology → vector → anopheles → mosq → extrinsicIncubationPeriod

<extrinsicIncubationPeriod
    value=int
  />

Documentation (element)

Units: Days

name:Extrinsic incubation period (days)

Attributes

Input parameter value

value=int

An integer value.

Proportion of mosquitoes host seeking on same day as ovipositing

→ scenario → entomology → vector → anopheles → mosq → mosqLaidEggsSameDayProportion

<mosqLaidEggsSameDayProportion
    value=double
  />

Documentation (element)

Units: Proportion

Proportion of mosquitoes host seeking on same day as ovipositing

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Duration of the host-seeking period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqSeekingDuration

<mosqSeekingDuration
    value=double
  />

Documentation (element)

Units: Days

Duration of the host-seeking period of the vector (days)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito survives the feeding cycle

→ scenario → entomology → vector → anopheles → mosq → mosqSurvivalFeedingCycleProbability

<mosqSurvivalFeedingCycleProbability
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito survives the feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Variance in human availability rate

→ scenario → entomology → vector → anopheles → mosq → availabilityVariance

<availabilityVariance
    value=double
  />

Documentation (element)

Variance in availability rate of humans to mosquitoes. The mean rate is calculated based on other parameters.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito succesfully bites chosen host

→ scenario → entomology → vector → anopheles → mosq → mosqProbBiting

<mosqProbBiting
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito succesfully bites chosen host

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → mosq → mosqProbFindRestSite

<mosqProbFindRestSite
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito escapes host and finds a resting place after biting

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → mosq → mosqProbResting

<mosqProbResting
    mean=double
    variance=double
  />

Documentation (element)

Probability of mosquito successfully resting after finding a resting site

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of a mosquito successfully laying eggs given that it has rested

→ scenario → entomology → vector → anopheles → mosq → mosqProbOvipositing

<mosqProbOvipositing
    value=double
  />

Documentation (element)

Probability of a mosquito successfully laying eggs given that it has rested

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human blood index

→ scenario → entomology → vector → anopheles → mosq → mosqHumanBloodIndex

<mosqHumanBloodIndex
    value=double
  />

Documentation (element)

Units: Proportion

The proportion of resting mosquitoes which fed on human blood during the last feed.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mosquito life cycle parameters

→ scenario → entomology → vector → anopheles → lifeCycle

<lifeCycle
  [ estimatedLarvalResources=double ] DEFAULT VALUE 1e8
  >
IN ANY ORDER:
|   <eggStage ... /> 
|   <larvalStage ... /> 
|   <pupalStage ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</lifeCycle>

Documentation (element)

Parameters describing the life-cycle of this species of mosquito

Attributes

Estimate of larval resources

estimatedLarvalResources=double

Units: X

Default value: 1e8

Egg stage

→ scenario → entomology → vector → anopheles → lifeCycle → eggStage

<eggStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the egg stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

larvalStage

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage

<larvalStage>
</larvalStage>

daily

Documentation (type)

Parameters for the larval stage of development

Documentation (base type)

Parameters associated with a mosquito development stage.

Daily development

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage → daily

<daily
    resourceUsage=double
    effectCompetition=double
  />

Documentation (element)

Attributes

Resource usage

resourceUsage=double

Units: X

Resource usage during larval stage of development. Units are arbitrary.

Effect of competition

effectCompetition=double

Units: none

Effect of competition over resources on development.

Pupal stage

→ scenario → entomology → vector → anopheles → lifeCycle → pupalStage

<pupalStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the pupal stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → lifeCycle → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Simple Mosq-Pop-Dynamics parameters

→ scenario → entomology → vector → anopheles → simpleMPD

<simpleMPD>
IN ANY ORDER:
|   <developmentDuration ... /> 
|   <developmentSurvival ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</simpleMPD>

Documentation (element)

Parameters describing the simple mosquito population dynamics model.

This is a simpler version of the life-cycle model, requiring less parameters and with much simpler initialisation.

Duration

→ scenario → entomology → vector → anopheles → simpleMPD → developmentDuration

<developmentDuration
    value=int
  />

Documentation (element)

Units: Days Min: 1

Duration from egg laying to emergence in days.

Attributes

Input parameter value

value=int

An integer value.

Probability of survival

→ scenario → entomology → vector → anopheles → simpleMPD → developmentSurvival

<developmentSurvival
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that mosquito survives from the egg being laid to emergence, given no resouce limitations (no density constraints).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → simpleMPD → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Alternative (non-human) host paramters

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN ANY ORDER:
|   <mosqRelativeEntoAvailability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
</nonHumanHosts>

Documentation (element)

Min: 0

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of non-human host (ξ_i)

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqRelativeEntoAvailability

<mosqRelativeEntoAvailability
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Name of this species of non human hosts (must match up with those described per anopheles section).

Population size of alternative host species

number=double

Units: Number

Population size of this non-human host.

Pharmacokinetics and pharmacodynamics

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
| ( <drug ... /> )+
</pharmacology>

drug

Documentation (element)

Drug model parameters

Library of drug parameters

→ scenario → pharmacology → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (element)

Sequence of drug descriptions forming a library of drug parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drug → PD

<PD>
IN THIS ORDER:
| ( <allele ... /> )+
</PD>

allele

PD parameters per allele

→ scenario → pharmacology → drug → PD → allele

<allele
    name=string
  >
IN THIS ORDER:
|   <initial_frequency ... /> 
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</allele>

Documentation (element)

PD parameters per allele, plus initial frequency of each allele.

Note: we assume a one-to-one correspondance of drugs to loci, hence each drug has an independent set of alleles here.

Attributes

name

name=string

Relative frequency

→ scenario → pharmacology → drug → PD → allele → initial_frequency

<initial_frequency>
    double
</initial_frequency>

Documentation (element)

Units: dimensionless Min: 0

Frequency, relative to the total frequency of all alleles for this drug/locus.

Maximal parasite killing rate

→ scenario → pharmacology → drug → PD → allele → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drug → PD → allele → IC50

<IC50>
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

Slope of effect curve

→ scenario → pharmacology → drug → PD → allele → slope

<slope>
    double
</slope>

Documentation (element)

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
|   <half_life ... /> 
|   <vol_dist ... /> 
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate (which is: ln(2) / half_life).

Volume of Distribution

→ scenario → pharmacology → drug → PK → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: include/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=int
  >
IN THIS ORDER:
| [ <NonMalariaFevers ... /> ]
</clinical>

NonMalariaFevers

Documentation (type)

Attributes

Follow-up period during which recurrence is treated as a failure

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
|   <prNeedTreatmentNMF ... /> 
|   <prNeedTreatmentMF ... /> 
</NonMalariaFevers>

Documentation (type)

Description of the incidence of non-malaria fever. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a non-malarial fever requires treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

Availability of humans to mosquitoes relative to an adult, categorized by age group

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ]
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → model → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 30 documentation

Generated from: scenario_30.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    name=string
    wuID=int
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_30.xsd"
  >
IN ANY ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entomology ... /> 
| [ <pharmacology ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Units: string

Name of intervention

Work unit identifier

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Attributes

Name of demography data

name=string

Units: string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: years Min: 0 Max: 100

Maximum age of simulated humans in years.

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Percentage of human population in age group

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ cohortOnly=boolean ]
  [ firstBoutOnly=boolean ]
  [ firstTreatmentOnly=boolean ]
  [ firstInfectionOnly=boolean ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Attributes

Name of monitoring information

name=string

Units: string

Name of monitoring data

Survey only cohort

cohortOnly=boolean

Time to first episode only

firstBoutOnly=boolean

Time to first treatment only

firstTreatmentOnly=boolean

Time to first infection only

firstInfectionOnly=boolean

continuous

→ scenario → monitoring → continuous

<continuous
    period=int
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Days between reports

period=int

Units: Days Min: 1 Max: unbounded

Number of timesteps between reports.

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Model options required

name=string

Options define different model structures. Option name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.

Indicator of whether option is required

value=boolean

Default value: true

Option value (true/false). Each option has a default value used if the option is not listed (usually false but sometimes true).

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/microlitre Min: 0

Limit above which a human's infection is reported as patent.

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time; 0 means just before start of main sim and is a valid survey-point. Reported data is either from a point-time survey (immediate data) or is collected over the previous year (data from previous timesteps-per-year period). Simulation will end immediately after last survey is taken.

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Preventative interventions

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <vaccine ... /> ]
| [ <IPT ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <vectorDeterrent ... /> ]
| [ <cohort ... /> ]
| [ <importedInfections ... /> ]
| [ <immuneSuppression ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <larviciding ... /> ]
</interventions>

Documentation (element)

Units: List of elements

Attributes

Intervention

name=string

Units: string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeHS>

timedDeployment

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Units: string

Name of intervention

timedDeployment

→ scenario → interventions → changeHS → timedDeployment

<timedDeployment
    time=int
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timedDeployment>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this replacement occurs, starting from 0, the first intervention-period time-step.

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</uncomplicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

decisions

→ scenario → interventions → MDA → description → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )*
</decisions>

decision

Documentation (type)

case (uncomplicated only): Returns "UC1" if there is no recent history of a malarial case, or "UC2" if there is.
result: Dependent on decision "test", this performs a parasite density test. Output is one of "none" (no test performed), "positive", "negative".

The following decisions must be described here:

test (uncomplicated only): Outputs must be "none", "microscopy" or "RDT" to describe which test the "result" decision uses.
treatment: Describes which treatment to use. Values aren't restricted but must match up with a treatment described in the corresponding "treatments" section.
hospitalisation (complicated only): none, immediate or delayed.

decision

→ scenario → interventions → MDA → description → decisions → decision

<decision
    name=string
    depends=string
    values=string
  >
    string
</decision>

Documentation (type)

A decision describes how to choose between a set of values.

Lexically, it can contain symbols matching "[_.a-zA-Z0-9]+", round brackets: (), braces: {} and colons. Whitespace is ignored except to separate symbols.

For each BRANCH_SET each BRANCH must have the same DECISION. This DECISION must be one of the dependencies mentioned in "depends". This may be:

another decision, in which case the VALUE immediately following in brackets must correspond to one of its output values. The BRANCH_SET immediately containing this BRANCH must represent each output value of the same decision exactly once, and no parent BRANCH_SET may be for the same DECISION.
"p": this indicates a probabilistic decision. In this case the value is a probability, the sum of all values for the BRANCH_SET must be 1 and the decision must be associated directly with OUTCOMEs (not sub-TREEs).
"age": this indicates an age-test. The VALUE must have the form "a-b", indicating that this branch will be taken for individuals aged such that a <= age < b, where a,b are non-negative real numbers or the special value "inf", and a <= b. All VALUEs in the BRANCH_SET must cover all possible (non-negative real) ages, with no overlap (hence, smallest a must be 0 and greatest b must be inf).

Semantically, each OUTCOME must be one of the values associated with this decision.

Attributes

Name of decision

name=string

The name of this decision. The name must match the regular expression "[_a-zA-Z0-9]+"; that is it can only contain letters, digits and _ characters (no spaces, punctuation, etc.).

Preceding decisions

depends=string

A comma-separated list of decisions that must have already been evaluated before this decision can be evaluated. Can be empty. Each must be hard-coded or described here. Can include the special decisions "p" and "age", though "age" cannot be combined with any other dependency.

Outcome values

values=string

A comma-separated list of outcome values this decision may have. The name of each value must be of the same form as decision names (i.e. only contain letters, digits and _ characters).

treatments

→ scenario → interventions → MDA → description → treatments

<treatments>
IN THIS ORDER:
| ( <treatment ... /> )*
</treatments>

treatment

Documentation (type)

Units: string

A list of drug treatment tables. Each should have a name corresponding to one of the "drug" decision's values.

treatment

→ scenario → interventions → MDA → description → treatments → treatment

<treatment
    name=string
  >
IN THIS ORDER:
|   <schedule ... /> 
| ( <modifier ... /> )*
</treatment>

Documentation (type)

Units: List of elements

A description of a base treatment schedule along with modifiers to handle delays, quality variations, etc.

Attributes

Treatment administered

name=string

Units: string

Name corresponding to one of the drug decision's output values.

schedule

→ scenario → interventions → MDA → description → treatments → treatment → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

Units: List of elements

The base (unmodified) schedule of drugs administered for this treatment.

medicate

→ scenario → interventions → MDA → description → treatments → treatment → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  [ duration=double ]
  />

Attributes

drug

drug=string

Units: string

Abbreviated name of drug compound

drug dose

mg=double

Units: mg

Quantity of drug compound

time of administration

hour=double

Units: hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

duration of administration

duration=double

Units: hours Min: 0

If this attribute is given, use IV administration instead of orally. Specifies the number of hours over which the dose is administered.

modifier

→ scenario → interventions → MDA → description → treatments → treatment → modifier

<modifier
    decision=string
  >
EXACTLY ONE OF:
| ( <multiplyQty ... /> )*
| ( <delay ... /> )*
| ( <selectTimeRange ... /> )*
</modifier>

Documentation (type)

Units: Choice of elements

A modifier for this treatment, according to the outputs of a decision.

Attributes

decision

decision=string

Units: string

Specifies the decision that this modifier acts on.

Active ingredient multipliers

→ scenario → interventions → MDA → description → treatments → treatment → modifier → multiplyQty

<multiplyQty
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Units: Comma separated list of values

Multiplies the quantity of active ingredients of drugs administered.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of multipliers for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0.5,1" the quantity of drug A is halved while that of B is unchanged.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

Active ingredient delays

→ scenario → interventions → MDA → description → treatments → treatment → modifier → delay

<delay
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Units: Comma separated list of values

Delays administration of drugs listed in the base schedule by so many hours.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of delays (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0,6", drug A is administered as in the base schedule while drug B is administered 6 hours later than specified.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

Active ingredient time-ranges

→ scenario → interventions → MDA → description → treatments → treatment → modifier → selectTimeRange

<selectTimeRange
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Units: Comma separated list of values

Selects which drug doses to administer according to time of administration (before times are modified by delays). Half-open interval: [x,y)

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of time-ranges (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. The time-ranges should be of the form x-y and are interpreted as the half-open interval [x,y); that is a drug listed with time t will only be administered if x <= t < y.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</complicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: days Min: 0 Max: unbounded

Maximum number of timesteps (including first of case) an individual will remember they are sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial/non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of a complicated/severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: none Min: 0 Max: 1

It is sometimes desirable to model delays to treatment seeking in uncomplicated cases. While treatment of drugs can be delayed within case management trees to provide a similar effect, this doesn't delay any of the decisions, including diagnostics using the current parasite density.

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: none Min: 0 Max: 1

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: none Min: 0 Max: 1

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: none Min: 0 Max: 1

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
    name=string
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
</ImmediateOutcomes>

Documentation (type)

Units: List of elements

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Case Management model

name=string

Units: string

Name of health system

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

ACT

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

QN

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

Probability that a patient with uncomplicated disease seeks official care immediately

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease self-treats

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Case fatality rate in inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: List of elements

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients, during a severe bout.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeEIR>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Units: string

Name of intervention

timedDeployment

→ scenario → interventions → changeEIR → timedDeployment

<timedDeployment
    eipDuration=int
    time=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timedDeployment>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

Time

time=int

Units: time-steps Min: 0

Time-step at which this replacement occurs, starting from 0, the first intervention-period time-step.

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

In the non-vector model, EIR is input as a sequence of daily values. There must be at least a years' worth of entries (365), and if there are more, values are wrapped and averaged (i.e. value for first day of year is taken as the mean of values for days 0, 365+0, 2*365+0, etc.).

Attributes

Time origin of EIR sequence

origin=string

Mass drug administration

→ scenario → interventions → MDA

<MDA
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | [ <diagnostic ... /> ]
| | [ <description ... /> ]
| [ <timed ... /> ]
</MDA>

Documentation (element)

Description and deployment of MDA interventions (can also be configured as screen and treat or intermittent preventative treatment with 1-day time-step models).

Currently neither diagnostic nor description need be provided for 5-day timestep model; this may change in the future.

Attributes

Name of intervention

name=string

Units: string

Name of intervention

Diagnostic (5-day)

→ scenario → interventions → MDA → diagnostic

<diagnostic>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterministic ... /> 
| |   <stochastic ... /> 
</diagnostic>

Documentation (element)

Description of diagnostic used by mass treatment option of five-day case management model — may be used to model MDA without diagnostic or MSAT.

Drugs are administered whenever the test outcome is positive.

Deterministic detection

→ scenario → interventions → MDA → diagnostic → deterministic

<deterministic
    minDensity=double
  />

Documentation (element)

Specify that an artificial deterministic test is used: drugs are administered if parasite density is at least the minimum given.

Attributes

Minimum detectible density

minDensity=double

Units: parasites/microlitre Min: 0

The minimum density at which parasites can be detected. If 0, the test outcome is always positive.

Non-deterministic detection

→ scenario → interventions → MDA → diagnostic → stochastic

<stochastic
    dens_50=double
    specificity=double
  />

Documentation (element)

An improved model of detection which is non-deterministic, including false positive results as well as false negatives.

Some parameterisations:

Microscopy sensitivity/specificity data in Africa; Source: expert opinion — Allan Schapira dens_50 = 20.0 specificity = .75

RDT sensitivity/specificity for Plasmodium falciparum in Africa Source: Murray et al (Clinical Microbiological Reviews, Jan. 2008) dens_50 = 50.0; specificity = .942;

Attributes

Density 50

dens_50=double

Units: parasites/microlitre Min: 0

The density at which the test outcome has a 50% chance of being positive.

Specificity

specificity=double

Units: none Min: 0 Max: 1

The probability of a positive test outcome in the absense of parasites.

Diagnostic and treatment (1-day)

→ scenario → interventions → MDA → description

<description
  [ name=string ]
  >
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</description>

Documentation (element)

Documentation (base type)

Units: List of elements

A set of decisions and a set of treatments.

Attributes

Intervention

name=string

Units: string

Name of set of interventions

Mass administration

→ scenario → interventions → MDA → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed deployments of mass-drug-administration.

deploy

→ scenario → interventions → MDA → timed → deploy

<deploy
    time=int
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Vaccines

→ scenario → interventions → vaccine

<vaccine
  [ name=string ]
  >
IN THIS ORDER:
| ( <description ... /> ){0,3}
| [ <continuous ... /> ]
| [ <timed ... /> ]
</vaccine>

Documentation (element)

Description and deployment of vaccine interventions.

Attributes

Name of intervention

name=string

Units: string

Name of intervention

description

→ scenario → interventions → vaccine → description

<description
    vaccineType=("PEV" or "BSV" or "TBV")
  [ name=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</description>

Documentation (type)

List of vaccine descriptions

Attributes

Type of vaccine

vaccineType=("PEV" or "BSV" or "TBV")

Units: Code

Type of vaccine

Vaccine

name=string

Units: string

Name of vaccine

Decay of effect

→ scenario → interventions → vaccine → description → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Specification of decay of efficacy. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Variance parameter for vaccine efficacy

→ scenario → interventions → vaccine → description → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial mean efficacy

→ scenario → interventions → vaccine → description → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Age-based vaccination

→ scenario → interventions → vaccine → continuous

<continuous>
IN THIS ORDER:
| ( <deploy ... /> )+
</continuous>

deploy

Documentation (element)

List of ages at which vaccination takes place (through EPI, post-natal and school-based programmes, etc.).

deploy

→ scenario → interventions → vaccine → continuous → deploy

<deploy
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Mass vaccination

→ scenario → interventions → vaccine → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed mass vaccinations in the community

deploy

→ scenario → interventions → vaccine → timed → deploy

<deploy
    time=int
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

Intermittent preventative treatment

→ scenario → interventions → IPT

<IPT
  [ name=string ]
  >
IN THIS ORDER:
|   <description ... /> 
| [ <continuous ... /> ]
| [ <timed ... /> ]
</IPT>

Documentation (element)

Description and deployment of IPT interventions.

Attributes

Name of intervention

name=string

Units: string

Name of intervention

description

→ scenario → interventions → IPT → description

<description
    iptiEffect=int
  [ name=string ]
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</description>

infGenotype

Attributes

Description of ipti effect

iptiEffect=int

Units: List of Elementes

Description of ipti effect

IPT name

name=string

Units: string

Name of IPT intervention

infGenotype

→ scenario → interventions → IPT → description → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

Age specific intervention

name=string

Units: string

Name of age specific intervention

Frequency

freq=double

Frequency of parasite genotype

ACR

ACR=double

Adequate clinical response (proportion)

Prophylactic period

proph=int

Prophylactic period

Tolerance period

tolPeriod=int

Tolerance period

atten=double

Tolerance period

Age-based IPT deployment

→ scenario → interventions → IPT → continuous

<continuous>
IN THIS ORDER:
| ( <deploy ... /> )+
</continuous>

deploy

Documentation (element)

List of ages at which IPTi/IPTc deployment takes place (through EPI, post-natal and school-based programmes, etc.).

Mass IPT administration

→ scenario → interventions → IPT → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed IPTi/IPTc distribution

Bed nets

→ scenario → interventions → ITN

<ITN
  [ name=string ]
  >
IN THIS ORDER:
|   <description ... /> 
| [ <continuous ... /> ]
| [ <timed ... /> ]
</ITN>

Documentation (element)

Description and deployment of bed-net interventions (ITNs, LLINs).

Attributes

Name of intervention

name=string

Units: string

Name of intervention

description

→ scenario → interventions → ITN → description

<description>
IN THIS ORDER:
|   <usage ... /> 
|   <holeRate ... /> 
|   <ripRate ... /> 
|   <ripFactor ... /> 
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
|   <attritionOfNets ... /> 
| ( <anophelesParams ... /> )+
</description>

Proportion of time nets are used by humans

→ scenario → interventions → ITN → description → usage

<usage
    value=double
  />

Documentation (element)

Units: none Min: 0 Max: 1

Usage of nets by humans, from 0 to 1.

At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing.

See also "propActing" (proportion of bits for which net acts).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Rate at which holes are made

→ scenario → interventions → ITN → description → holeRate

<holeRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Holes per annum Min: 0

The rate at which new holes are made in nets.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ log N( log(mean)-sigma²/2, sigma² ).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rate at which holes are enlarged

→ scenario → interventions → ITN → description → ripRate

<ripRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Rips per existing hole per annum Min: 0

Each existing hole has a probability of being ripped bigger according to a Poisson process with this rate as (only) parameter.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ log N( log(mean)-sigma²/2, sigma² ).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rip factor

→ scenario → interventions → ITN → description → ripFactor

<ripFactor
    value=double
  />

Documentation (element)

Units: none Min: 0

This factor expresses how important rips are in increasing the hole.

The hole index of a net is h + F×x where h and x are the total numbers of holes and rips respectively and F is the rip factor.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → ITN → description → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: mg/m² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → ITN → description → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of nets. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Attrition of nets

→ scenario → interventions → ITN → description → attritionOfNets

<attritionOfNets
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Specifies the rate at which nets are disposed of over time. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → ITN → description → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which net acts

propActive=double

Units: none Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → ITN → description → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
  />

Documentation (element)

Units: none Min: 0 Max: 1

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → ITN → description → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: none Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: none

Post-prandial killing effect

→ scenario → interventions → ITN → description → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: none Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: none

Age-based bed-net deployment

→ scenario → interventions → ITN → continuous

<continuous>
IN THIS ORDER:
| ( <deploy ... /> )+
</continuous>

deploy

Documentation (element)

List of ages at which bed-net deployment takes place (through EPI, post-natal and school-based programmes, etc.).

Mass ITN deployment

→ scenario → interventions → ITN → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed ITN deployment in the community

Indoor residual spraying

→ scenario → interventions → IRS

<IRS
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <description ... /> 
| |   <description_v2 ... /> 
| [ <timed ... /> ]
</IRS>

Documentation (element)

Description and deployment of indoor insecticide interventions (IRS, durable wall linings, insecticide-treated-paint, etc.)

User must choose between using (the old model, where effect decays directly) and <description_v2> (the new model where effect decays indirectly based on decay of insecticide).

Attributes

Name of intervention

name=string

Units: string

Name of intervention

description

→ scenario → interventions → IRS → description

<description>
IN THIS ORDER:
|   <decay ... /> 
| ( <anophelesParams ... /> )+
</description>

Documentation (type)

Description of effect for the simple model: IRS has three effects, whos strength is calculated as the product of an input parameter and "survival of effect", which is given by a decay function.

Decay

→ scenario → interventions → IRS → description → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Description of decay of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → IRS → description → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: none Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → IRS → description → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: none Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied this factor times survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → IRS → description → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: none Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → IRS → description → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: none Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

description_v2

→ scenario → interventions → IRS → description_v2

<description_v2>
IN THIS ORDER:
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
| ( <anophelesParams ... /> )+
</description_v2>

Documentation (type)

Description of effect for the more complex and probably more realistic Briet model: IRS has three effects, whos strength is calculated as a function of surviving insecticide content.

Initial insecticide

→ scenario → interventions → IRS → description_v2 → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: μg/cm² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → IRS → description_v2 → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → IRS → description_v2 → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: none Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → IRS → description_v2 → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: none Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied by exp(P×log(p)) where P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → IRS → description_v2 → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: none Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: none

Post-prandial killing effect

→ scenario → interventions → IRS → description_v2 → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: none Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: none

Mass IRS deployment

→ scenario → interventions → IRS → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed IRS deployment in the community

Vector deterrents

<vectorDeterrent
  [ name=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
| ( <anophelesParams ... /> )+
| [ <timed ... /> ]
</vectorDeterrent>

Documentation (element)

Description and deployment of interventions affecting only human-mosquito availability (deterrents).

Attributes

Name of intervention

name=string

Units: string

Name of intervention

Decay

→ scenario → interventions → vectorDeterrent → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Description of decay of vector deterrent. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → vectorDeterrent → anophelesParams

<anophelesParams
    mosquito=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</anophelesParams>

deterrency

Documentation (type)

Units: None Min: 0 Max: 1

Descriptions of initial effectiveness of each of the effects of interventions. Decay is specified by a separate element (ITNDecay etc.)

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Deterrency

→ scenario → interventions → vectorDeterrent → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mass deployment

→ scenario → interventions → vectorDeterrent → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed mosquito deterrent deployment in the community

Cohort recruitment

→ scenario → interventions → cohort

<cohort
  [ name=string ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
| [ <timed ... /> ]
</cohort>

Documentation (element)

Recruitment of cohort as a pseudo-intervention.

Attributes

Name of intervention

name=string

Units: string

Name of intervention

Age-based cohort recruitment

→ scenario → interventions → cohort → continuous

<continuous>
IN THIS ORDER:
| ( <deploy ... /> )+
</continuous>

deploy

Documentation (element)

List of ages at which cohort recruitment takes place.

Mass cohort selection

→ scenario → interventions → cohort → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of times of mass cohort selection.

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Units: string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=int ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=int

Units: time-steps Min: 0

Default value: 0

If period is 0 (or effectively infinite), the last specified value remains indefinitely in effect, otherwise the times of all values specified must be less than the period, and values are repeated modulo period (timestep period+2 has same value as timestep 2, etc.).

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=int
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time

time=int

Units: time-steps Min: 0

Immune suppression

<immuneSuppression>
IN THIS ORDER:
| [ <timed ... /> ]
</immuneSuppression>

timed

Documentation (element)

Removes all exposure-related immunity gained over time by hosts without removing infections.

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

timed

→ scenario → interventions → immuneSuppression → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Insert R_0 case

<insertR_0Case>
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</insertR_0Case>

timedDeployment

Documentation (element)

timedDeployment

→ scenario → interventions → insertR_0Case → timedDeployment

<timedDeployment
    time=int
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Uninfect vectors

<uninfectVectors>
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</uninfectVectors>

timedDeployment

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

timedDeployment

→ scenario → interventions → uninfectVectors → timedDeployment

<timedDeployment
    time=int
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Simple larviciding intervention

→ scenario → interventions → larviciding

<larviciding
  [ name=string ]
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</larviciding>

Documentation (element)

Units: List of elements

Simple larviciding intervention description.

Attributes

Name of intervention

name=string

Units: string

Name of intervention

description

→ scenario → interventions → larviciding → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → larviciding → description → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
|   <duration ... /> 
|   <effectiveness ... /> 
</anopheles>

Documentation (type)

Units: None Min: 0 Max: 1

Descriptions of initial effectiveness of the effects of larviciding interventions.

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Duration

→ scenario → interventions → larviciding → description → anopheles → duration

<duration
    value=int
  />

Documentation (element)

Units: time-steps

Specifies how long the larviciding is effective

Attributes

Input parameter value

value=int

An integer value.

Effectiveness

→ scenario → interventions → larviciding → description → anopheles → effectiveness

<effectiveness
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

Give the proportion of larvae killed by the larviciding

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Larviciding deployment

→ scenario → interventions → larviciding → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed mosquito larviding deployment

deploy

→ scenario → interventions → larviciding → timed → deploy

<deploy
    time=int
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Units: List of elements

Description of health system.

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("forced" or "dynamic")
  [ scaledAnnualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Units: List of elements

Description of entomological data

Attributes

Entomology dataset

name=string

Units: string

Name of entomology data

Transmission model mode

mode=("forced" or "dynamic")

Override annual EIR

scaledAnnualEIR=double

Units: Infectious bites per adult per year

If set, the annual EIR (for all species of vector) is scaled to this level; can be omitted if not needed.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Units: List of elements

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Units: List of elements

Parameters of the transmission model.

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <seasonality ... /> 
|   <mosq ... /> 
| [ <lifeCycle ... /> ]
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial guess of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial guess of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Seasonality of transmission

→ scenario → entomology → vector → anopheles → seasonality

<seasonality
    input=("EIR")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <fourierSeries ... /> 
| |   <monthlyValues ... /> 
| |   <dailyValues ... /> 
</seasonality>

Documentation (element)

Some specifier for the seasonality of transmission and optionally the level of annual transmission.

Attributes

Seasonality input

input=("EIR")

Annual EIR

annualEIR=double

Units: inoculations per adult per annum Min: 0

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries

<fourierSeries
    EIRRotateAngle=double
  >
IN THIS ORDER:
| ( <coeffic ... /> )*
</fourierSeries>

coeffic

Documentation (element)

Units: Infectious bites per adult per day

Attributes

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Pair of Fourier coefficients

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries → coeffic

<coeffic
    a=double
    b=double
  />

Documentation (element)

Units: none

A pair of Fourier series coefficients. The first element specifies a1 and b1, the second a2 and b2, etc. Any number (from 0 up) of pairs may be given.

Attributes

a_n parameter of Fourier approximation to ln(EIR)

a=double

a_n parameter of Fourier approximation to ln(EIR) for some natural number n.

b_n parameter of Fourier approximation to ln(EIR)

b=double

b_n parameter of Fourier approximation to ln(EIR) for some natural number n.

List of montly values

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues

<monthlyValues
    smoothing=("none" or "fourier")
  >
IN THIS ORDER:
| ( <value ... /> ){12,12}
</monthlyValues>

value

Documentation (element)

Description of seasonality from monthly values. Multiple smoothing methods are possible (see smoothing attribute).

List should contain twelve entries: January to December.

Attributes

Smoothing function

smoothing=("none" or "fourier")

How the monthly values are converted into a daily sequence of values:

none: no smoothing (step function)
fourier: a Fourier series (with terms up to a2/b2) is fit to the sequence of monthly values and used to generate a smoothed list of daily values.

Monthly value

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Monthly value

List of daily values

→ scenario → entomology → vector → anopheles → seasonality → dailyValues

<dailyValues>
IN THIS ORDER:
| ( <value ... /> ){365,365}
</dailyValues>

value

Documentation (element)

Description of seasonality from daily values.

List should contain 365 entries: 1st January to 31st December.

Daily value

→ scenario → entomology → vector → anopheles → seasonality → dailyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Daily value

Mosquito feeding cycle parameters

→ scenario → entomology → vector → anopheles → mosq

<mosq
    minInfectedThreshold=double
  >
IN ANY ORDER:
|   <mosqRestDuration ... /> 
|   <extrinsicIncubationPeriod ... /> 
|   <mosqLaidEggsSameDayProportion ... /> 
|   <mosqSeekingDuration ... /> 
|   <mosqSurvivalFeedingCycleProbability ... /> 
|   <availabilityVariance ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <mosqProbOvipositing ... /> 
|   <mosqHumanBloodIndex ... /> 
</mosq>

Documentation (element)

Units: List of elements

Parameters describing the feeding cycle and human mosquito interaction of a single species of anopheles mosquito.

Attributes

Min infected threshold

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

Duration of the resting period of the vector (days)

→ scenario → entomology → vector → anopheles → mosq → mosqRestDuration

<mosqRestDuration
    value=int
  />

Documentation (element)

name:Duration of the resting period of the vector (days);

Attributes

Input parameter value

value=int

An integer value.

Extrinsic incubation period (days)

→ scenario → entomology → vector → anopheles → mosq → extrinsicIncubationPeriod

<extrinsicIncubationPeriod
    value=int
  />

Documentation (element)

name:Extrinsic incubation period (days)

Attributes

Input parameter value

value=int

An integer value.

Proportion of mosquitoes host seeking on same day as ovipositing

→ scenario → entomology → vector → anopheles → mosq → mosqLaidEggsSameDayProportion

<mosqLaidEggsSameDayProportion
    value=double
  />

Documentation (element)

Proportion of mosquitoes host seeking on same day as ovipositing

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Duration of the host-seeking period of the vector (days)

→ scenario → entomology → vector → anopheles → mosq → mosqSeekingDuration

<mosqSeekingDuration
    value=double
  />

Documentation (element)

Duration of the host-seeking period of the vector (days)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito survives the feeding cycle

→ scenario → entomology → vector → anopheles → mosq → mosqSurvivalFeedingCycleProbability

<mosqSurvivalFeedingCycleProbability
    value=double
  />

Documentation (element)

Probability that the mosquito survives the feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Variance in human availability rate

→ scenario → entomology → vector → anopheles → mosq → availabilityVariance

<availabilityVariance
    value=double
  />

Documentation (element)

Variance in availability rate of humans to mosquitoes. The mean rate is calculated based on other parameters.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito succesfully bites chosen host

→ scenario → entomology → vector → anopheles → mosq → mosqProbBiting

<mosqProbBiting
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito succesfully bites chosen host

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → mosq → mosqProbFindRestSite

<mosqProbFindRestSite
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito escapes host and finds a resting place after biting

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → mosq → mosqProbResting

<mosqProbResting
    mean=double
    variance=double
  />

Documentation (element)

Probability of mosquito successfully resting after finding a resting site

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of a mosquito successfully laying eggs given that it has rested

→ scenario → entomology → vector → anopheles → mosq → mosqProbOvipositing

<mosqProbOvipositing
    value=double
  />

Documentation (element)

Probability of a mosquito successfully laying eggs given that it has rested

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human blood index

→ scenario → entomology → vector → anopheles → mosq → mosqHumanBloodIndex

<mosqHumanBloodIndex
    value=double
  />

Documentation (element)

The proportion of resting mosquitoes which fed on human blood during the last feed.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mosquito life cycle parameters

→ scenario → entomology → vector → anopheles → lifeCycle

<lifeCycle
  [ estimatedLarvalResources=double ] DEFAULT VALUE 1e8
  >
IN ANY ORDER:
|   <eggStage ... /> 
|   <larvalStage ... /> 
|   <pupalStage ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</lifeCycle>

Documentation (element)

Parameters describing the life-cycle of this species of mosquito

Attributes

Estimate of larval resources

estimatedLarvalResources=double

Units: X

Default value: 1e8

An estimate of mean annual availability of resources to larvae. Used to set the resource usage fitting algorithm going; if this algorithm fails to fit the resource availability then tweaking this parameter may help. In other cases tweaking this parameter shouldn't be necessary. Default value is 10⁸ (1e8). Units are arbitrary but the same as those used by the resourceUsage parameter.

Egg stage

→ scenario → entomology → vector → anopheles → lifeCycle → eggStage

<eggStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the egg stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

larvalStage

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage

<larvalStage>
</larvalStage>

daily

Documentation (type)

Parameters for the larval stage of development

Documentation (base type)

Parameters associated with a mosquito development stage.

Daily development

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage → daily

<daily
    resourceUsage=double
    effectCompetition=double
  />

Documentation (element)

Attributes

Resource usage

resourceUsage=double

Units: X

Resource usage over larval stage of development. Units are arbitrary.

Effect competition

effectCompetition=double

Units: none

Effect of competition over resources on development.

Pupal stage

→ scenario → entomology → vector → anopheles → lifeCycle → pupalStage

<pupalStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the pupal stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → lifeCycle → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

nonHumanHosts

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN ANY ORDER:
|   <mosqRelativeEntoAvailability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
</nonHumanHosts>

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of non-human host (ξ_i)

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqRelativeEntoAvailability

<mosqRelativeEntoAvailability
    value=double
  />

Documentation (element)

Relative availability of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Name of this species of non human hosts (must match up with those described per anopheles section).

number

number=double

Population size of this non-human host.

Pharmacokinetics and pharmacodynamics

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
| ( <drug ... /> )+
</pharmacology>

drug

Documentation (element)

Units: List of elements

Drug model parameters

Library of drug parameters

→ scenario → pharmacology → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (element)

Sequence of drug descriptions forming a library of drug parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drug → PD

<PD>
IN THIS ORDER:
| ( <allele ... /> )+
</PD>

allele

PD parameters per allele

→ scenario → pharmacology → drug → PD → allele

<allele
    name=string
  >
IN THIS ORDER:
|   <initial_frequency ... /> 
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</allele>

Documentation (element)

PD parameters per allele, plus initial frequency of each allele.

Note: we assume a one-to-one correspondance of drugs to loci, hence each drug has an independent set of alleles here.

Attributes

name

name=string

Relative frequency

→ scenario → pharmacology → drug → PD → allele → initial_frequency

<initial_frequency>
    double
</initial_frequency>

Documentation (element)

Units: relative frequency Min: 0

Frequency, relative to the total frequency of all alleles for this drug/locus.

Maximal parasite killing rate

→ scenario → pharmacology → drug → PD → allele → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drug → PD → allele → IC50

<IC50>
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

Slope of effect curve

→ scenario → pharmacology → drug → PD → allele → slope

<slope>
    double
</slope>

Documentation (element)

Units: no units

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
|   <half_life ... /> 
|   <vol_dist ... /> 
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate (which is: ln(2) / half_life).

Volume of Distribution

→ scenario → pharmacology → drug → PK → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
|   <parameters ... /> 
</model>

Documentation (element)

Units: List of elements

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

Units: List of elements

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: include/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=int
  >
IN THIS ORDER:
| [ <NonMalariaFevers ... /> ]
</clinical>

NonMalariaFevers

Documentation (type)

Units: List of elements

Description of clinical parameters.

This is related to the health-system description, but contains data which can't be changed as part of an intervention and is not restricted to treatment.

Attributes

Follow-up period during which recurrence is treated as a failure

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
|   <prNeedTreatmentNMF ... /> 
|   <prNeedTreatmentMF ... /> 
</NonMalariaFevers>

Documentation (type)

Description of non-malaria fever incidence. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: none Min: 0 Max: 1

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: none Min: 0 Max: 1

Probability that a non-malaria fever needs treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: none Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

By age group data on availability of humans to mosquitoes relative to an adult.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ]
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Units: List of elements

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → model → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 30-3 documentation

Generated from: scenario_30_3.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    name=string
    wuID=int
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_30_3.xsd"
  >
IN ANY ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entomology ... /> 
| [ <pharmacology ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Name of intervention

Work unit identifier

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Description of demography

Attributes

Name of demography data

name=string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Years Min: 0 Max: 100

Maximum age of simulated humans in years

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

list of age groups included in demography

Documentation (type)

list of age groups included in demography or surveys

Attributes

Lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Units: Percentage Min: 0 Max: 100

Percentage of human population in age group

Upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ cohortOnly=boolean ]
  [ firstBoutOnly=boolean ]
  [ firstTreatmentOnly=boolean ]
  [ firstInfectionOnly=boolean ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Description of surveys

Attributes

Name of monitoring information

name=string

Name of monitoring data

Survey only cohort

cohortOnly=boolean

Time to first episode only

firstBoutOnly=boolean

Time to first treatment only

firstTreatmentOnly=boolean

Time to first infection only

firstInfectionOnly=boolean

continuous

→ scenario → monitoring → continuous

<continuous
    period=int
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Days between reports

period=int

Units: Days Min: 1 Max: unbounded

Number of timesteps between reports.

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Model options required

name=string

Options define different model structures. Option name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.

Indicator of whether option is required

value=boolean

Default value: true

Option value (true/false). Each option has a default value used if the option is not listed (usually false but sometimes true).

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

Units: list of elements

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/microlitre Min: 0

Limit above which a human's infection is reported as patent.

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

List of age groups included in demography or surveys

Documentation (type)

List of age groups included in surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Preventative interventions

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <vaccine ... /> ]
| [ <IPT ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <vectorDeterrent ... /> ]
| [ <cohort ... /> ]
| [ <importedInfections ... /> ]
| [ <immuneSuppression ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <larviciding ... /> ]
</interventions>

Documentation (element)

Attributes

Intervention

name=string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeHS>

timedDeployment

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeHS → timedDeployment

<timedDeployment
    time=int
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timedDeployment>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this replacement occurs, starting from 0, the first intervention-period time-step.

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</uncomplicated>

Documentation (type)

A set of decisions and a set of treatments.

decisions

→ scenario → interventions → MDA → description → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )*
</decisions>

decision

Documentation (type)

case (uncomplicated only): Returns "UC1" if there is no recent history of a malarial case, or "UC2" if there is.
result: Dependent on decision "test", this performs a parasite density test. Output is one of "none" (no test performed), "positive", "negative".

The following decisions must be described here:

test (uncomplicated only): Outputs must be "none", "microscopy" or "RDT" to describe which test the "result" decision uses.
treatment: Describes which treatment to use. Values aren't restricted but must match up with a treatment described in the corresponding "treatments" section.
hospitalisation (complicated only): none, immediate or delayed.

decision

→ scenario → interventions → MDA → description → decisions → decision

<decision
    name=string
    depends=string
    values=string
  >
    string
</decision>

Documentation (type)

A decision describes rules for choosing between a set of values.

Lexically, it can contain symbols matching "[_.a-zA-Z0-9]+", round brackets: (), braces: {} and colons. Whitespace is ignored except to separate symbols.

For each BRANCH_SET each BRANCH must result in the same DECISION. The DECISION must be one of the dependencies mentioned in "depends". This may be:

another decision, in which case the VALUE immediately following in brackets must correspond to one of its output values. The BRANCH_SET immediately containing this BRANCH must represent each output value of the same decision exactly once, and no parent BRANCH_SET may be for the same DECISION.
"p": this entry indicates a probabilistic decision. Where the value is a probability, the sum of all values for the BRANCH_SET must be 1 and the decision must be associated directly with OUTCOMEs (not sub-TREEs).
"age": this entry indicates an age-test. The VALUE must have the form "a-b", indicating that this branch will be taken for individuals aged such that a <= age < b, where a,b are non-negative real numbers or the special value "inf", and a <= b. All VALUEs in the BRANCH_SET must cover all possible (non-negative real) ages, with no overlap (hence, smallest a must be 0 and greatest b must be inf).

Semantically, each OUTCOME must be one of the values associated with this decision.

Attributes

Name of decision

name=string

The name of this decision. The name must match the regular expression "[_a-zA-Z0-9]+"; that is it can only contain letters, digits and _ characters (no spaces, punctuation, etc.).

Preceding decisions

depends=string

Outcome values

values=string

A comma-separated list of outcome values this decision may have. The name of each value must be of the same form as decision names (i.e. only contain letters, digits and _ characters).

treatments

→ scenario → interventions → MDA → description → treatments

<treatments>
IN THIS ORDER:
| ( <treatment ... /> )*
</treatments>

treatment

Documentation (type)

A list of drug treatment tables. Each should have a name corresponding to one of the "drug" decision's values.

treatment

→ scenario → interventions → MDA → description → treatments → treatment

<treatment
    name=string
  >
IN THIS ORDER:
|   <schedule ... /> 
| ( <modifier ... /> )*
</treatment>

Documentation (type)

A description of a base treatment schedule that includes modifiers to handle delays, quality variations, etc.

Attributes

Treatment administered

name=string

Units: string

Name corresponding to one of the drug decision's output values.

schedule

→ scenario → interventions → MDA → description → treatments → treatment → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

The base (unmodified)schedule of drugs administered for this treatment.

medicate

→ scenario → interventions → MDA → description → treatments → treatment → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  [ duration=double ]
  />

Attributes

drug

drug=string

Abbreviated name of drug compound

drug dose

mg=double

Units: mg

Quantity of drug compound

Time of administration

hour=double

Units: Hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

Duration of administration

duration=double

Units: Hours Min: 0

If this attribute is given, use IV administration instead of orally. Specifies the number of hours during which the dose is administered.

modifier

→ scenario → interventions → MDA → description → treatments → treatment → modifier

<modifier
    decision=string
  >
EXACTLY ONE OF:
| ( <multiplyQty ... /> )*
| ( <delay ... /> )*
| ( <selectTimeRange ... /> )*
</modifier>

Documentation (type)

Units: Choice of elements

A modifier for this treatment, according to the outputs of a decision.

Attributes

Decision

decision=string

Units: string

Specifies the decision that this modifier acts on.

Active ingredient multipliers

→ scenario → interventions → MDA → description → treatments → treatment → modifier → multiplyQty

<multiplyQty
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Units: Comma-separated list of values

Multiplies the quantity of active ingredients of drugs administered.

Attributes

Value of decision

value=string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: None

Does this affect the cost? If false, the effective drug usage (w.r.t. cost)is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

Active ingredient delays

→ scenario → interventions → MDA → description → treatments → treatment → modifier → delay

<delay
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Units: Comma-separated list of values

Delays administration of drugs listed in the base schedule by so many hours.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of delays (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0,6", drug A is administered as in the base schedule while drug B is administered 6 hours later than specified.

Attributes

Value of decision

value=string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: None

Does this affect the cost? If false, the effective drug usage (w.r.t. cost)is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

Active ingredient time-ranges

→ scenario → interventions → MDA → description → treatments → treatment → modifier → selectTimeRange

<selectTimeRange
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Selects which drug doses to administer according to time of administration (before times are modified by delays). Half-open interval: [x,y)

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of time-ranges (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. The time-ranges should be of the form x-y and are interpreted as the half-open interval [x,y); that is a drug listed with time t will only be administered if x <= t < y.

Attributes

Value of decision

value=string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: None

Does this affect the cost? If false, the effective drug usage (w.r.t. cost)is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</complicated>

Documentation (type)

A set of decisions and a set of treatments.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: Days Min: 0 Max: unbounded

Maximum number of timesteps (including first day of case) that an individual with an uncomplicated case of malaria will remember he/she was sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial or non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Fixed length of a complicated or severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: Days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
    name=string
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
</ImmediateOutcomes>

Documentation (type)

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Case Management model

name=string

Name of health system

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Description of drug regimen.

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Artemisinine combination therapy

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

QN

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0 Max: 1name:P(self-treat)

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Effectiveness of treatment for non-compliant patients

Probability that a patient with uncomplicated disease seeks official care immediately.

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease will self-treat.

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with uncomplicated disease will self-treat

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Case fatality rate for inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: Dimensionless

List of age-specific probabilities of sequelae in inpatients, during a severe bout of malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</changeEIR>

timedDeployment

Documentation (element)

Attributes

Name of intervention

name=string

Name of intervention

timedDeployment

→ scenario → interventions → changeEIR → timedDeployment

<timedDeployment
    eipDuration=int
    time=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timedDeployment>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Time

time=int

Units: time-steps Min: 0

Time-step at which this replacement occurs, starting from 0, the first intervention-period time-step.

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Mass drug administration

→ scenario → interventions → MDA

<MDA
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | [ <diagnostic ... /> ]
| | [ <description ... /> ]
| [ <timed ... /> ]
</MDA>

Documentation (element)

Description and deployment of MDA interventions (can also be configured as screen and treat or intermittent preventative treatment with 1-day time-step models).

Currently neither diagnostic nor description need be provided for 5-day timestep model; this may change in the future.

Attributes

Name of intervention

name=string

Name of intervention

Diagnostic (5-day)

→ scenario → interventions → MDA → diagnostic

<diagnostic>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterministic ... /> 
| |   <stochastic ... /> 
</diagnostic>

Documentation (element)

Description of diagnostic used by mass treatment option of five-day case management model — may be used to model MDA without diagnostic or MSAT.

Drugs are administered whenever the test outcome is positive.

Deterministic detection

→ scenario → interventions → MDA → diagnostic → deterministic

<deterministic
    minDensity=double
  />

Documentation (element)

Specify that an artificial deterministic test is used: drugs are administered if parasite density is at least the minimum given.

Attributes

Minimum detectible density

minDensity=double

Units: parasites/microlitre Min: 0

The minimum density at which parasites can be detected. If 0, the test outcome is always positive.

Non-deterministic detection

→ scenario → interventions → MDA → diagnostic → stochastic

<stochastic
    dens_50=double
    specificity=double
  />

Documentation (element)

An improved model of detection which is non-deterministic, including false positive results as well as false negatives.

Some parameterisations:

Microscopy sensitivity/specificity data in Africa; Source: expert opinion — Allan Schapira dens_50 = 20.0 specificity = .75

RDT sensitivity/specificity for Plasmodium falciparum in Africa Source: Murray et al (Clinical Microbiological Reviews, Jan. 2008) dens_50 = 50.0; specificity = .942;

Attributes

Density 50

dens_50=double

Units: parasites/microlitre Min: 0

The density at which the test outcome has a 50% chance of being positive.

Specificity

specificity=double

Units: Dimensionless Min: 0 Max: 1

The probability of a positive test outcome in the absense of parasites.

Diagnostic and treatment (1-day)

→ scenario → interventions → MDA → description

<description
  [ name=string ]
  >
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</description>

Documentation (element)

Documentation (base type)

A set of decisions and a set of treatments.

Attributes

Intervention

name=string

Name of set of interventions

Mass administration

→ scenario → interventions → MDA → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed deployments of mass-drug-administration.

deploy

→ scenario → interventions → MDA → timed → deploy

<deploy
    time=int
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: dimensionless Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Vaccines

→ scenario → interventions → vaccine

<vaccine
  [ name=string ]
  >
IN THIS ORDER:
| ( <description ... /> ){0,3}
| [ <continuous ... /> ]
| [ <timed ... /> ]
</vaccine>

Documentation (element)

Description and deployment of vaccine interventions.

Attributes

Name of intervention

name=string

Name of intervention

description

→ scenario → interventions → vaccine → description

<description
    vaccineType=("PEV" or "BSV" or "TBV")
  [ name=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</description>

Documentation (type)

List of vaccine descriptions

Attributes

Type of vaccine

vaccineType=("PEV" or "BSV" or "TBV")

Units: Code

Type of vaccine

Vaccine

name=string

Name of vaccine

Decay of effect

→ scenario → interventions → vaccine → description → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Specification of decay of efficacy. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Variance parameter for vaccine efficacy

→ scenario → interventions → vaccine → description → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial mean efficacy

→ scenario → interventions → vaccine → description → initialEfficacy

<initialEfficacy
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Age-based vaccination

→ scenario → interventions → vaccine → continuous

<continuous>
IN THIS ORDER:
| ( <deploy ... /> )+
</continuous>

deploy

Documentation (element)

List of ages at which vaccination takes place (through EPI, post-natal and school-based programmes, etc.).

deploy

→ scenario → interventions → vaccine → continuous → deploy

<deploy
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: dimensionless Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: dimensionless Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Mass vaccination

→ scenario → interventions → vaccine → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed mass vaccinations in the communitsy

deploy

→ scenario → interventions → vaccine → timed → deploy

<deploy
    time=int
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: dimensionless Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: dimensionless Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

Intermittent preventative treatment

→ scenario → interventions → IPT

<IPT
  [ name=string ]
  >
IN THIS ORDER:
|   <description ... /> 
| [ <continuous ... /> ]
| [ <timed ... /> ]
</IPT>

Documentation (element)

Description and deployment of IPT interventions.

Attributes

Name of intervention

name=string

Name of intervention

description

→ scenario → interventions → IPT → description

<description
    iptiEffect=int
  [ name=string ]
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</description>

infGenotype

Attributes

Description of ipti effect

iptiEffect=int

Description of ipti effect

IPT name

name=string

Name of IPT intervention

infGenotype

→ scenario → interventions → IPT → description → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

Age specific intervention

name=string

Name of age specific intervention

Frequency

freq=double

Frequency of parasite genotype

ACR

ACR=double

Units: dimensionless Min: 0, max:1.0

Adequate clinical response (proportion)

Prophylactic period

proph=int

Units: time-step

Prophylactic period

Tolerance period

tolPeriod=int

Units: time-step

Tolerance period

atten=double

Units: time-step

Tolerance period

Age-based IPT deployment

→ scenario → interventions → IPT → continuous

<continuous>
IN THIS ORDER:
| ( <deploy ... /> )+
</continuous>

deploy

Documentation (element)

List of ages at which IPTi/IPTc deployment takes place (through EPI, post-natal and school-based programmes, etc.).

Mass IPT administration

→ scenario → interventions → IPT → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed IPTi/IPTc distribution

Bed nets

→ scenario → interventions → ITN

<ITN
  [ name=string ]
  >
IN THIS ORDER:
|   <description ... /> 
| [ <continuous ... /> ]
| [ <timed ... /> ]
</ITN>

Documentation (element)

Description and deployment of bed-net interventions (ITNs, LLINs).

Attributes

Name of intervention

name=string

Name of intervention

description

→ scenario → interventions → ITN → description

<description>
IN THIS ORDER:
|   <usage ... /> 
|   <holeRate ... /> 
|   <ripRate ... /> 
|   <ripFactor ... /> 
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
|   <attritionOfNets ... /> 
| ( <anophelesParams ... /> )+
</description>

Proportion of time nets are used by humans

→ scenario → interventions → ITN → description → usage

<usage
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Usage of nets by humans, from 0 to 1.

At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagepropActing) + intervention_factorusage*propActing.

See also "propActing" (proportion of bits for which net acts).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Rate at which holes are made

→ scenario → interventions → ITN → description → holeRate

<holeRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Holes per annum Min: 0

The rate at which new holes are made in nets.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ log N( log(mean)-sigma²/2, sigma² ).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rate at which holes are enlarged

→ scenario → interventions → ITN → description → ripRate

<ripRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Rips per existing hole per annum Min: 0

Each existing hole has a probability of being ripped bigger according to a Poisson process with this rate as (only) parameter.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ log N( log(mean)-sigma²/2, sigma² ).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rip factor

→ scenario → interventions → ITN → description → ripFactor

<ripFactor
    value=double
  />

Documentation (element)

Units: none Min: 0

This factor expresses how important rips are in increasing the hole.

The hole index of a net is h + F×x where h and x are the total numbers of holes and rips respectively and F is the rip factor.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → ITN → description → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: mg/m² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → ITN → description → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of nets. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Attrition of nets

→ scenario → interventions → ITN → description → attritionOfNets

<attritionOfNets
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: dimensionless

Specifies the rate at which nets are disposed of over time. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → ITN → description → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterrency ... /> 
| |   <twoStageDeterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which net acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → ITN → description → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Relative attractiveness

→ scenario → interventions → ITN → description → anophelesParams → twoStageDeterrency

<twoStageDeterrency>
IN ANY ORDER:
|   <entering ... /> 
|   <attacking ... /> 
</twoStageDeterrency>

Documentation (element)

Units: dimensionless

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

This deterrency model multiplies human attractiveness by pEnt×pAtt divided by a base factor to normalise the output to 1 when there are no nets.

RA (entering)

→ scenario → interventions → ITN → description → anophelesParams → twoStageDeterrency → entering

<entering
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless

pEnt represents the relative probability of entering due to ITNs: pEnt = exp(log(P)×p) where P is the insecticide factor and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

RA (attacking)

→ scenario → interventions → ITN → description → anophelesParams → twoStageDeterrency → attacking

<attacking
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless

pAtt represents the relative probability of attacking a human after entering a house due to ITNs (i.e. of feeding/dying vs. flying off): pAtt = B + H×h + P×p + I×h×p where B is the base (without net) probability; H, P and I are the hole, insecticide and interaction factors respectively, h=exp(-holeIndex×holeScalingFactor) and p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Pre-prandial killing effect

→ scenario → interventions → ITN → description → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → ITN → description → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    holeFactor=double
    interactionFactor=double
    holeScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Age-based bed-net deployment

→ scenario → interventions → ITN → continuous

<continuous>
IN THIS ORDER:
| ( <deploy ... /> )+
</continuous>

deploy

Documentation (element)

List of ages at which bed-net deployment takes place (through EPI, post-natal and school-based programmes, etc.).

Mass ITN deployment

→ scenario → interventions → ITN → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed ITN deployment in the communitsy

Indoor residual spraying

→ scenario → interventions → IRS

<IRS
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <description ... /> 
| |   <description_v2 ... /> 
| [ <timed ... /> ]
</IRS>

Documentation (element)

Description and deployment of indoor insecticide interventions (IRS, durable wall linings, insecticide-treated-paint, etc.)

User must choose between using (the old model, where effect decays directly) and <description_v2> (the new model where effect decays indirectly based on decay of insecticide).

Attributes

Name of intervention

name=string

Name of intervention

description

→ scenario → interventions → IRS → description

<description>
IN THIS ORDER:
|   <decay ... /> 
| ( <anophelesParams ... /> )+
</description>

Documentation (type)

Description of effect for the simple model: IRS has three effects, whos strength is calculated as the product of an input parameter and "survival of effect", which is given by a decay function.

Decay

→ scenario → interventions → IRS → description → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Description of decay of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → IRS → description → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → IRS → description → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied this factor times survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → IRS → description → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → IRS → description → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Killing proportion is this factor multiplied by survival of effect.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

description_v2

→ scenario → interventions → IRS → description_v2

<description_v2>
IN THIS ORDER:
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
| ( <anophelesParams ... /> )+
</description_v2>

Documentation (type)

Description of effect for the more complex and probably more realistic Briet model: IRS has three effects, whos strength is calculated as a function of surviving insecticide content.

Initial insecticide

→ scenario → interventions → IRS → description_v2 → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: μg/cm² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → IRS → description_v2 → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of IRS. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Per-mosquito species parameters

→ scenario → interventions → IRS → description_v2 → anophelesParams

<anophelesParams
    mosquito=string
  [ propActive=double ] DEFAULT VALUE 1
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Proportion of bites for which IRS acts

propActive=double

Units: dimensionless Min: 0 Max: 1

Default value: 1

Relative attractiveness

→ scenario → interventions → IRS → description_v2 → anophelesParams → deterrency

<deterrency
    insecticideFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Effect of IRS on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attractiveness of the human is multiplied by exp(P×log(p)) where P is the insecticide factor, p=1−exp(-insecticideContent×insecticideScalingFactor).

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → IRS → description_v2 → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Post-prandial killing effect

→ scenario → interventions → IRS → description_v2 → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    insecticideFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+P ≤ 1 and P ≥ 0.

Attributes

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: dimensionless

Mass IRS deployment

→ scenario → interventions → IRS → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed IRS deployment in the communitsy

Vector deterrents

<vectorDeterrent
  [ name=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
| ( <anophelesParams ... /> )+
| [ <timed ... /> ]
</vectorDeterrent>

Documentation (element)

Description and deployment of interventions affecting only human-mosquito availability (deterrents).

Attributes

Name of intervention

name=string

Name of intervention

Decay

→ scenario → interventions → vectorDeterrent → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Description of decay of vector deterrent. Documentation: see DecayFunction type or https://github.com/SwissTPH/openmalaria/wiki/ModelDecayFunctions

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → vectorDeterrent → anophelesParams

<anophelesParams
    mosquito=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</anophelesParams>

deterrency

Documentation (type)

Units: dimensionless Min: 0 Max: 1

Descriptions of initial effectiveness of each of the effects of interventions. Decay is specified by a separate element (ITNDecay etc.)

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Deterrency

→ scenario → interventions → vectorDeterrent → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

One minus this multiplies the host's availability.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mass deployment

→ scenario → interventions → vectorDeterrent → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed mosquito deterrent deployment in the communitsy

Cohort recruitment

→ scenario → interventions → cohort

<cohort
  [ name=string ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
| [ <timed ... /> ]
</cohort>

Documentation (element)

Recruitment of cohort as a pseudo-intervention.

Attributes

Name of intervention

name=string

Name of intervention

Age-based cohort recruitment

→ scenario → interventions → cohort → continuous

<continuous>
IN THIS ORDER:
| ( <deploy ... /> )+
</continuous>

deploy

Documentation (element)

List of ages at which cohort recruitment takes place.

Mass cohort selection

→ scenario → interventions → cohort → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of times of mass cohort selection.

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=int ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=int

Units: time-steps Min: 0

Default value: 0

If period is 0 (or effectively infinite), the last specified value remains indefinitely in effect, otherwise the times of all values specified must be less than the period, and values are repeated modulo period (timestep period+2 has same value as timestep 2, etc.).

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=int
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time

time=int

Units: time-steps Min: 0

Immune suppression

<immuneSuppression>
IN THIS ORDER:
| [ <timed ... /> ]
</immuneSuppression>

timed

Documentation (element)

Removes all exposure-related immunitsy gained over time by hosts without removing infections.

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

timed

→ scenario → interventions → immuneSuppression → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Insert R_0 case

<insertR_0Case>
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</insertR_0Case>

timedDeployment

Documentation (element)

timedDeployment

→ scenario → interventions → insertR_0Case → timedDeployment

<timedDeployment
    time=int
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Uninfect vectors

<uninfectVectors>
IN THIS ORDER:
| ( <timedDeployment ... /> )*
</uninfectVectors>

timedDeployment

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

timedDeployment

→ scenario → interventions → uninfectVectors → timedDeployment

<timedDeployment
    time=int
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Simple larviciding intervention

→ scenario → interventions → larviciding

<larviciding
  [ name=string ]
  >
IN THIS ORDER:
|   <description ... /> 
| [ <timed ... /> ]
</larviciding>

Documentation (element)

Units: List of elements

Simple larviciding intervention description.

Attributes

Name of intervention

name=string

Name of intervention

description

→ scenario → interventions → larviciding → description

<description>
IN THIS ORDER:
| ( <anopheles ... /> )+
</description>

anopheles

anopheles

→ scenario → interventions → larviciding → description → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
|   <duration ... /> 
|   <effectiveness ... /> 
</anopheles>

Documentation (type)

Units: dimensionless Min: 0 Max: 1

Descriptions of initial effectiveness of the effects of larviciding interventions.

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Duration

→ scenario → interventions → larviciding → description → anopheles → duration

<duration
    value=int
  />

Documentation (element)

Units: time-steps

Specifies how long the larviciding is effective

Attributes

Input parameter value

value=int

An integer value.

Effectiveness

→ scenario → interventions → larviciding → description → anopheles → effectiveness

<effectiveness
    value=double
  />

Documentation (element)

Units: dimensionless Min: 0 Max: 1

Give the proportion of larvae killed by the larviciding

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Larviciding deployment

→ scenario → interventions → larviciding → timed

<timed>
IN THIS ORDER:
| ( <deploy ... /> )+
</timed>

deploy

Documentation (element)

List of timed mosquito larviding deployment

deploy

→ scenario → interventions → larviciding → timed → deploy

<deploy
    time=int
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Description of health system.

Documentation (type)

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("forced" or "dynamic")
  [ scaledAnnualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Description of entomological data

Attributes

Entomology dataset name

name=string

Name of entomology data

Transmission model mode

mode=("forced" or "dynamic")

Override annual EIR

scaledAnnualEIR=double

Units: Infectious bites per adult per year

If set, the annual EIR (for all species of vector) is scaled to this level; can be omitted if not needed.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony

eipDuration=int

Units: Days

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters of the transmission model

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <seasonality ... /> 
|   <mosq ... /> 
| [ <lifeCycle ... /> ]
| [ <simpleMPD ... /> ]
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial estimate of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial estimate of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial estimate of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Seasonality of transmission

→ scenario → entomology → vector → anopheles → seasonality

<seasonality
    input=("EIR")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <fourierSeries ... /> 
| |   <monthlyValues ... /> 
| |   <dailyValues ... /> 
</seasonality>

Documentation (element)

Specifies the seasonality of transmission and optionally the level of annual transmission.

Attributes

Seasonality input

input=("EIR")

Annual EIR

annualEIR=double

Units: Inoculations per adult per annum Min: 0

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries

<fourierSeries
    EIRRotateAngle=double
  >
IN THIS ORDER:
| ( <coeffic ... /> )*
</fourierSeries>

coeffic

Documentation (element)

Units: Infectious bites per adult per day

Attributes

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: Radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Pair of Fourier coefficients

→ scenario → entomology → vector → anopheles → seasonality → fourierSeries → coeffic

<coeffic
    a=double
    b=double
  />

Documentation (element)

A pair of Fourier series coefficients. The first element specifies a1 and b1, the second a2 and b2, etc. Any number (from 0 up) of pairs may be given.

Attributes

a_n parameter of Fourier approximation to ln(EIR)

a=double

a_n parameter of Fourier approximation to ln(EIR) for some natural number n.

b_n parameter of Fourier approximation to ln(EIR)

b=double

b_n parameter of Fourier approximation to ln(EIR) for some natural number n.

List of monthly values

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues

<monthlyValues
    smoothing=("none" or "fourier")
  >
IN THIS ORDER:
| ( <value ... /> ){12,12}
</monthlyValues>

value

Documentation (element)

Description of seasonality from monthly values. Multiple smoothing methods are possible (see smoothing attribute).

List should contain twelve entries: January to December.

Attributes

Smoothing function

smoothing=("none" or "fourier")

How the monthly values are converted into a daily sequence of values:

none: no smoothing (step function)
Fourier: a Fourier series (with terms up to a2/b2) is fit to the sequence of monthly values and used to generate a smoothed list of daily values.

Monthly value

→ scenario → entomology → vector → anopheles → seasonality → monthlyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Monthly value

List of daily values

→ scenario → entomology → vector → anopheles → seasonality → dailyValues

<dailyValues>
IN THIS ORDER:
| ( <value ... /> ){365,365}
</dailyValues>

value

Documentation (element)

Description of seasonality from daily values.

List should contain 365 entries: 1st January to 31st December.

Daily value

→ scenario → entomology → vector → anopheles → seasonality → dailyValues → value

<value>
    double
</value>

Documentation (element)

Units: (see "seasonality input" parameter)

Daily value

Mosquito feeding cycle parameters

→ scenario → entomology → vector → anopheles → mosq

<mosq
    minInfectedThreshold=double
  >
IN ANY ORDER:
|   <mosqRestDuration ... /> 
|   <extrinsicIncubationPeriod ... /> 
|   <mosqLaidEggsSameDayProportion ... /> 
|   <mosqSeekingDuration ... /> 
|   <mosqSurvivalFeedingCycleProbability ... /> 
|   <availabilityVariance ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
|   <mosqProbOvipositing ... /> 
|   <mosqHumanBloodIndex ... /> 
</mosq>

Documentation (element)

Parameters describing the feeding cycle and human mosquito interaction of a single species of anopheles mosquito.

Attributes

Mininum infected threshold for mosquitos

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

Duration of the resting period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqRestDuration

<mosqRestDuration
    value=int
  />

Documentation (element)

Units: Days

name:Duration of the resting period of the vector (days);

Attributes

Input parameter value

value=int

An integer value.

Extrinsic incubation period

→ scenario → entomology → vector → anopheles → mosq → extrinsicIncubationPeriod

<extrinsicIncubationPeriod
    value=int
  />

Documentation (element)

Units: Days

name:Extrinsic incubation period (days)

Attributes

Input parameter value

value=int

An integer value.

Proportion of mosquitoes host seeking on same day as ovipositing

→ scenario → entomology → vector → anopheles → mosq → mosqLaidEggsSameDayProportion

<mosqLaidEggsSameDayProportion
    value=double
  />

Documentation (element)

Units: Proportion

Proportion of mosquitoes host seeking on same day as ovipositing

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Duration of the host-seeking period of the vector

→ scenario → entomology → vector → anopheles → mosq → mosqSeekingDuration

<mosqSeekingDuration
    value=double
  />

Documentation (element)

Units: Days

Duration of the host-seeking period of the vector (days)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito survives the feeding cycle

→ scenario → entomology → vector → anopheles → mosq → mosqSurvivalFeedingCycleProbability

<mosqSurvivalFeedingCycleProbability
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito survives the feeding cycle

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Variance in human availability rate

→ scenario → entomology → vector → anopheles → mosq → availabilityVariance

<availabilityVariance
    value=double
  />

Documentation (element)

Variance in availability rate of humans to mosquitoes. The mean rate is calculated based on other parameters.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito succesfully bites chosen host

→ scenario → entomology → vector → anopheles → mosq → mosqProbBiting

<mosqProbBiting
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito succesfully bites chosen host

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → mosq → mosqProbFindRestSite

<mosqProbFindRestSite
    mean=double
    variance=double
  />

Documentation (element)

Probability that the mosquito escapes host and finds a resting place after biting

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → mosq → mosqProbResting

<mosqProbResting
    mean=double
    variance=double
  />

Documentation (element)

Probability of mosquito successfully resting after finding a resting site

Documentation (type)

Parameters of a normal distribution, provided as mean and variance.

Attributes

mean

mean=double

Units: none

The mean of the beta distribution (must be in the open range (0,1)).

variance

variance=double

Units: none

The standard deviation of variates.

Probability of a mosquito successfully laying eggs given that it has rested

→ scenario → entomology → vector → anopheles → mosq → mosqProbOvipositing

<mosqProbOvipositing
    value=double
  />

Documentation (element)

Probability of a mosquito successfully laying eggs given that it has rested

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Human blood index

→ scenario → entomology → vector → anopheles → mosq → mosqHumanBloodIndex

<mosqHumanBloodIndex
    value=double
  />

Documentation (element)

Units: Proportion

The proportion of resting mosquitoes which fed on human blood during the last feed.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mosquito life cycle parameters

→ scenario → entomology → vector → anopheles → lifeCycle

<lifeCycle
  [ estimatedLarvalResources=double ] DEFAULT VALUE 1e8
  >
IN ANY ORDER:
|   <eggStage ... /> 
|   <larvalStage ... /> 
|   <pupalStage ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</lifeCycle>

Documentation (element)

Parameters describing the life-cycle of this species of mosquito

Attributes

Estimate of larval resources

estimatedLarvalResources=double

Units: X

Default value: 1e8

Egg stage

→ scenario → entomology → vector → anopheles → lifeCycle → eggStage

<eggStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the egg stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

larvalStage

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage

<larvalStage>
</larvalStage>

daily

Documentation (type)

Parameters for the larval stage of development

Documentation (base type)

Parameters associated with a mosquito development stage.

Daily development

→ scenario → entomology → vector → anopheles → lifeCycle → larvalStage → daily

<daily
    resourceUsage=double
    effectCompetition=double
  />

Documentation (element)

Attributes

Resource usage

resourceUsage=double

Units: X

Resource usage during larval stage of development. Units are arbitrary.

Effect of competition

effectCompetition=double

Units: none

Effect of competition over resources on development.

Pupal stage

→ scenario → entomology → vector → anopheles → lifeCycle → pupalStage

<pupalStage
    duration=int
    survival=double
  />

Documentation (element)

Parameters for the pupal stage of development

Documentation (type)

Parameters associated with a mosquito development stage.

Attributes

Duration

duration=int

Units: Days

Duration of the stage (i.e. length of time mosquito is an egg/larva/pupa).

Probability of survival

survival=double

Units: Proportion

Probability that mosquito survives this size (probability of egg hatching, a larva becoming a pupa or a pupa emerging as an adult, at the start of that stage).

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → lifeCycle → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Simple Mosq-Pop-Dynamics parameters

→ scenario → entomology → vector → anopheles → simpleMPD

<simpleMPD>
IN ANY ORDER:
|   <developmentDuration ... /> 
|   <developmentSurvival ... /> 
|   <femaleEggsLaidByOviposit ... /> 
</simpleMPD>

Documentation (element)

Parameters describing the simple mosquito population dynamics model.

This is a simpler version of the life-cycle model, requiring less parameters and with much simpler initialisation.

Duration

→ scenario → entomology → vector → anopheles → simpleMPD → developmentDuration

<developmentDuration
    value=int
  />

Documentation (element)

Units: Days Min: 1

Duration from egg laying to emergence in days.

Attributes

Input parameter value

value=int

An integer value.

Probability of survival

→ scenario → entomology → vector → anopheles → simpleMPD → developmentSurvival

<developmentSurvival
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that mosquito survives from the egg being laid to emergence, given no resouce limitations (no density constraints).

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Eggs laid by ovipositing mosquito

→ scenario → entomology → vector → anopheles → simpleMPD → femaleEggsLaidByOviposit

<femaleEggsLaidByOviposit
    value=double
  />

Documentation (element)

Units: Eggs per feeding cycle

The total number of female eggs laid by a female mosquito at the conclusion to a feeding cycle.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Alternative (non-human) host paramters

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
  >
IN ANY ORDER:
|   <mosqRelativeEntoAvailability ... /> 
|   <mosqProbBiting ... /> 
|   <mosqProbFindRestSite ... /> 
|   <mosqProbResting ... /> 
</nonHumanHosts>

Documentation (element)

Min: 0

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of non-human host (ξ_i)

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqRelativeEntoAvailability

<mosqRelativeEntoAvailability
    value=double
  />

Documentation (element)

Units: Proportion

Relative availability of non-human hosts of type i to other non-human hosts; the sum of this across all non-human hosts must be 1.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully biting host

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbBiting

<mosqProbBiting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully biting host

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that the mosquito escapes host and finds a resting place after biting

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbFindRestSite

<mosqProbFindRestSite
    value=double
  />

Documentation (element)

Units: Proportion

Probability that the mosquito escapes host and finds a resting place after biting

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability of mosquito successfully resting after finding a resting site

→ scenario → entomology → vector → anopheles → nonHumanHosts → mosqProbResting

<mosqProbResting
    value=double
  />

Documentation (element)

Units: Proportion

Probability of mosquito successfully resting after finding a resting site

Attributes

Input parameter value

value=double

A double-precision floating-point value.

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Name of this species of non human hosts (must match up with those described per anopheles section).

Population size of alternative host species

number=double

Units: Number

Population size of this non-human host.

Pharmacokinetics and pharmacodynamics

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
| ( <drug ... /> )+
</pharmacology>

drug

Documentation (element)

Drug model parameters

Library of drug parameters

→ scenario → pharmacology → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (element)

Sequence of drug descriptions forming a library of drug parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drug → PD

<PD>
IN THIS ORDER:
| ( <allele ... /> )+
</PD>

allele

PD parameters per allele

→ scenario → pharmacology → drug → PD → allele

<allele
    name=string
  >
IN THIS ORDER:
|   <initial_frequency ... /> 
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</allele>

Documentation (element)

PD parameters per allele, plus initial frequency of each allele.

Note: we assume a one-to-one correspondance of drugs to loci, hence each drug has an independent set of alleles here.

Attributes

name

name=string

Relative frequency

→ scenario → pharmacology → drug → PD → allele → initial_frequency

<initial_frequency>
    double
</initial_frequency>

Documentation (element)

Units: dimensionless Min: 0

Frequency, relative to the total frequency of all alleles for this drug/locus.

Maximal parasite killing rate

→ scenario → pharmacology → drug → PD → allele → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drug → PD → allele → IC50

<IC50>
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

Slope of effect curve

→ scenario → pharmacology → drug → PD → allele → slope

<slope>
    double
</slope>

Documentation (element)

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
|   <half_life ... /> 
|   <vol_dist ... /> 
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate (which is: ln(2) / half_life).

Volume of Distribution

→ scenario → pharmacology → drug → PK → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: include/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=int
  >
IN THIS ORDER:
| [ <NonMalariaFevers ... /> ]
</clinical>

NonMalariaFevers

Documentation (type)

Attributes

Follow-up period during which recurrence is treated as a failure

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
|   <prNeedTreatmentNMF ... /> 
|   <prNeedTreatmentMF ... /> 
</NonMalariaFevers>

Documentation (type)

Description of the incidence of non-malaria fever. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: Dimensionless Min: 0.0 Max: 1.0

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a non-malarial fever requires treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: Dimensionless Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

Availability of humans to mosquitoes relative to an adult, categorized by age group

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ]
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → model → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 29 documentation

Generated from: scenario_29.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    name=string
    wuID=int
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_29.xsd"
  >
IN ANY ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entomology ... /> 
| [ <pharmacology ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Units: string

Name of intervention

Work unit identifier

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Attributes

Name of demography data

name=string

Units: string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: years Min: 0 Max: 100

Maximum age of simulated humans in years.

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Percentage of human population in age group

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ cohortOnly=boolean ]
  [ firstBoutOnly=boolean ]
  [ firstTreatmentOnly=boolean ]
  [ firstInfectionOnly=boolean ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Attributes

Name of monitoring information

name=string

Units: string

Name of monitoring data

Survey only cohort

cohortOnly=boolean

Time to first episode only

firstBoutOnly=boolean

Time to first treatment only

firstTreatmentOnly=boolean

Time to first infection only

firstInfectionOnly=boolean

continuous

→ scenario → monitoring → continuous

<continuous
    period=int
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Days between reports

period=int

Units: Days Min: 1 Max: unbounded

Number of timesteps between reports.

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Model options required

name=string

Options define different model structures. Option name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.

Indicator of whether option is required

value=boolean

Default value: true

Option value (true/false). Each option has a default value used if the option is not listed (usually false but sometimes true).

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/microlitre Min: 0

Limit above which a human's infection is reported as patent.

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time; 0 means just before start of main sim and is a valid survey-point. Reported data is either from a point-time survey (immediate data) or is collected over the previous year (data from previous timesteps-per-year period). Simulation will end immediately after last survey is taken.

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Preventative interventions

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <vaccine ... /> ]
| [ <IPT ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <vectorDeterrent ... /> ]
| [ <cohort ... /> ]
| [ <importedInfections ... /> ]
| [ <immuneSuppression ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <larviciding ... /> ]
</interventions>

Documentation (element)

Units: List of elements

Attributes

Intervention

name=string

Units: string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timed ... /> )*
</changeHS>

timed

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Units: string

Name of intervention

timed

→ scenario → interventions → changeHS → timed

<timed
    time=int
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timed>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this replacement occurs, starting from 0, the first intervention-period time-step.

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</uncomplicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

decisions

→ scenario → interventions → MDA → description → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )*
</decisions>

decision

Documentation (type)

case (uncomplicated only): Returns "UC1" if there is no recent history of a malarial case, or "UC2" if there is.
result: Dependent on decision "test", this performs a parasite density test. Output is one of "none" (no test performed), "positive", "negative".

The following decisions must be described here:

test (uncomplicated only): Outputs must be "none", "microscopy" or "RDT" to describe which test the "result" decision uses.
treatment: Describes which treatment to use. Values aren't restricted but must match up with a treatment described in the corresponding "treatments" section.
hospitalisation (complicated only): none, immediate or delayed.

decision

→ scenario → interventions → MDA → description → decisions → decision

<decision
    name=string
    depends=string
    values=string
  >
    string
</decision>

Documentation (type)

A decision describes how to choose between a set of values.

Lexically, it can contain symbols matching "[_.a-zA-Z0-9]+", round brackets: (), braces: {} and colons. Whitespace is ignored except to separate symbols.

For each BRANCH_SET each BRANCH must have the same DECISION. This DECISION must be one of the dependencies mentioned in "depends". This may be:

another decision, in which case the VALUE immediately following in brackets must correspond to one of its output values. The BRANCH_SET immediately containing this BRANCH must represent each output value of the same decision exactly once, and no parent BRANCH_SET may be for the same DECISION.
"p": this indicates a probabilistic decision. In this case the value is a probability, the sum of all values for the BRANCH_SET must be 1 and the decision must be associated directly with OUTCOMEs (not sub-TREEs).
"age": this indicates an age-test. The VALUE must have the form "a-b", indicating that this branch will be taken for individuals aged such that a <= age < b, where a,b are non-negative real numbers or the special value "inf", and a <= b. All VALUEs in the BRANCH_SET must cover all possible (non-negative real) ages, with no overlap (hence, smallest a must be 0 and greatest b must be inf).

Semantically, each OUTCOME must be one of the values associated with this decision.

Attributes

Name of decision

name=string

The name of this decision. The name must match the regular expression "[_a-zA-Z0-9]+"; that is it can only contain letters, digits and _ characters (no spaces, punctuation, etc.).

Preceding decisions

depends=string

Outcome values

values=string

A comma-separated list of outcome values this decision may have. The name of each value must be of the same form as decision names (i.e. only contain letters, digits and _ characters).

treatments

→ scenario → interventions → MDA → description → treatments

<treatments>
IN THIS ORDER:
| ( <treatment ... /> )*
</treatments>

treatment

Documentation (type)

Units: string

A list of drug treatment tables. Each should have a name corresponding to one of the "drug" decision's values.

treatment

→ scenario → interventions → MDA → description → treatments → treatment

<treatment
    name=string
  >
IN THIS ORDER:
|   <schedule ... /> 
| ( <modifier ... /> )*
</treatment>

Documentation (type)

Units: List of elements

A description of a base treatment schedule along with modifiers to handle delays, quality variations, etc.

Attributes

Treatment administered

name=string

Units: string

Name corresponding to one of the drug decision's output values.

schedule

→ scenario → interventions → MDA → description → treatments → treatment → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

Units: List of elements

The base (unmodified) schedule of drugs administered for this treatment.

medicate

→ scenario → interventions → MDA → description → treatments → treatment → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  [ duration=double ]
  />

Attributes

drug

drug=string

Units: string

Abbreviated name of drug compound

drug dose

mg=double

Units: mg

Quantity of drug compound

time of administration

hour=double

Units: hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

duration of administration

duration=double

Units: hours Min: 0

If this attribute is given, use IV administration instead of orally. Specifies the number of hours over which the dose is administered.

modifier

→ scenario → interventions → MDA → description → treatments → treatment → modifier

<modifier
    decision=string
  >
EXACTLY ONE OF:
| ( <multiplyQty ... /> )*
| ( <delay ... /> )*
| ( <selectTimeRange ... /> )*
</modifier>

Documentation (type)

Units: Choice of elements

A modifier for this treatment, according to the outputs of a decision.

Attributes

decision

decision=string

Units: string

Specifies the decision that this modifier acts on.

Active ingredient multipliers

→ scenario → interventions → MDA → description → treatments → treatment → modifier → multiplyQty

<multiplyQty
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Units: Comma separated list of values

Multiplies the quantity of active ingredients of drugs administered.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of multipliers for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0.5,1" the quantity of drug A is halved while that of B is unchanged.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

Active ingredient delays

→ scenario → interventions → MDA → description → treatments → treatment → modifier → delay

<delay
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Units: Comma separated list of values

Delays administration of drugs listed in the base schedule by so many hours.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of delays (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0,6", drug A is administered as in the base schedule while drug B is administered 6 hours later than specified.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

Active ingredient time-ranges

→ scenario → interventions → MDA → description → treatments → treatment → modifier → selectTimeRange

<selectTimeRange
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Units: Comma separated list of values

Selects which drug doses to administer according to time of administration (before times are modified by delays). Half-open interval: [x,y)

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of time-ranges (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. The time-ranges should be of the form x-y and are interpreted as the half-open interval [x,y); that is a drug listed with time t will only be administered if x <= t < y.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</complicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: days Min: 0 Max: unbounded

Maximum number of timesteps (including first of case) an individual will remember they are sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial/non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of a complicated/severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: none Min: 0 Max: 1

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: none Min: 0 Max: 1

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: none Min: 0 Max: 1

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: none Min: 0 Max: 1

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
    name=string
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
</ImmediateOutcomes>

Documentation (type)

Units: List of elements

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Case Management model

name=string

Units: string

Name of health system

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

ACT

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

QN

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

Probability that a patient with uncomplicated disease seeks official care immediately

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease self-treats

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Case fatality rate in inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: List of elements

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients, during a severe bout.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timed ... /> )*
</changeEIR>

timed

Documentation (element)

Attributes

Name of intervention

name=string

Units: string

Name of intervention

timed

→ scenario → interventions → changeEIR → timed

<timed
    eipDuration=int
    time=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timed>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

Time

time=int

Units: time-steps Min: 0

Time-step at which this replacement occurs, starting from 0, the first intervention-period time-step.

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Mass drug administration

→ scenario → interventions → MDA

<MDA
  [ name=string ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | [ <diagnostic ... /> ]
| | [ <description ... /> ]
| ( <timed ... /> )*
</MDA>

Documentation (element)

Description and deployment of MDA interventions (can also be configured as screen and treat or intermittent preventative treatment with 1-day time-step models).

Currently neither diagnostic nor description need be provided for 5-day timestep model; this may change in the future.

Attributes

Name of intervention

name=string

Units: string

Name of intervention

Diagnostic (5-day)

→ scenario → interventions → MDA → diagnostic

<diagnostic>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <deterministic ... /> 
| |   <stochastic ... /> 
</diagnostic>

Documentation (element)

Description of diagnostic used by mass treatment option of five-day case management model — may be used to model MDA without diagnostic or MSAT.

Drugs are administered whenever the test outcome is positive.

Deterministic detection

→ scenario → interventions → MDA → diagnostic → deterministic

<deterministic
    minDensity=double
  />

Documentation (element)

Specify that an artificial deterministic test is used: drugs are administered if parasite density is at least the minimum given.

Attributes

Minimum detectible density

minDensity=double

Units: parasites/microlitre Min: 0

The minimum density at which parasites can be detected. If 0, the test outcome is always positive.

Non-deterministic detection

→ scenario → interventions → MDA → diagnostic → stochastic

<stochastic
    dens_50=double
    specificity=double
  />

Documentation (element)

An improved model of detection which is non-deterministic, including false positive results as well as false negatives.

Some parameterisations:

Microscopy sensitivity/specificity data in Africa; Source: expert opinion — Allan Schapira dens_50 = 20.0 specificity = .75

RDT sensitivity/specificity for Plasmodium falciparum in Africa Source: Murray et al (Clinical Microbiological Reviews, Jan. 2008) dens_50 = 50.0; specificity = .942;

Attributes

Density 50

dens_50=double

Units: parasites/microlitre Min: 0

The density at which the test outcome has a 50% chance of being positive.

Specificity

specificity=double

Units: none Min: 0 Max: 1

The probability of a positive test outcome in the absense of parasites.

Diagnostic and treatment (1-day)

→ scenario → interventions → MDA → description

<description
  [ name=string ]
  >
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</description>

Documentation (element)

Documentation (base type)

Units: List of elements

A set of decisions and a set of treatments.

Attributes

Intervention

name=string

Units: string

Name of set of interventions

Mass administration

→ scenario → interventions → MDA → timed

<timed
    time=int
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  />

Documentation (element)

List of timed deployments of mass-drug-administration.

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Vaccines

→ scenario → interventions → vaccine

<vaccine
  [ name=string ]
  >
IN THIS ORDER:
| ( <description ... /> ){0,3}
| ( <continuous ... /> )*
| ( <timed ... /> )*
</vaccine>

Documentation (element)

Description and deployment of vaccine interventions.

Attributes

Name of intervention

name=string

Units: string

Name of intervention

description

→ scenario → interventions → vaccine → description

<description
    vaccineType=("PEV" or "BSV" or "TBV")
  [ name=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</description>

Documentation (type)

List of vaccine descriptions

Attributes

Type of vaccine

vaccineType=("PEV" or "BSV" or "TBV")

Units: Code

Type of vaccine

Vaccine

name=string

Units: string

Name of vaccine

Decay of effect

→ scenario → interventions → vaccine → description → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Specification of decay of efficacy

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Variance parameter for vaccine efficacy

→ scenario → interventions → vaccine → description → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

initialEfficacy

→ scenario → interventions → vaccine → description → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Age-based vaccination

→ scenario → interventions → vaccine → continuous

<continuous
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

List of ages at which vaccination takes place (through EPI, post-natal and school-based programmes, etc.).

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Mass vaccination

→ scenario → interventions → vaccine → timed

<timed
    time=int
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

List of timed mass vaccinations in the community

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

Intermittent preventative treatment

→ scenario → interventions → IPT

<IPT
  [ name=string ]
  >
IN THIS ORDER:
|   <description ... /> 
| ( <continuous ... /> )*
| ( <timed ... /> )*
</IPT>

Documentation (element)

Description and deployment of IPT interventions.

Attributes

Name of intervention

name=string

Units: string

Name of intervention

description

→ scenario → interventions → IPT → description

<description
    iptiEffect=int
  [ name=string ]
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</description>

infGenotype

Attributes

Description of ipti effect

iptiEffect=int

Units: List of Elementes

Description of ipti effect

IPT name

name=string

Units: string

Name of IPT intervention

infGenotype

→ scenario → interventions → IPT → description → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

Age specific intervention

name=string

Units: string

Name of age specific intervention

Frequency

freq=double

Frequency of parasite genotype

ACR

ACR=double

Adequate clinical response (proportion)

Prophylactic period

proph=int

Prophylactic period

Tolerance period

tolPeriod=int

Tolerance period

atten=double

Tolerance period

Age-based IPT deployment

→ scenario → interventions → IPT → continuous

<continuous
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

List of ages at which IPTi/IPTc deployment takes place (through EPI, post-natal and school-based programmes, etc.).

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Mass IPT administration

→ scenario → interventions → IPT → timed

<timed
    time=int
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

List of timed IPTi/IPTc distribution

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

Bed nets

→ scenario → interventions → ITN

<ITN
  [ name=string ]
  >
IN THIS ORDER:
|   <description ... /> 
| ( <continuous ... /> )*
| ( <timed ... /> )*
</ITN>

Documentation (element)

Description and deployment of bed-net interventions (ITNs, LLINs).

Attributes

Name of intervention

name=string

Units: string

Name of intervention

description

→ scenario → interventions → ITN → description

<description>
IN THIS ORDER:
|   <usage ... /> 
|   <holeRate ... /> 
|   <ripRate ... /> 
|   <ripFactor ... /> 
|   <initialInsecticide ... /> 
|   <insecticideDecay ... /> 
|   <attritionOfNets ... /> 
| ( <anophelesParams ... /> )+
</description>

Usage level of nets by humans

→ scenario → interventions → ITN → description → usage

<usage
    value=double
  />

Documentation (element)

Units: none Min: 0 Max: 0

The proportion of the time during the night that humans use nets while indoors (fixed parameter).

At the moment this is constant across humans and deterministic: relative attractiveness and survival factors are base*(1-usagem) + intervention_factorusage*m where m is the proportion of time mosquitoes bite while humans are indoors.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Rate at which holes are made

→ scenario → interventions → ITN → description → holeRate

<holeRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Holes per annum Min: 0

The rate at which new holes are made in nets.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ log N( log(mean)-sigma²/2, sigma² ).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rate at which holes are enlarged

→ scenario → interventions → ITN → description → ripRate

<ripRate
    mean=double
    sigma=double
  />

Documentation (element)

Units: Rips per existing hole per annum Min: 0

Each existing hole has a probability of being ripped bigger according to a Poisson process with this rate as (only) parameter.

Documentation (type)

Parameters of a log-normal distribution.

Variates are sampled as: X ~ log N( log(mean)-sigma²/2, sigma² ).

Attributes

mean

mean=double

Units: (same as base units)

The mean of the lognormal distribution.

sigma

sigma=double

Sigma parameter of the lognormal distribution; sigma squared is the variance of the log of samples.

Rip factor

→ scenario → interventions → ITN → description → ripFactor

<ripFactor
    value=double
  />

Documentation (element)

Units: none Min: 0

This factor expresses how important rips are in increasing the hole.

The hole index of a net is h + F×x where h and x are the total numbers of holes and rips respectively and F is the rip factor.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Initial insecticide

→ scenario → interventions → ITN → description → initialInsecticide

<initialInsecticide
    mu=double
    sigma=double
  />

Documentation (element)

Units: mg/m² Min: 0

Documentation (type)

Parameters of a normal distribution.

Variates are sampled as: X ~ N( mu, sigma² ).

Attributes

mu

mu=double

Units: (same as base units)

The mean of the normal distribution.

sigma

sigma=double

Units: (same as base units)

The standard deviation of variates.

Decay of insecticide

→ scenario → interventions → ITN → description → insecticideDecay

<insecticideDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Decay curve for insecticide content of nets.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

Attrition of nets

→ scenario → interventions → ITN → description → attritionOfNets

<attritionOfNets
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Units: none

Specifies the rate at which nets are disposed of over time.

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → ITN → description → anophelesParams

<anophelesParams
    mosquito=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anophelesParams>

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Relative attractiveness

→ scenario → interventions → ITN → description → anophelesParams → deterrency

<deterrency
    holeFactor=double
    insecticideFactor=double
    interactionFactor=double
    holeScalingFactor=double
    insecticideScalingFactor=double
  />

Documentation (element)

Units: none Min: 0 Max: 1

Effect of net on attractiveness of humans to mosquitoes relative to an unprotected adult human. Parameterisations should take into account that mosquitoes do not always bite indoors.

Attributes

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Pre-prandial killing effect

→ scenario → interventions → ITN → description → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    holeFactor=double
    insecticideFactor=double
    interactionFactor=double
    holeScalingFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: none Min: 0 Max: 1

Effect of net on survival mosquitoes as they seek to bite a human after choosing that human relative to the same person not sleeping under a net. Parameterisations should take into account that mosquitoes do not always bite indoors.

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: none

Post-prandial killing effect

→ scenario → interventions → ITN → description → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    holeFactor=double
    insecticideFactor=double
    interactionFactor=double
    holeScalingFactor=double
    insecticideScalingFactor=double
    baseFactor=double
  />

Documentation (element)

Units: none Min: 0 Max: 1

Effect of net on survival mosquitoes as they seek to escape from a human host after a blood meal, relative to the same person not sleeping under a net. Parameterisations should take into account that mosquitoes do not always bite indoors.

Survival of mosquitoes is adjusted via multiplication by (1−K) / (1−B). To keep this in the range [0,1], we require that B+H ≤ 1, B+P ≤ 1, B+H+P+I ≤ 1, H ≥ 0, P ≥ 0 and H+P+I ≥ 0.

Attributes

Hole factor

holeFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Insecticide factor

insecticideFactor=double

Units: none Max: 1

Value expected to be at least 0. Negative values are not necessarily invalid, but allow nets to increase transmission.

Interaction factor

interactionFactor=double

Units: none Max: 1

holeFactor + insecticideFactor + interactionFactor must not be greater than 1, and is expected to be at least 0. A negative value is not necessarily invalid, but allows nets to increase transmission.

Hole scaling factor

holeScalingFactor=double

Units: none Min: 0

Insecticide scaling factor

insecticideScalingFactor=double

Units: none Min: 0

Probability of mosquito death without intervention

baseFactor=double

Units: none

Age-based bed-net deployment

→ scenario → interventions → ITN → continuous

<continuous
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

List of ages at which bed-net deployment takes place (through EPI, post-natal and school-based programmes, etc.).

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Mass ITN deployment

→ scenario → interventions → ITN → timed

<timed
    time=int
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

List of timed ITN deployment in the community

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

Indoor residual spraying

→ scenario → interventions → IRS

<IRS
  [ name=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
| ( <anophelesParams ... /> )+
| ( <timed ... /> )*
</IRS>

Documentation (element)

Description and deployment of indoor insecticide interventions (IRS, durable wall linings, insecticide-treated-paint, etc.)

Attributes

Name of intervention

name=string

Units: string

Name of intervention

decay

→ scenario → interventions → IRS → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → IRS → anophelesParams

<anophelesParams>
IN THIS ORDER:
|   <deterrency ... /> 
</anophelesParams>

Documentation (base type)

Units: None Min: 0 Max: 1

Descriptions of initial effectiveness of each of the effects of interventions. Decay is specified by a separate element (ITNDecay etc.)

Deterrency

→ scenario → interventions → IRS → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

killing effect

→ scenario → interventions → IRS → anophelesParams → killingEffect

<killingEffect
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mass IRS deployment

→ scenario → interventions → IRS → timed

<timed
    time=int
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

List of timed IRS deployment in the community

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

Vector deterrents

<vectorDeterrent
  [ name=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
| ( <anophelesParams ... /> )+
| ( <timed ... /> )*
</vectorDeterrent>

Documentation (element)

Description and deployment of interventions affecting only human-mosquito availability (deterrents).

Attributes

Name of intervention

name=string

Units: string

Name of intervention

decay

→ scenario → interventions → vectorDeterrent → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ mu=double ] DEFAULT VALUE 0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

μ (mu)

mu=double

Min: 0

Default value: 0

σ (sigma)

sigma=double

Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → vectorDeterrent → anophelesParams

<anophelesParams
    mosquito=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</anophelesParams>

deterrency

Documentation (type)

Units: None Min: 0 Max: 1

Descriptions of initial effectiveness of each of the effects of interventions. Decay is specified by a separate element (ITNDecay etc.)

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Mass deployment

→ scenario → interventions → vectorDeterrent → timed

<timed
    time=int
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

List of timed mosquito deterrent deployment in the community

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

Cohort recruitment

→ scenario → interventions → cohort

<cohort
  [ name=string ]
  >
IN THIS ORDER:
| ( <continuous ... /> )*
| ( <timed ... /> )*
</cohort>

Documentation (element)

Recruitment of cohort as a pseudo-intervention.

Attributes

Name of intervention

name=string

Units: string

Name of intervention

Age-based cohort recruitment

→ scenario → interventions → cohort → continuous

<continuous
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

List of ages at which cohort recruitment takes place.

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Mass cohort selection

→ scenario → interventions → cohort → timed

<timed
    time=int
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

List of times of mass cohort selection.

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Units: string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=int ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=int

Units: time-steps Min: 0

Default value: 0

If period is 0 (or effectively infinite), the last specified value remains indefinitely in effect, otherwise the times of all values specified must be less than the period, and values are repeated modulo period (timestep period+2 has same value as timestep 2, etc.).

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=int
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time

time=int

Units: time-steps Min: 0

Immune suppression

<immuneSuppression>
IN THIS ORDER:
| ( <timed ... /> )*
</immuneSuppression>

timed

Documentation (element)

Removes all exposure-related immunity gained over time by hosts without removing infections.

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

timed

→ scenario → interventions → immuneSuppression → timed

<timed
    time=int
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Insert R_0 case

<insertR_0Case>
IN THIS ORDER:
| ( <timed ... /> )*
</insertR_0Case>

timed

Documentation (element)

timed

→ scenario → interventions → insertR_0Case → timed

<timed
    time=int
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Uninfect vectors

<uninfectVectors>
IN THIS ORDER:
| ( <timed ... /> )*
</uninfectVectors>

timed

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

timed

→ scenario → interventions → uninfectVectors → timed

<timed
    time=int
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Simple larviciding intervention

→ scenario → interventions → larviciding

<larviciding
  [ name=string ]
  >
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

anopheles

Documentation (element)

Units: List of elements

Simple larviciding intervention description.

Attributes

Name of intervention

name=string

Units: string

Name of intervention

anopheles

→ scenario → interventions → larviciding → anopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

Mosquito to be larvicided

mosquito=string

Mosquito to be larvicided

Proportionate reduction in emergence

effectiveness=double

Units: none Min: 0 Max: 1

Proportional reduction in emergence rate

Duration of activity

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Units: List of elements

Description of health system.

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("2" or "4")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Units: List of elements

Description of entomological data

Attributes

Entomology dataset

name=string

Units: string

Name of entomology data

Transmission simulation mode

mode=("2" or "4")

Units: Code

Transmission simulation mode -- enter dynamic mode (4) or forced mode (2) at start of intervention period. Mode 3 (transient EIR from data provided as intervention) is set when intervention data is applied, and is no longer a valid value to specify here.

Override annual EIR

annualEIR=double

Units: Infectious bites per adult per year

If set, overrides the annual EIR by scaling it to this level. If ommitted, EIR levels are as specified elsewhere.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Units: List of elements

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Units: List of elements

Parameters of the transmission model.

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EIR ... /> 
| |   <monthlyEIR ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial guess of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial guess of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → EIR

<EIR
    a0=double
    a1=double
    b1=double
    a2=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Infectious bites per adult per day

Description of target entomological inoculation rate as a Fourier series. This is used to estimate a suitible vector emergence rate. The annual (target) EIR is thus the exponent of the fourier series with these parameters, with period scaled to 365 days.

Attributes

a0 parameter of Fourier approximation to ln(EIR)

a0=double

a0 parameter of Fourier approximation to ln(EIR)

a1 parameter of Fourier approximation to ln(EIR)

a1=double

a1 parameter of Fourier approximation to ln(EIR)

b1 parameter of Fourier approximation to ln(EIR)

b1=double

b1 parameter of Fourier approximation to ln(EIR)

a2 parameter of Fourier approximation to ln(EIR)

a2=double

a2 parameter of Fourier approximation to ln(EIR)

b2 parameter of Fourier approximation to ln(EIR)

b2=double

b2 parameter of Fourier approximation to ln(EIR)

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Monthly values for pre-intervention EIR

→ scenario → entomology → vector → anopheles → monthlyEIR

<monthlyEIR
    annualEIR=double
  >
IN THIS ORDER:
| ( <item ... /> ){12,12}
</monthlyEIR>

item

Documentation (element)

Units: Infectious bites per adult per month

Description of target entomological inoculation rate as monthly values plus an annual override (monthly values are scaled to fit the annual EIR described). This is used to estimate a suitible vector emergence rate. The annual (target) EIR is derived from a Fourier series fit to these monthly values (used as a smoothing factor). List should contain twelve entries: January to December.

Attributes

Annual EIR

annualEIR=double

Units: Infectious bites per adult per year Min: 0

Scales the monthly values to give this annual innoculation rate.

Monthly pre-intervention EIR

→ scenario → entomology → vector → anopheles → monthlyEIR → item

<item>
    double
</item>

Documentation (element)

Units: Inoculations per person per month

Inoculations per person per month

Vector Species

→ scenario → entomology → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqLaidEggsSameDayProportion=double
    mosqSeekingDuration=double
    mosqSurvivalFeedingCycleProbability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
    mosqHumanBloodIndex=double
    minInfectedThreshold=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

Duration of the resting period of the vector (days)

mosqRestDuration=int

name:Duration of the resting period of the vector (days);

Extrinsic incubation period (days)

extrinsicIncubationPeriod=int

name:Extrinsic incubation period (days)

Proportion of mosquitoes host seeking on same day as ovipositing

mosqLaidEggsSameDayProportion=double

Proportion of mosquitoes host seeking on same day as ovipositing

Duration of the host-seeking period of the vector (days)

mosqSeekingDuration=double

Duration of the host-seeking period of the vector (days)

Probability that the mosquito survives the feeding cycle

mosqSurvivalFeedingCycleProbability=double

Probability that the mosquito survives the feeding cycle

Probability that the mosquito succesfully bites chosen host

mosqProbBiting=double

Probability that the mosquito succesfully bites chosen host

Probability that the mosquito escapes host and finds a resting place after biting

mosqProbFindRestSite=double

Probability that the mosquito escapes host and finds a resting place after biting

Probability of mosquito successfully resting after finding a resting site

mosqProbResting=double

Probability of mosquito successfully resting after finding a resting site

Probability of a mosquito successfully laying eggs given that it has rested

mosqProbOvipositing=double

Probability of a mosquito successfully laying eggs given that it has rested

Human blood index

mosqHumanBloodIndex=double

The proportion of resting mosquitoes which fed on human blood during the last feed.

Min infected threshold

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

nonHumanHosts

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
    mosqRelativeEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of nonhuman hosts of type i (to other nonhuman hosts)

mosqRelativeEntoAvailability=double

Relative availability of nonhuman hosts of type i (to other nonhuman hosts)

Probability of mosquito successfully biting host

mosqProbBiting=double

Probability of mosquito successfully biting host

Probability that the mosquito escapes host and finds a resting place after biting

mosqProbFindRestSite=double

Probability that the mosquito escapes host and finds a resting place after biting

Probability of mosquito successfully resting after finding a resting site

mosqProbResting=double

Probability of mosquito successfully resting after finding a resting site

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Units: List of elements

Name of this species of non human hosts (must match up with those described per anopheles section)

number

number=double

Pharmacokinetics and pharmacodynamics

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
| ( <drug ... /> )+
</pharmacology>

drug

Documentation (element)

Units: List of elements

Drug model parameters

Library of drug parameters

→ scenario → pharmacology → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (element)

Sequence of drug descriptions forming a library of drug parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drug → PD

<PD>
IN THIS ORDER:
| ( <allele ... /> )+
</PD>

allele

PD parameters per allele

→ scenario → pharmacology → drug → PD → allele

<allele
    name=string
  >
IN THIS ORDER:
|   <initial_frequency ... /> 
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</allele>

Documentation (element)

PD parameters per allele, plus initial frequency of each allele.

Note: we assume a one-to-one correspondance of drugs to loci, hence each drug has an independent set of alleles here.

Attributes

name

name=string

Relative frequency

→ scenario → pharmacology → drug → PD → allele → initial_frequency

<initial_frequency>
    double
</initial_frequency>

Documentation (element)

Units: relative frequency Min: 0

Frequency, relative to the total frequency of all alleles for this drug/locus.

Maximal parasite killing rate

→ scenario → pharmacology → drug → PD → allele → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drug → PD → allele → IC50

<IC50>
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

Slope of effect curve

→ scenario → pharmacology → drug → PD → allele → slope

<slope>
    double
</slope>

Documentation (element)

Units: no units

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
|   <half_life ... /> 
|   <vol_dist ... /> 
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate (which is: ln(2) / half_life).

Volume of Distribution

→ scenario → pharmacology → drug → PK → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
|   <parameters ... /> 
</model>

Documentation (element)

Units: List of elements

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

Units: List of elements

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: include/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=int
  >
IN THIS ORDER:
| [ <NonMalariaFevers ... /> ]
</clinical>

NonMalariaFevers

Documentation (type)

Units: List of elements

Description of clinical parameters.

This is related to the health-system description, but contains data which can't be changed as part of an intervention and is not restricted to treatment.

Attributes

Follow-up period during which recurrence is treated as a failure

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
|   <prNeedTreatmentNMF ... /> 
|   <prNeedTreatmentMF ... /> 
</NonMalariaFevers>

Documentation (type)

Description of non-malaria fever incidence. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: none Min: 0 Max: 1

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: none Min: 0 Max: 1

Probability that a non-malaria fever needs treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: none Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ]
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

By age group data on availability of humans to mosquitoes relative to an adult.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ]
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Units: List of elements

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → model → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 28 documentation

Generated from: scenario_28.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    name=string
    wuID=int
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_28.xsd"
  >
IN ANY ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entomology ... /> 
| [ <pharmacology ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Units: string

Name of intervention

Work unit identifier

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Attributes

Name of demography data

name=string

Units: string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: years Min: 0 Max: 100

Maximum age of simulated humans in years.

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Percentage of human population in age group

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ cohortOnly=boolean ]
  [ firstBoutOnly=boolean ]
  [ firstTreatmentOnly=boolean ]
  [ firstInfectionOnly=boolean ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Attributes

Name of monitoring information

name=string

Units: string

Name of monitoring data

Survey only cohort

cohortOnly=boolean

Time to first episode only

firstBoutOnly=boolean

Time to first treatment only

firstTreatmentOnly=boolean

Time to first infection only

firstInfectionOnly=boolean

continuous

→ scenario → monitoring → continuous

<continuous
    period=int
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Days between reports

period=int

Units: Days Min: 1 Max: unbounded

Number of timesteps between reports.

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Model options required

name=string

Options define different model structures. Option name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.

Indicator of whether option is required

value=boolean

Default value: true

Option value (true/false). Each option has a default value used if the option is not listed (usually false but sometimes true).

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time; 0 means just before start of main sim and is a valid survey-point. Reported data is either from a point-time survey (immediate data) or is collected over the previous year (data from previous timesteps-per-year period). Simulation will end immediately after last survey is taken.

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Preventative interventions

<interventions
    name=string
  >
IN ANY ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <vaccine ... /> ]
| [ <IPT ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <vectorDeterrent ... /> ]
| [ <cohort ... /> ]
| [ <importedInfections ... /> ]
| [ <immuneSuppression ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <larviciding ... /> ]
</interventions>

Documentation (element)

Units: List of elements

Attributes

Intervention

name=string

Units: string

Name of set of interventions

Change health system

→ scenario → interventions → changeHS

<changeHS
  [ name=string ]
  >
IN THIS ORDER:
| ( <timed ... /> )*
</changeHS>

timed

Documentation (element)

Changes to the health system

Attributes

Name of intervention

name=string

Units: string

Name of intervention

timed

→ scenario → interventions → changeHS → timed

<timed
    time=int
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</timed>

Documentation (type)

A complete replacement health system. Replaces all previous properties. (Health system can be replaced multiple times if necessary.)

Documentation (base type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this replacement occurs, starting from 0, the first intervention-period time-step.

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</uncomplicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

decisions

→ scenario → interventions → MDA → description → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )*
</decisions>

decision

Documentation (type)

case (uncomplicated only): Returns "UC1" if there is no recent history of a malarial case, or "UC2" if there is.
result: Dependent on decision "test", this performs a parasite density test. Output is one of "none" (no test performed), "positive", "negative".

The following decisions must be described here:

test (uncomplicated only): Outputs must be "none", "microscopy" or "RDT" to describe which test the "result" decision uses.
treatment: Describes which treatment to use. Values aren't restricted but must match up with a treatment described in the corresponding "treatments" section.
hospitalisation (complicated only): none, immediate or delayed.

decision

→ scenario → interventions → MDA → description → decisions → decision

<decision
    name=string
    depends=string
    values=string
  >
    string
</decision>

Documentation (type)

A decision describes how to choose between a set of values.

Lexically, it can contain symbols matching "[_.a-zA-Z0-9]+", round brackets: (), braces: {} and colons. Whitespace is ignored except to separate symbols.

For each BRANCH_SET each BRANCH must have the same DECISION. This DECISION must be one of the dependencies mentioned in "depends". This may be:

another decision, in which case the VALUE immediately following in brackets must correspond to one of its output values. The BRANCH_SET immediately containing this BRANCH must represent each output value of the same decision exactly once, and no parent BRANCH_SET may be for the same DECISION.
"p": this indicates a probabilistic decision. In this case the value is a probability, the sum of all values for the BRANCH_SET must be 1 and the decision must be associated directly with OUTCOMEs (not sub-TREEs).
"age": this indicates an age-test. The VALUE must have the form "a-b", indicating that this branch will be taken for individuals aged such that a <= age < b, where a,b are non-negative real numbers or the special value "inf", and a <= b. All VALUEs in the BRANCH_SET must cover all possible (non-negative real) ages, with no overlap (hence, smallest a must be 0 and greatest b must be inf).

Semantically, each OUTCOME must be one of the values associated with this decision.

Attributes

Name of decision

name=string

The name of this decision. The name must match the regular expression "[_a-zA-Z0-9]+"; that is it can only contain letters, digits and _ characters (no spaces, punctuation, etc.).

Preceding decisions

depends=string

Outcome values

values=string

A comma-separated list of outcome values this decision may have. The name of each value must be of the same form as decision names (i.e. only contain letters, digits and _ characters).

treatments

→ scenario → interventions → MDA → description → treatments

<treatments>
IN THIS ORDER:
| ( <treatment ... /> )*
</treatments>

treatment

Documentation (type)

Units: string

A list of drug treatment tables. Each should have a name corresponding to one of the "drug" decision's values.

treatment

→ scenario → interventions → MDA → description → treatments → treatment

<treatment
    name=string
  >
IN THIS ORDER:
|   <schedule ... /> 
| ( <modifier ... /> )*
</treatment>

Documentation (type)

Units: List of elements

A description of a base treatment schedule along with modifiers to handle delays, quality variations, etc.

Attributes

Treatment administered

name=string

Units: string

Name corresponding to one of the drug decision's output values.

schedule

→ scenario → interventions → MDA → description → treatments → treatment → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

Units: List of elements

The base (unmodified) schedule of drugs administered for this treatment.

medicate

→ scenario → interventions → MDA → description → treatments → treatment → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  [ duration=double ]
  />

Attributes

drug

drug=string

Units: string

Abbreviated name of drug compound

drug dose

mg=double

Units: mg

Quantity of drug compound

time of administration

hour=double

Units: hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

duration of administration

duration=double

Units: hours Min: 0

If this attribute is given, use IV administration instead of orally. Specifies the number of hours over which the dose is administered.

modifier

→ scenario → interventions → MDA → description → treatments → treatment → modifier

<modifier
    decision=string
  >
EXACTLY ONE OF:
| ( <multiplyQty ... /> )*
| ( <delay ... /> )*
| ( <selectTimeRange ... /> )*
</modifier>

Documentation (type)

Units: Choice of elements

A modifier for this treatment, according to the outputs of a decision.

Attributes

decision

decision=string

Units: string

Specifies the decision that this modifier acts on.

Active ingredient multipliers

→ scenario → interventions → MDA → description → treatments → treatment → modifier → multiplyQty

<multiplyQty
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Units: Comma separated list of values

Multiplies the quantity of active ingredients of drugs administered.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of multipliers for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0.5,1" the quantity of drug A is halved while that of B is unchanged.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

Active ingredient delays

→ scenario → interventions → MDA → description → treatments → treatment → modifier → delay

<delay
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Units: Comma separated list of values

Delays administration of drugs listed in the base schedule by so many hours.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of delays (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0,6", drug A is administered as in the base schedule while drug B is administered 6 hours later than specified.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

Active ingredient time-ranges

→ scenario → interventions → MDA → description → treatments → treatment → modifier → selectTimeRange

<selectTimeRange
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Units: Comma separated list of values

Selects which drug doses to administer according to time of administration (before times are modified by delays). Half-open interval: [x,y)

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of time-ranges (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. The time-ranges should be of the form x-y and are interpreted as the half-open interval [x,y); that is a drug listed with time t will only be administered if x <= t < y.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</complicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: days Min: 0 Max: unbounded

Maximum number of timesteps (including first of case) an individual will remember they are sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial/non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of a complicated/severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: none Min: 0 Max: 1

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: none Min: 0 Max: 1

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: none Min: 0 Max: 1

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: none Min: 0 Max: 1

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
    name=string
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
</ImmediateOutcomes>

Documentation (type)

Units: List of elements

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Case Management model

name=string

Units: string

Name of health system

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

ACT

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

QN

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

Probability that a patient with uncomplicated disease seeks official care immediately

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease self-treats

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Case fatality rate in inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: List of elements

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients, during a severe bout.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Change transmission levels

→ scenario → interventions → changeEIR

<changeEIR
  [ name=string ]
  >
IN THIS ORDER:
| ( <timed ... /> )*
</changeEIR>

timed

Documentation (element)

Attributes

Name of intervention

name=string

Units: string

Name of intervention

timed

→ scenario → interventions → changeEIR → timed

<timed
    eipDuration=int
    time=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</timed>

EIRDaily

Documentation (type)

Replacement transmission levels. Disables feedback of human infectiousness to mosquitoes on further mosquito to human transmission. Must last until end of simulation.

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

Time

time=int

Units: time-steps Min: 0

Time-step at which this replacement occurs, starting from 0, the first intervention-period time-step.

EIRDaily

→ scenario → entomology → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Mass drug administration

→ scenario → interventions → MDA

<MDA
  [ name=string ]
  >
IN THIS ORDER:
| [ <description ... /> ]
| ( <timed ... /> )*
</MDA>

Documentation (element)

Description and deployment of MDA interventions (can also be configured as screen and treat or intermittent preventative treatment with 1-day time-step models).

Attributes

Name of intervention

name=string

Units: string

Name of intervention

Description of MDA

→ scenario → interventions → MDA → description

<description
  [ name=string ]
  >
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</description>

Documentation (element)

Documentation (base type)

Units: List of elements

A set of decisions and a set of treatments.

Attributes

Intervention

name=string

Units: string

Name of set of interventions

Mass administration

→ scenario → interventions → MDA → timed

<timed
    time=int
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  />

Documentation (element)

List of timed deployments of mass-drug-administration.

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Vaccines

→ scenario → interventions → vaccine

<vaccine
  [ name=string ]
  >
IN THIS ORDER:
| ( <description ... /> ){0,3}
| ( <continuous ... /> )*
| ( <timed ... /> )*
</vaccine>

Documentation (element)

Description and deployment of vaccine interventions.

Attributes

Name of intervention

name=string

Units: string

Name of intervention

description

→ scenario → interventions → vaccine → description

<description
    vaccineType=("PEV" or "BSV" or "TBV")
  [ name=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</description>

Documentation (type)

List of vaccine descriptions

Attributes

Type of vaccine

vaccineType=("PEV" or "BSV" or "TBV")

Units: Code

Type of vaccine

Vaccine

name=string

Units: string

Name of vaccine

Decay of effect

→ scenario → interventions → vaccine → description → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Specification of decay of efficacy

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

σ (sigma)

sigma=double

Units: none Min: 0

Default value: 0

If non-zero, heterogeneity of decay is introduced via a variate sampled from the log-normal distribution with mu zero (i.e. median is 1) and this sigma. Age is then divided by this variate before being passed to the decay function.

Variance parameter for vaccine efficacy

→ scenario → interventions → vaccine → description → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

initialEfficacy

→ scenario → interventions → vaccine → description → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Age-based vaccination

→ scenario → interventions → vaccine → continuous

<continuous
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

List of ages at which vaccination takes place (through EPI, post-natal and school-based programmes, etc.).

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Mass vaccination

→ scenario → interventions → vaccine → timed

<timed
    time=int
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

List of timed mass vaccinations in the community

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

Intermittent preventative treatment

→ scenario → interventions → IPT

<IPT
  [ name=string ]
  >
IN THIS ORDER:
|   <description ... /> 
| ( <continuous ... /> )*
| ( <timed ... /> )*
</IPT>

Documentation (element)

Description and deployment of IPT interventions.

Attributes

Name of intervention

name=string

Units: string

Name of intervention

description

→ scenario → interventions → IPT → description

<description
    iptiEffect=int
  [ name=string ]
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</description>

infGenotype

Attributes

Description of ipti effect

iptiEffect=int

Units: List of Elementes

Description of ipti effect

IPT name

name=string

Units: string

Name of IPT intervention

infGenotype

→ scenario → interventions → IPT → description → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

Age specific intervention

name=string

Units: string

Name of age specific intervention

Frequency

freq=double

Frequency of parasite genotype

ACR

ACR=double

Adequate clinical response (proportion)

Prophylactic period

proph=int

Prophylactic period

Tolerance period

tolPeriod=int

Tolerance period

atten=double

Tolerance period

Age-based IPT deployment

→ scenario → interventions → IPT → continuous

<continuous
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

List of ages at which IPTi/IPTc deployment takes place (through EPI, post-natal and school-based programmes, etc.).

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Mass IPT administration

→ scenario → interventions → IPT → timed

<timed
    time=int
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

List of timed IPTi/IPTc distribution

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

Bed nets

→ scenario → interventions → ITN

<ITN
  [ name=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
| ( <anophelesParams ... /> )+
| ( <continuous ... /> )*
| ( <timed ... /> )*
</ITN>

Documentation (element)

Description and deployment of bed-net interventions (ITNs, LLINs).

Attributes

Name of intervention

name=string

Units: string

Name of intervention

decay

→ scenario → interventions → ITN → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

σ (sigma)

sigma=double

Units: none Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → ITN → anophelesParams

<anophelesParams
    mosquito=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</anophelesParams>

Documentation (base type)

Units: None Min: 0 Max: 1

Descriptions of initial effectiveness of each of the effects of interventions. Decay is specified by a separate element (ITNDecay etc.)

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Deterrency

→ scenario → interventions → ITN → anophelesParams → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → ITN → anophelesParams → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → ITN → anophelesParams → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Age-based bed-net deployment

→ scenario → interventions → ITN → continuous

<continuous
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

List of ages at which bed-net deployment takes place (through EPI, post-natal and school-based programmes, etc.).

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Mass ITN deployment

→ scenario → interventions → ITN → timed

<timed
    time=int
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

List of timed ITN deployment in the community

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

Indoor residual spraying

→ scenario → interventions → IRS

<IRS
  [ name=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
| ( <anophelesParams ... /> )+
| ( <timed ... /> )*
</IRS>

Documentation (element)

Description and deployment of indoor insecticide interventions (IRS, durable wall linings, insecticide-treated-paint, etc.)

Attributes

Name of intervention

name=string

Units: string

Name of intervention

decay

→ scenario → interventions → IRS → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

σ (sigma)

sigma=double

Units: none Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → IRS → anophelesParams

<anophelesParams
    mosquito=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</anophelesParams>

Documentation (base type)

Units: None Min: 0 Max: 1

Descriptions of initial effectiveness of each of the effects of interventions. Decay is specified by a separate element (ITNDecay etc.)

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

killing effect

→ scenario → interventions → IRS → anophelesParams → killingEffect

<killingEffect
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Mass IRS deployment

→ scenario → interventions → IRS → timed

<timed
    time=int
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

List of timed IRS deployment in the community

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

Vector deterrents

<vectorDeterrent
  [ name=string ]
  >
IN THIS ORDER:
|   <decay ... /> 
| ( <anophelesParams ... /> )+
| ( <timed ... /> )*
</vectorDeterrent>

Documentation (element)

Description and deployment of interventions affecting only human-mosquito availability (deterrents).

Attributes

Name of intervention

name=string

Units: string

Name of intervention

decay

→ scenario → interventions → vectorDeterrent → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

σ (sigma)

sigma=double

Units: none Min: 0

Default value: 0

anophelesParams

→ scenario → interventions → vectorDeterrent → anophelesParams

<anophelesParams
    mosquito=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</anophelesParams>

deterrency

Documentation (base type)

Units: None Min: 0 Max: 1

Descriptions of initial effectiveness of each of the effects of interventions. Decay is specified by a separate element (ITNDecay etc.)

Attributes

Mosquito species

mosquito=string

Name of the affected anopheles-mosquito species.

Mass deployment

→ scenario → interventions → vectorDeterrent → timed

<timed
    time=int
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

List of timed mosquito deterrent deployment in the community

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

Cohort recruitment

→ scenario → interventions → cohort

<cohort
  [ name=string ]
  >
IN THIS ORDER:
| ( <continuous ... /> )*
| ( <timed ... /> )*
</cohort>

Documentation (element)

Recruitment of cohort as a pseudo-intervention.

Attributes

Name of intervention

name=string

Units: string

Name of intervention

Age-based cohort recruitment

→ scenario → interventions → cohort → continuous

<continuous
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

List of ages at which cohort recruitment takes place.

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Mass cohort selection

→ scenario → interventions → cohort → timed

<timed
    time=int
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

List of times of mass cohort selection.

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

Imported infections

<importedInfections
  [ name=string ]
  >
IN THIS ORDER:
|   <timed ... /> 
</importedInfections>

timed

Documentation (element)

Models importation of P. falciparum infections directly into humans from an external source. This is infections, not inoculations or EIR being imported.

Attributes

Name of intervention

name=string

Units: string

Name of intervention

Rate of importation

→ scenario → interventions → importedInfections → timed

<timed
  [ period=int ] DEFAULT VALUE 0
  >
IN THIS ORDER:
| ( <rate ... /> )+
</timed>

rate

Documentation (element)

Rate of case importation, as a step function. Each value is valid until replaced by the next value.

Attributes

Period of repetition

period=int

Units: time-steps Min: 0

Default value: 0

If period is 0 (or effectively infinite), the last specified value remains indefinitely in effect, otherwise the times of all values specified must be less than the period, and values are repeated modulo period (timestep period+2 has same value as timestep 2, etc.).

rate

→ scenario → interventions → importedInfections → timed → rate

<rate
    value=double
    time=int
  />

Documentation (type)

Units: Imported cases per thousand people per year

A time-rate pair.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Time

time=int

Units: time-steps Min: 0

Immune suppression

<immuneSuppression>
IN THIS ORDER:
| ( <timed ... /> )*
</immuneSuppression>

timed

Documentation (element)

Removes all exposure-related immunity gained over time by hosts without removing infections.

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

timed

→ scenario → interventions → immuneSuppression → timed

<timed
    time=int
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Insert R_0 case

<insertR_0Case>
IN THIS ORDER:
| ( <timed ... /> )*
</insertR_0Case>

timed

Documentation (element)

timed

→ scenario → interventions → insertR_0Case → timed

<timed
    time=int
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Uninfect vectors

<uninfectVectors>
IN THIS ORDER:
| ( <timed ... /> )*
</uninfectVectors>

timed

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

timed

→ scenario → interventions → uninfectVectors → timed

<timed
    time=int
  />

Attributes

Time

time=int

Units: time-steps Min: 0

Time-step at which this intervention occurs, starting from 0, the first intervention-period time-step.

Simple larviciding intervention

→ scenario → interventions → larviciding

<larviciding
  [ name=string ]
  >
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

anopheles

Documentation (element)

Units: List of elements

Simple larviciding intervention description.

Attributes

Name of intervention

name=string

Units: string

Name of intervention

anopheles

→ scenario → interventions → larviciding → anopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

Mosquito to be larvicided

mosquito=string

Mosquito to be larvicided

Proportionate reduction in emergence

effectiveness=double

Units: none Min: 0 Max: 1

Proportional reduction in emergence rate

Duration of activity

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Units: List of elements

Description of health system.

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entomology

<entomology
    name=string
    mode=("2" or "4")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entomology>

Documentation (element)

Units: List of elements

Description of entomological data

Attributes

Entomology dataset

name=string

Units: string

Name of entomology data

Transmission simulation mode

mode=("2" or "4")

Units: Code

Override annual EIR

annualEIR=double

Units: Infectious bites per adult per year

If set, overrides the annual EIR by scaling it to this level. If ommitted, EIR levels are as specified elsewhere.

Transmission setting (vector control not enabled)

→ scenario → entomology → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Units: List of elements

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entomology → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Units: List of elements

Parameters of the transmission model.

anopheles

→ scenario → entomology → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EIR ... /> 
| |   <monthlyEIR ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial guess of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial guess of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Fourier approximation to pre-intervention EIR

→ scenario → entomology → vector → anopheles → EIR

<EIR
    a0=double
    a1=double
    b1=double
    a2=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Infectious bites per adult per day

Attributes

a0 parameter of Fourier approximation to ln(EIR)

a0=double

a0 parameter of Fourier approximation to ln(EIR)

a1 parameter of Fourier approximation to ln(EIR)

a1=double

a1 parameter of Fourier approximation to ln(EIR)

b1 parameter of Fourier approximation to ln(EIR)

b1=double

b1 parameter of Fourier approximation to ln(EIR)

a2 parameter of Fourier approximation to ln(EIR)

a2=double

a2 parameter of Fourier approximation to ln(EIR)

b2 parameter of Fourier approximation to ln(EIR)

b2=double

b2 parameter of Fourier approximation to ln(EIR)

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Monthly values for pre-intervention EIR

→ scenario → entomology → vector → anopheles → monthlyEIR

<monthlyEIR
    annualEIR=double
  >
IN THIS ORDER:
| ( <item ... /> ){12,12}
</monthlyEIR>

item

Documentation (element)

Units: Infectious bites per adult per month

Attributes

Annual EIR

annualEIR=double

Units: Infectious bites per adult per year Min: 0

Scales the monthly values to give this annual innoculation rate.

Monthly pre-intervention EIR

→ scenario → entomology → vector → anopheles → monthlyEIR → item

<item>
    double
</item>

Documentation (element)

Units: Inoculations per person per month

Inoculations per person per month

Vector Species

→ scenario → entomology → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqLaidEggsSameDayProportion=double
    mosqSeekingDuration=double
    mosqSurvivalFeedingCycleProbability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
    mosqHumanBloodIndex=double
    minInfectedThreshold=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

Duration of the resting period of the vector (days)

mosqRestDuration=int

name:Duration of the resting period of the vector (days);

Extrinsic incubation period (days)

extrinsicIncubationPeriod=int

name:Extrinsic incubation period (days)

Proportion of mosquitoes host seeking on same day as ovipositing

mosqLaidEggsSameDayProportion=double

Proportion of mosquitoes host seeking on same day as ovipositing

Duration of the host-seeking period of the vector (days)

mosqSeekingDuration=double

Duration of the host-seeking period of the vector (days)

Probability that the mosquito survives the feeding cycle

mosqSurvivalFeedingCycleProbability=double

Probability that the mosquito survives the feeding cycle

Probability that the mosquito succesfully bites chosen host

mosqProbBiting=double

Probability that the mosquito succesfully bites chosen host

Probability that the mosquito escapes host and finds a resting place after biting

mosqProbFindRestSite=double

Probability that the mosquito escapes host and finds a resting place after biting

Probability of mosquito successfully resting after finding a resting site

mosqProbResting=double

Probability of mosquito successfully resting after finding a resting site

Probability of a mosquito successfully laying eggs given that it has rested

mosqProbOvipositing=double

Probability of a mosquito successfully laying eggs given that it has rested

Human blood index

mosqHumanBloodIndex=double

The proportion of resting mosquitoes which fed on human blood during the last feed.

Min infected threshold

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

nonHumanHosts

→ scenario → entomology → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
    mosqRelativeEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of nonhuman hosts of type i (to other nonhuman hosts)

mosqRelativeEntoAvailability=double

Relative availability of nonhuman hosts of type i (to other nonhuman hosts)

Probability of mosquito successfully biting host

mosqProbBiting=double

Probability of mosquito successfully biting host

Probability that the mosquito escapes host and finds a resting place after biting

mosqProbFindRestSite=double

Probability that the mosquito escapes host and finds a resting place after biting

Probability of mosquito successfully resting after finding a resting site

mosqProbResting=double

Probability of mosquito successfully resting after finding a resting site

nonHumanHosts

→ scenario → entomology → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Units: List of elements

Name of this species of non human hosts (must match up with those described per anopheles section)

number

number=double

Pharmacokinetics and pharmacodynamics

→ scenario → pharmacology

<pharmacology>
IN THIS ORDER:
| ( <drug ... /> )+
</pharmacology>

drug

Documentation (element)

Units: List of elements

Drug model parameters

Library of drug parameters

→ scenario → pharmacology → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (element)

Sequence of drug descriptions forming a library of drug parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → pharmacology → drug → PD

<PD>
IN THIS ORDER:
| ( <allele ... /> )+
</PD>

allele

PD parameters per allele

→ scenario → pharmacology → drug → PD → allele

<allele
    name=string
  >
IN THIS ORDER:
|   <initial_frequency ... /> 
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</allele>

Documentation (element)

PD parameters per allele, plus initial frequency of each allele.

Note: we assume a one-to-one correspondance of drugs to loci, hence each drug has an independent set of alleles here.

Attributes

name

name=string

Relative frequency

→ scenario → pharmacology → drug → PD → allele → initial_frequency

<initial_frequency>
    double
</initial_frequency>

Documentation (element)

Units: relative frequency Min: 0

Frequency, relative to the total frequency of all alleles for this drug/locus.

Maximal parasite killing rate

→ scenario → pharmacology → drug → PD → allele → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → pharmacology → drug → PD → allele → IC50

<IC50>
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

Slope of effect curve

→ scenario → pharmacology → drug → PD → allele → slope

<slope>
    double
</slope>

Documentation (element)

Units: no units

n — Slope of the concentration effect curve

PK

→ scenario → pharmacology → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
|   <half_life ... /> 
|   <vol_dist ... /> 
</PK>

Drug concentration considered negligible

→ scenario → pharmacology → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → pharmacology → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate (which is: ln(2) / half_life).

Volume of Distribution

→ scenario → pharmacology → drug → PK → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Model options and parameters

→ scenario → model

<model>
IN ANY ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
|   <parameters ... /> 
</model>

Documentation (element)

Units: List of elements

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

Units: List of elements

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: include/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=int
  >
IN THIS ORDER:
| [ <NonMalariaFevers ... /> ]
</clinical>

NonMalariaFevers

Documentation (type)

Units: List of elements

Description of clinical parameters.

This is related to the health-system description, but contains data which can't be changed as part of an intervention and is not restricted to treatment.

Attributes

Follow-up period during which recurrence is treated as a failure

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
|   <prNeedTreatmentNMF ... /> 
|   <prNeedTreatmentMF ... /> 
</NonMalariaFevers>

Documentation (type)

Description of non-malaria fever incidence. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: none Min: 0 Max: 1

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: none Min: 0 Max: 1

Probability that a non-malaria fever needs treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: none Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

By age group data on availability of humans to mosquitoes relative to an adult.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Units: List of elements

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → model → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 27 documentation

Generated from: scenario_27.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    name=string
    wuID=int
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_27.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entoData ... /> 
| [ <drugDescription ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Units: string

Name of intervention

Work unit identifier

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Attributes

Name of demography data

name=string

Units: string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: years Min: 0 Max: 100

Maximum age of simulated humans in years.

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Percentage of human population in age group

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ cohortOnly=boolean ]
  [ firstBoutOnly=boolean ]
  [ firstTreatmentOnly=boolean ]
  [ firstInfectionOnly=boolean ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Attributes

Name of monitoring information

name=string

Units: string

Name of monitoring data

Survey only cohort

cohortOnly=boolean

Time to first episode only

firstBoutOnly=boolean

Time to first treatment only

firstTreatmentOnly=boolean

Time to first infection only

firstInfectionOnly=boolean

continuous

→ scenario → monitoring → continuous

<continuous
    period=int
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Days between reports

period=int

Units: Days Min: 1 Max: unbounded

Number of timesteps between reports.

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Model options required

name=string

Options define different model structures. Option name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.

Indicator of whether option is required

value=boolean

Default value: true

Option value (true/false). Each option has a default value used if the option is not listed (usually false but sometimes true).

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time; 0 means just before start of main sim and is a valid survey-point. Reported data is either from a point-time survey (immediate data) or is collected over the previous year (data from previous timesteps-per-year period). Simulation will end immediately after last survey is taken.

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Preventative interventions

<interventions
    name=string
  >
IN THIS ORDER:
|   <descriptions ... /> 
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

Attributes

Intervention

name=string

Units: string

Name of age specific intervention

descriptions

<descriptions>
IN THIS ORDER:
| [ <MDADescription ... /> ]
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| [ <ITNDecay ... /> ]
| [ <IRSDecay ... /> ]
| [ <VADecay ... /> ]
| ( <anopheles ... /> )*
</descriptions>

Documentation (element)

Descriptions applying across all uses of an intervention.

Description of MDA

→ scenario → interventions → descriptions → MDADescription

<MDADescription>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</MDADescription>

Documentation (element)

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

decisions

→ scenario → interventions → descriptions → MDADescription → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )*
</decisions>

decision

Documentation (type)

case (uncomplicated only): Returns "UC1" if there is no recent history of a malarial case, or "UC2" if there is.
result: Dependent on decision "test", this performs a parasite density test. Output is one of "none" (no test performed), "positive", "negative".

The following decisions must be described here:

test (uncomplicated only): Outputs must be "none", "microscopy" or "RDT" to describe which test the "result" decision uses.
treatment: Describes which treatment to use. Values aren't restricted but must match up with a treatment described in the corresponding "treatments" section.
hospitalisation (complicated only): none, immediate or delayed.

decision

→ scenario → interventions → descriptions → MDADescription → decisions → decision

<decision
    name=string
    depends=string
    values=string
  >
    string
</decision>

Documentation (type)

A decision describes how to choose between a set of values.

Lexically, it can contain symbols matching "[_.a-zA-Z0-9]+", round brackets: (), braces: {} and colons. Whitespace is ignored except to separate symbols.

For each BRANCH_SET each BRANCH must have the same DECISION. This DECISION must be one of the dependencies mentioned in "depends". This may be:

another decision, in which case the VALUE immediately following in brackets must correspond to one of its output values. The BRANCH_SET immediately containing this BRANCH must represent each output value of the same decision exactly once, and no parent BRANCH_SET may be for the same DECISION.
"p": this indicates a probabilistic decision. In this case the value is a probability, the sum of all values for the BRANCH_SET must be 1 and the decision must be associated directly with OUTCOMEs (not sub-TREEs).
"age": this indicates an age-test. The VALUE must have the form "a-b", indicating that this branch will be taken for individuals aged such that a <= age < b, where a,b are non-negative real numbers or the special value "inf", and a <= b. All VALUEs in the BRANCH_SET must cover all possible (non-negative real) ages, with no overlap (hence, smallest a must be 0 and greatest b must be inf).

Semantically, each OUTCOME must be one of the values associated with this decision.

Attributes

Name of decision

name=string

The name of this decision. The name must match the regular expression "[_a-zA-Z0-9]+"; that is it can only contain letters, digits and _ characters (no spaces, punctuation, etc.).

Preceding decisions

depends=string

Outcome values

values=string

A comma-separated list of outcome values this decision may have. The name of each value must be of the same form as decision names (i.e. only contain letters, digits and _ characters).

treatments

→ scenario → interventions → descriptions → MDADescription → treatments

<treatments>
IN THIS ORDER:
| ( <treatment ... /> )*
</treatments>

treatment

Documentation (type)

Units: string

A list of drug treatment tables. Each should have a name corresponding to one of the "drug" decision's values.

treatment

→ scenario → interventions → descriptions → MDADescription → treatments → treatment

<treatment
    name=string
  >
IN THIS ORDER:
|   <schedule ... /> 
| ( <modifier ... /> )*
</treatment>

Documentation (type)

Units: List of elements

A description of a base treatment schedule along with modifiers to handle delays, quality variations, etc.

Attributes

Treatment administered

name=string

Units: string

Name corresponding to one of the drug decision's output values.

schedule

→ scenario → interventions → descriptions → MDADescription → treatments → treatment → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

Units: List of elements

The base (unmodified) schedule of drugs administered for this treatment.

medicate

→ scenario → interventions → descriptions → MDADescription → treatments → treatment → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  [ duration=double ]
  />

Attributes

drug

drug=string

Units: string

Abbreviated name of drug compound

drug dose

mg=double

Units: mg

Quantity of drug compound

time of administration

hour=double

Units: hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

duration of administration

duration=double

Units: hours Min: 0

If this attribute is given, use IV administration instead of orally. Specifies the number of hours over which the dose is administered.

modifier

→ scenario → interventions → descriptions → MDADescription → treatments → treatment → modifier

<modifier
    decision=string
  >
EXACTLY ONE OF:
| ( <multiplyQty ... /> )*
| ( <delay ... /> )*
| ( <selectTimeRange ... /> )*
</modifier>

Documentation (type)

Units: Choice of elements

A modifier for this treatment, according to the outputs of a decision.

Attributes

decision

decision=string

Units: string

Specifies the decision that this modifier acts on.

Active ingredient multipliers

→ scenario → interventions → descriptions → MDADescription → treatments → treatment → modifier → multiplyQty

<multiplyQty
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Units: Comma separated list of values

Multiplies the quantity of active ingredients of drugs administered.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of multipliers for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0.5,1" the quantity of drug A is halved while that of B is unchanged.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

Active ingredient delays

→ scenario → interventions → descriptions → MDADescription → treatments → treatment → modifier → delay

<delay
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Units: Comma separated list of values

Delays administration of drugs listed in the base schedule by so many hours.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of delays (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0,6", drug A is administered as in the base schedule while drug B is administered 6 hours later than specified.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

Active ingredient time-ranges

→ scenario → interventions → descriptions → MDADescription → treatments → treatment → modifier → selectTimeRange

<selectTimeRange
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Units: Comma separated list of values

Selects which drug doses to administer according to time of administration (before times are modified by delays). Half-open interval: [x,y)

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of time-ranges (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. The time-ranges should be of the form x-y and are interpreted as the half-open interval [x,y); that is a drug listed with time t will only be administered if x <= t < y.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

vaccineDescription

→ scenario → interventions → descriptions → vaccineDescription

<vaccineDescription
    vaccineType=("PEV" or "BSV" or "TBV")
  >
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

Type of vaccine

vaccineType=("PEV" or "BSV" or "TBV")

Units: Code

Type of vaccine

Decay of effect

→ scenario → interventions → descriptions → vaccineDescription → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Specification of decay of efficacy

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

σ (sigma)

sigma=double

Units: none Min: 0

Default value: 0

Variance parameter for vaccine efficacy

→ scenario → interventions → descriptions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

initialEfficacy

→ scenario → interventions → descriptions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

iptiDescription

→ scenario → interventions → descriptions → iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

Description of ipti effect

iptiEffect=int

Units: List of Elementes

Description of ipti effect

infGenotype

→ scenario → interventions → descriptions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

Age specific intervention

name=string

Units: string

Name of age specific intervention

Frequency

freq=double

Frequency of parasite genotype

ACR

ACR=double

Adequate clinical response (proportion)

Prophylactic period

proph=int

Prophylactic period

Tolerance period

tolPeriod=int

Tolerance period

atten=double

Tolerance period

ITNDecay

→ scenario → interventions → descriptions → ITNDecay

<ITNDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

σ (sigma)

sigma=double

Units: none Min: 0

Default value: 0

IRSDecay

→ scenario → interventions → descriptions → IRSDecay

<IRSDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

σ (sigma)

sigma=double

Units: none Min: 0

Default value: 0

VADecay

→ scenario → interventions → descriptions → VADecay

<VADecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "smooth-compact")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

σ (sigma)

sigma=double

Units: none Min: 0

Default value: 0

anopheles

→ scenario → interventions → descriptions → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <VADescription ... /> ]
</anopheles>

Attributes

Entomological effects of interventions

mosquito=string

Description of the entomological effects of interventions

ITNDescription

→ scenario → interventions → descriptions → anopheles → ITNDescription

<ITNDescription>
IN THIS ORDER:
|   <deterrency ... /> 
</ITNDescription>

Documentation (base type)

Units: None Min: 0 Max: 1

Descriptions of initial effectiveness of each of the effects of interventions. Decay is specified by a separate element (ITNDecay etc.)

Deterrency

→ scenario → interventions → descriptions → anopheles → ITNDescription → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → descriptions → anopheles → ITNDescription → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → descriptions → anopheles → ITNDescription → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

IRSDescription

→ scenario → interventions → descriptions → anopheles → IRSDescription

<IRSDescription>
IN THIS ORDER:
|   <deterrency ... /> 
</IRSDescription>

Documentation (base type)

Units: None Min: 0 Max: 1

Descriptions of initial effectiveness of each of the effects of interventions. Decay is specified by a separate element (ITNDecay etc.)

killing effect

→ scenario → interventions → descriptions → anopheles → IRSDescription → killingEffect

<killingEffect
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

VADescription

→ scenario → interventions → descriptions → anopheles → VADescription

<VADescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</VADescription>

deterrency

Documentation (type)

Units: None Min: 0 Max: 1

Descriptions of initial effectiveness of each of the effects of interventions. Decay is specified by a separate element (ITNDecay etc.)

Attributes

Name of intervention

name=string

Units: string

Name of intervention

Continuously applied interventions

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
| ( <cohort ... /> )*
</continuous>

Documentation (element)

Continuously applied interventions

Documentation (type)

Interventions to be deployed continuously

List of age groups for vaccination

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Description of ITN deployment

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

List of age groups for IPTi

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Continuous cohort selection

→ scenario → interventions → continuous → cohort

<cohort
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

Description of continuous selection of individuals for a cohort study.

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Timed interventions

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfectionsPerThousandHosts ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <VectorAvailability ... /> ]
| [ <ipti ... /> ]
| [ <immuneSuppression ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <larviciding ... /> ]
| [ <cohort ... /> ]
</intervention>

Attributes

Time step of intervention

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</uncomplicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</complicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: days Min: 0 Max: unbounded

Maximum number of timesteps (including first of case) an individual will remember they are sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial/non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of a complicated/severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: none Min: 0 Max: 1

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: none Min: 0 Max: 1

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: none Min: 0 Max: 1

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: none Min: 0 Max: 1

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
    name=string
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
</ImmediateOutcomes>

Documentation (type)

Units: List of elements

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Case Management model

name=string

Units: string

Name of health system

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

ACT

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

QN

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

Probability that a patient with uncomplicated disease seeks official care immediately

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease self-treats

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Case fatality rate in inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: List of elements

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients, during a severe bout.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Replacement transmission setting (vector control not enabled)

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (element)

Units: List of elements

New description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

EIRDaily

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Import infections

→ scenario → interventions → timed → intervention → importedInfectionsPerThousandHosts

<importedInfectionsPerThousandHosts>
    double
</importedInfectionsPerThousandHosts>

Documentation (element)

Units: Number per 1000 hosts Min: 0

Import infections (as if a mosquito bites a human). Imported via a Bernoulli trial per host.

Mass Drug Administration

→ scenario → interventions → timed → intervention → MDA

<MDA
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Vaccination

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

ITN deployment

→ scenario → interventions → timed → intervention → ITN

<ITN
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

IRS deployment

→ scenario → interventions → timed → intervention → IRS

<IRS
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

Units: List of elements

Description of IRS deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

Mosquito deterrent

→ scenario → interventions → timed → intervention → VectorAvailability

<VectorAvailability
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

Units: List of elements

Description of a mosquito deterrent deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

IPTi deployment

→ scenario → interventions → timed → intervention → ipti

<ipti
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

Immune suppression deployment

→ scenario → interventions → timed → intervention → immuneSuppression

<immuneSuppression
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  />

Documentation (element)

Units: List of elements

Removes all exposure-related immunity gained over time by hosts without removing infections.

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Insert R_0 case

→ scenario → interventions → timed → intervention → insertR_0Case

<insertR_0Case/>

Documentation (element)

Units: List of elements

Uninfect vectors

→ scenario → interventions → timed → intervention → uninfectVectors

<uninfectVectors/>

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

Simple larviciding intervention

→ scenario → interventions → timed → intervention → larviciding

<larviciding>
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

anopheles

Documentation (element)

Units: List of elements

Simple larviciding intervention description.

anopheles

→ scenario → interventions → timed → intervention → larviciding → anopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

Mosquito to be larvicided

mosquito=string

Mosquito to be larvicided

Proportionate reduction in emergence

effectiveness=double

Units: none Min: 0 Max: 1

Proportional reduction in emergence rate

Duration of activity

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

Mass Cohort Selection

→ scenario → interventions → timed → intervention → cohort

<cohort
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

Units: List of elements

Description of mass cohort selection.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Units: List of elements

Description of health system.

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entoData

<entoData
    name=string
    mode=("2" or "4")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Attributes

Entomology dataset

name=string

Units: string

Name of entomology data

Transmission simulation mode

mode=("2" or "4")

Units: Code

Override annual EIR

annualEIR=double

Units: Infectious bites per adult per year

If set, overrides the annual EIR by scaling it to this level. If ommitted, EIR levels are as specified elsewhere.

Transmission setting (vector control not enabled)

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Units: List of elements

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Units: List of elements

Parameters of the transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <eir ... /> 
| |   <monthlyEir ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial guess of proportion of mosquitoes infected (ρ_O)

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial guess of proportion of mosquitoes infectious (ρ_S)

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Fourier approximation to pre-intervention EIR

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    b1=double
    a2=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Infectious bites per adult per day

Attributes

a0 parameter of Fourier approximation to ln(EIR)

a0=double

a0 parameter of Fourier approximation to ln(EIR)

a1 parameter of Fourier approximation to ln(EIR)

a1=double

a1 parameter of Fourier approximation to ln(EIR)

b1 parameter of Fourier approximation to ln(EIR)

b1=double

b1 parameter of Fourier approximation to ln(EIR)

a2 parameter of Fourier approximation to ln(EIR)

a2=double

a2 parameter of Fourier approximation to ln(EIR)

b2 parameter of Fourier approximation to ln(EIR)

b2=double

b2 parameter of Fourier approximation to ln(EIR)

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Monthly values for pre-intervention EIR

→ scenario → entoData → vector → anopheles → monthlyEir

<monthlyEir
    annualEIR=double
  >
IN THIS ORDER:
| ( <item ... /> ){12,12}
</monthlyEir>

item

Documentation (element)

Units: Infectious bites per adult per month

Attributes

Annual EIR

annualEIR=double

Units: Infectious bites per adult per year Min: 0

Scales the monthly values to give this annual innoculation rate.

Monthly pre-intervention EIR

→ scenario → entoData → vector → anopheles → monthlyEir → item

<item>
    double
</item>

Documentation (element)

Units: Inoculations per person per month

Inoculations per person per month

Vector Species

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqLaidEggsSameDayProportion=double
    mosqSeekingDuration=double
    mosqSurvivalFeedingCycleProbability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
    mosqHumanBloodIndex=double
    minInfectedThreshold=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

Duration of the resting period of the vector (days)

mosqRestDuration=int

name:Duration of the resting period of the vector (days);

Extrinsic incubation period (days)

extrinsicIncubationPeriod=int

name:Extrinsic incubation period (days)

Proportion of mosquitoes host seeking on same day as ovipositing

mosqLaidEggsSameDayProportion=double

Proportion of mosquitoes host seeking on same day as ovipositing

Duration of the host-seeking period of the vector (days)

mosqSeekingDuration=double

Duration of the host-seeking period of the vector (days)

Probability that the mosquito survives the feeding cycle

mosqSurvivalFeedingCycleProbability=double

Probability that the mosquito survives the feeding cycle

Probability that the mosquito succesfully bites chosen host

mosqProbBiting=double

Probability that the mosquito succesfully bites chosen host

Probability that the mosquito escapes host and finds a resting place after biting

mosqProbFindRestSite=double

Probability that the mosquito escapes host and finds a resting place after biting

Probability of mosquito successfully resting after finding a resting site

mosqProbResting=double

Probability of mosquito successfully resting after finding a resting site

Probability of a mosquito successfully laying eggs given that it has rested

mosqProbOvipositing=double

Probability of a mosquito successfully laying eggs given that it has rested

Human blood index

mosqHumanBloodIndex=double

The proportion of resting mosquitoes which fed on human blood during the last feed.

Min infected threshold

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
    mosqRelativeEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of nonhuman hosts of type i (to other nonhuman hosts)

mosqRelativeEntoAvailability=double

Relative availability of nonhuman hosts of type i (to other nonhuman hosts)

Probability of mosquito successfully biting host

mosqProbBiting=double

Probability of mosquito successfully biting host

Probability that the mosquito escapes host and finds a resting place after biting

mosqProbFindRestSite=double

Probability that the mosquito escapes host and finds a resting place after biting

Probability of mosquito successfully resting after finding a resting site

mosqProbResting=double

Probability of mosquito successfully resting after finding a resting site

nonHumanHosts

→ scenario → entoData → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Units: List of elements

Name of this species of non human hosts (must match up with those described per anopheles section)

number

number=double

Pharmacokinetics and pharmacodynamics

<drugDescription>
IN THIS ORDER:
| ( <drug ... /> )+
</drugDescription>

drug

Documentation (element)

Units: List of elements

Drug model parameters

Library of drug parameters

→ scenario → drugDescription → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (element)

Sequence of drug descriptions forming a library of drug parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → drugDescription → drug → PD

<PD>
IN THIS ORDER:
| ( <allele ... /> )+
</PD>

allele

PD parameters per allele

→ scenario → drugDescription → drug → PD → allele

<allele
    name=string
  >
IN THIS ORDER:
|   <initial_frequency ... /> 
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</allele>

Documentation (element)

PD parameters per allele, plus initial frequency of each allele.

Note: we assume a one-to-one correspondance of drugs to loci, hence each drug has an independent set of alleles here.

Attributes

name

name=string

Relative frequency

→ scenario → drugDescription → drug → PD → allele → initial_frequency

<initial_frequency>
    double
</initial_frequency>

Documentation (element)

Units: relative frequency Min: 0

Frequency, relative to the total frequency of all alleles for this drug/locus.

Maximal parasite killing rate

→ scenario → drugDescription → drug → PD → allele → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → drugDescription → drug → PD → allele → IC50

<IC50>
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

Slope of effect curve

→ scenario → drugDescription → drug → PD → allele → slope

<slope>
    double
</slope>

Documentation (element)

Units: no units

n — Slope of the concentration effect curve

PK

→ scenario → drugDescription → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
|   <half_life ... /> 
|   <vol_dist ... /> 
</PK>

Drug concentration considered negligible

→ scenario → drugDescription → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → drugDescription → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate (which is: ln(2) / half_life).

Volume of Distribution

→ scenario → drugDescription → drug → PK → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Model options and parameters

→ scenario → model

<model>
IN THIS ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
|   <parameters ... /> 
</model>

Documentation (element)

Units: List of elements

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

Units: List of elements

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: include/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=int
  >
IN THIS ORDER:
| [ <NonMalariaFevers ... /> ]
</clinical>

NonMalariaFevers

Documentation (type)

Units: List of elements

Description of clinical parameters.

This is related to the health-system description, but contains data which can't be changed as part of an intervention and is not restricted to treatment.

Attributes

Follow-up period during which recurrence is treated as a failure

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
|   <prNeedTreatmentNMF ... /> 
|   <prNeedTreatmentMF ... /> 
</NonMalariaFevers>

Documentation (type)

Description of non-malaria fever incidence. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: none Min: 0 Max: 1

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: none Min: 0 Max: 1

Probability that a non-malaria fever needs treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: none Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

By age group data on availability of humans to mosquitoes relative to an adult.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Units: List of elements

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → model → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 26 documentation

Generated from: scenario_26.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    name=string
    wuID=int
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_26.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entoData ... /> 
| [ <drugDescription ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Units: string

Name of intervention

Work unit identifier

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Attributes

Name of demography data

name=string

Units: string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: years Min: 0 Max: 100

Maximum age of simulated humans in years.

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Percentage of human population in age group

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ cohortOnly=boolean ]
  [ firstBoutOnly=boolean ]
  [ firstTreatmentOnly=boolean ]
  [ firstInfectionOnly=boolean ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Attributes

Name of monitoring information

name=string

Units: string

Name of monitoring data

Survey only cohort

cohortOnly=boolean

Time to first episode only

firstBoutOnly=boolean

Time to first treatment only

firstTreatmentOnly=boolean

Time to first infection only

firstInfectionOnly=boolean

continuous

→ scenario → monitoring → continuous

<continuous
    period=int
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Days between reports

period=int

Units: Days Min: 1 Max: unbounded

Number of timesteps between reports.

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Model options required

name=string

Options define different model structures. Option name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.

Indicator of whether option is required

value=boolean

Default value: true

Option value (true/false). Each option has a default value used if the option is not listed (usually false but sometimes true).

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time; 0 means just before start of main sim and is a valid survey-point. Reported data is either from a point-time survey (immediate data) or is collected over the previous year (data from previous timesteps-per-year period). Simulation will end immediately after last survey is taken.

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Preventative interventions

<interventions
    name=string
  >
IN THIS ORDER:
|   <descriptions ... /> 
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

Attributes

Intervention

name=string

Units: string

Name of age specific intervention

descriptions

<descriptions>
IN THIS ORDER:
| [ <MDADescription ... /> ]
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| [ <ITNDecay ... /> ]
| [ <IRSDecay ... /> ]
| [ <VADecay ... /> ]
| ( <anopheles ... /> )*
</descriptions>

Documentation (element)

Descriptions applying across all uses of an intervention.

Description of MDA

→ scenario → interventions → descriptions → MDADescription

<MDADescription>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</MDADescription>

Documentation (element)

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

decisions

→ scenario → interventions → descriptions → MDADescription → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )*
</decisions>

decision

Documentation (type)

case (uncomplicated only): Returns "UC1" if there is no recent history of a malarial case, or "UC2" if there is.
result: Dependent on decision "test", this performs a parasite density test. Output is one of "none" (no test performed), "positive", "negative".

The following decisions must be described here:

test (uncomplicated only): Outputs must be "none", "microscopy" or "RDT" to describe which test the "result" decision uses.
treatment: Describes which treatment to use. Values aren't restricted but must match up with a treatment described in the corresponding "treatments" section.
hospitalisation (complicated only): none, immediate or delayed.

decision

→ scenario → interventions → descriptions → MDADescription → decisions → decision

<decision
    name=string
    depends=string
    values=string
  >
    string
</decision>

Documentation (type)

A decision describes how to choose between a set of values.

Lexically, it can contain symbols matching "[_.a-zA-Z0-9]+", round brackets: (), braces: {} and colons. Whitespace is ignored except to separate symbols.

For each BRANCH_SET each BRANCH must have the same DECISION. This DECISION must be one of the dependencies mentioned in "depends". This may be:

another decision, in which case the VALUE immediately following in brackets must correspond to one of its output values. The BRANCH_SET immediately containing this BRANCH must represent each output value of the same decision exactly once, and no parent BRANCH_SET may be for the same DECISION.
"p": this indicates a probabilistic decision. In this case the value is a probability, the sum of all values for the BRANCH_SET must be 1 and the decision must be associated directly with OUTCOMEs (not sub-TREEs).
"age": this indicates an age-test. The VALUE must have the form "a-b", indicating that this branch will be taken for individuals aged such that a <= age < b, where a,b are non-negative real numbers or the special value "inf", and a <= b. All VALUEs in the BRANCH_SET must cover all possible (non-negative real) ages, with no overlap (hence, smallest a must be 0 and greatest b must be inf).

Semantically, each OUTCOME must be one of the values associated with this decision.

Attributes

Name of decision

name=string

The name of this decision. The name must match the regular expression "[_a-zA-Z0-9]+"; that is it can only contain letters, digits and _ characters (no spaces, punctuation, etc.).

Preceding decisions

depends=string

Outcome values

values=string

A comma-separated list of outcome values this decision may have. The name of each value must be of the same form as decision names (i.e. only contain letters, digits and _ characters).

treatments

→ scenario → interventions → descriptions → MDADescription → treatments

<treatments>
IN THIS ORDER:
| ( <treatment ... /> )*
</treatments>

treatment

Documentation (type)

Units: string

A list of drug treatment tables. Each should have a name corresponding to one of the "drug" decision's values.

treatment

→ scenario → interventions → descriptions → MDADescription → treatments → treatment

<treatment
    name=string
  >
IN THIS ORDER:
|   <schedule ... /> 
| ( <modifier ... /> )*
</treatment>

Documentation (type)

Units: List of elements

A description of a base treatment schedule along with modifiers to handle delays, quality variations, etc.

Attributes

Treatment administered

name=string

Units: string

Name corresponding to one of the drug decision's output values.

schedule

→ scenario → interventions → descriptions → MDADescription → treatments → treatment → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

Units: List of elements

The base (unmodified) schedule of drugs administered for this treatment.

medicate

→ scenario → interventions → descriptions → MDADescription → treatments → treatment → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  [ duration=double ]
  />

Attributes

drug

drug=string

Units: string

Abbreviated name of drug compound

drug dose

mg=double

Units: mg

Quantity of drug compound

time of administration

hour=double

Units: hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

duration of administration

duration=double

Units: hours Min: 0

If this attribute is given, use IV administration instead of orally. Specifies the number of hours over which the dose is administered.

modifier

→ scenario → interventions → descriptions → MDADescription → treatments → treatment → modifier

<modifier
    decision=string
  >
EXACTLY ONE OF:
| ( <multiplyQty ... /> )*
| ( <delay ... /> )*
| ( <selectTimeRange ... /> )*
</modifier>

Documentation (type)

Units: Choice of elements

A modifier for this treatment, according to the outputs of a decision.

Attributes

decision

decision=string

Units: string

Specifies the decision that this modifier acts on.

Active ingredient multipliers

→ scenario → interventions → descriptions → MDADescription → treatments → treatment → modifier → multiplyQty

<multiplyQty
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Units: Comma separated list of values

Multiplies the quantity of active ingredients of drugs administered.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of multipliers for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0.5,1" the quantity of drug A is halved while that of B is unchanged.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

Active ingredient delays

→ scenario → interventions → descriptions → MDADescription → treatments → treatment → modifier → delay

<delay
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Units: Comma separated list of values

Delays administration of drugs listed in the base schedule by so many hours.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of delays (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0,6", drug A is administered as in the base schedule while drug B is administered 6 hours later than specified.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

Active ingredient time-ranges

→ scenario → interventions → descriptions → MDADescription → treatments → treatment → modifier → selectTimeRange

<selectTimeRange
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Units: Comma separated list of values

Selects which drug doses to administer according to time of administration (before times are modified by delays). Half-open interval: [x,y)

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of time-ranges (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. The time-ranges should be of the form x-y and are interpreted as the half-open interval [x,y); that is a drug listed with time t will only be administered if x <= t < y.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

vaccineDescription

→ scenario → interventions → descriptions → vaccineDescription

<vaccineDescription
    vaccineType=("PEV" or "BSV" or "TBV")
  >
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

Type of vaccine

vaccineType=("PEV" or "BSV" or "TBV")

Units: Code

Type of vaccine

Decay of effect

→ scenario → interventions → descriptions → vaccineDescription → decay

<decay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "chitnis")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (element)

Specification of decay of efficacy

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "chitnis")

Units: None Min: 0 Max: 1

Determines which decay function to use. Available decay functions, for age t in years: constant: 1 step: 1 for t less than L, otherwise 0 linear: 1 - t/L for t less than L, otherwise 0 exponential: exp( - t/L * log(2) ) weibull: exp( -(t/L)^k * log(2) ) hill: 1 / (1 + (t/L)^k) chitnis: exp( k - k / (1 - (t/L)^2) ) for t less than L, otherwise 0

L

L=double

Units: Years Min: 0

Scale parameter of distribution. With Chintnis' function, this is the age at which the parameter has decayed to 0; with the other three functions, this is the age at which the parameter has decayed to half its original value. Not used for constant decay (though must be specified anyway).

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

σ (sigma)

sigma=double

Units: none Min: 0

Default value: 0

Variance parameter for vaccine efficacy

→ scenario → interventions → descriptions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

initialEfficacy

→ scenario → interventions → descriptions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

iptiDescription

→ scenario → interventions → descriptions → iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

Description of ipti effect

iptiEffect=int

Units: List of Elementes

Description of ipti effect

infGenotype

→ scenario → interventions → descriptions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

Age specific intervention

name=string

Units: string

Name of age specific intervention

Frequency

freq=double

Frequency of parasite genotype

ACR

ACR=double

Adequate clinical response (proportion)

Prophylactic period

proph=int

Prophylactic period

Tolerance period

tolPeriod=int

Tolerance period

atten=double

Tolerance period

ITNDecay

→ scenario → interventions → descriptions → ITNDecay

<ITNDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "chitnis")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "chitnis")

Units: None Min: 0 Max: 1

Determines which decay function to use. Available decay functions, for age t in years: constant: 1 step: 1 for t less than L, otherwise 0 linear: 1 - t/L for t less than L, otherwise 0 exponential: exp( - t/L * log(2) ) weibull: exp( -(t/L)^k * log(2) ) hill: 1 / (1 + (t/L)^k) chitnis: exp( k - k / (1 - (t/L)^2) ) for t less than L, otherwise 0

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

σ (sigma)

sigma=double

Units: none Min: 0

Default value: 0

IRSDecay

→ scenario → interventions → descriptions → IRSDecay

<IRSDecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "chitnis")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "chitnis")

Units: None Min: 0 Max: 1

Determines which decay function to use. Available decay functions, for age t in years: constant: 1 step: 1 for t less than L, otherwise 0 linear: 1 - t/L for t less than L, otherwise 0 exponential: exp( - t/L * log(2) ) weibull: exp( -(t/L)^k * log(2) ) hill: 1 / (1 + (t/L)^k) chitnis: exp( k - k / (1 - (t/L)^2) ) for t less than L, otherwise 0

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

σ (sigma)

sigma=double

Units: none Min: 0

Default value: 0

VADecay

→ scenario → interventions → descriptions → VADecay

<VADecay
    function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "chitnis")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  [ sigma=double ] DEFAULT VALUE 0
  />

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "step" or "linear" or "exponential" or "weibull" or "hill" or "chitnis")

Units: None Min: 0 Max: 1

Determines which decay function to use. Available decay functions, for age t in years: constant: 1 step: 1 for t less than L, otherwise 0 linear: 1 - t/L for t less than L, otherwise 0 exponential: exp( - t/L * log(2) ) weibull: exp( -(t/L)^k * log(2) ) hill: 1 / (1 + (t/L)^k) chitnis: exp( k - k / (1 - (t/L)^2) ) for t less than L, otherwise 0

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

σ (sigma)

sigma=double

Units: none Min: 0

Default value: 0

anopheles

→ scenario → interventions → descriptions → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <VADescription ... /> ]
</anopheles>

Attributes

Entomological effects of interventions

mosquito=string

Description of the entomological effects of interventions

ITNDescription

→ scenario → interventions → descriptions → anopheles → ITNDescription

<ITNDescription>
IN THIS ORDER:
|   <deterrency ... /> 
</ITNDescription>

Documentation (base type)

Units: None Min: 0 Max: 1

Descriptions of initial effectiveness of each of the effects of interventions. Decay is specified by a separate element (ITNDecay etc.)

Deterrency

→ scenario → interventions → descriptions → anopheles → ITNDescription → deterrency

<deterrency
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Pre-prandial killing effect

→ scenario → interventions → descriptions → anopheles → ITNDescription → preprandialKillingEffect

<preprandialKillingEffect
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Post-prandial killing effect

→ scenario → interventions → descriptions → anopheles → ITNDescription → postprandialKillingEffect

<postprandialKillingEffect
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

IRSDescription

→ scenario → interventions → descriptions → anopheles → IRSDescription

<IRSDescription>
IN THIS ORDER:
|   <deterrency ... /> 
</IRSDescription>

Documentation (base type)

Units: None Min: 0 Max: 1

Descriptions of initial effectiveness of each of the effects of interventions. Decay is specified by a separate element (ITNDecay etc.)

killing effect

→ scenario → interventions → descriptions → anopheles → IRSDescription → killingEffect

<killingEffect
    value=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Attributes

Input parameter value

value=double

A double-precision floating-point value.

VADescription

→ scenario → interventions → descriptions → anopheles → VADescription

<VADescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</VADescription>

deterrency

Documentation (type)

Units: None Min: 0 Max: 1

Descriptions of initial effectiveness of each of the effects of interventions. Decay is specified by a separate element (ITNDecay etc.)

Attributes

Name of intervention

name=string

Units: string

Name of intervention

Continuously applied interventions

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
| ( <cohort ... /> )*
</continuous>

Documentation (element)

Continuously applied interventions

Documentation (type)

Interventions to be deployed continuously

List of age groups for vaccination

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Description of ITN deployment

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

List of age groups for IPTi

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Continuous cohort selection

→ scenario → interventions → continuous → cohort

<cohort
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

Description of continuous selection of individuals for a cohort study.

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Timed interventions

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfectionsPerThousandHosts ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <VectorAvailability ... /> ]
| [ <ipti ... /> ]
| [ <immuneSuppression ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <larviciding ... /> ]
| [ <cohort ... /> ]
</intervention>

Attributes

Time step of intervention

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</uncomplicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</complicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
| ( <dailyPrImmUCTS ... /> )+
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: days Min: 0 Max: unbounded

Maximum number of timesteps (including first of case) an individual will remember they are sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial/non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of a complicated/severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Daily probability of immediate treatment seeking for uncomplicated cases

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → dailyPrImmUCTS

<dailyPrImmUCTS>
    double
</dailyPrImmUCTS>

Documentation (element)

Units: none Min: 0 Max: 1

For no delay, use one element with a value of 1.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: none Min: 0 Max: 1

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: none Min: 0 Max: 1

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: none Min: 0 Max: 1

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
    name=string
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
</ImmediateOutcomes>

Documentation (type)

Units: List of elements

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Case Management model

name=string

Units: string

Name of health system

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

ACT

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

QN

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

Probability that a patient with uncomplicated disease seeks official care immediately

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease self-treats

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Case fatality rate in inpatients

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: List of elements

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients, during a severe bout.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Replacement transmission setting (vector control not enabled)

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (element)

Units: List of elements

New description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

EIRDaily

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Import infections

→ scenario → interventions → timed → intervention → importedInfectionsPerThousandHosts

<importedInfectionsPerThousandHosts>
    double
</importedInfectionsPerThousandHosts>

Documentation (element)

Units: Number per 1000 hosts Min: 0

Import infections (as if a mosquito bites a human). Imported via a Bernoulli trial per host.

Mass Drug Administration

→ scenario → interventions → timed → intervention → MDA

<MDA
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Vaccination

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

ITN deployment

→ scenario → interventions → timed → intervention → ITN

<ITN
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

IRS deployment

→ scenario → interventions → timed → intervention → IRS

<IRS
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

Units: List of elements

Description of IRS deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

Mosquito deterrent

→ scenario → interventions → timed → intervention → VectorAvailability

<VectorAvailability
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

Units: List of elements

Description of a mosquito deterrent deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

IPTi deployment

→ scenario → interventions → timed → intervention → ipti

<ipti
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

Immune suppression deployment

→ scenario → interventions → timed → intervention → immuneSuppression

<immuneSuppression
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  />

Documentation (element)

Units: List of elements

Removes all exposure-related immunity gained over time by hosts without removing infections.

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Insert R_0 case

→ scenario → interventions → timed → intervention → insertR_0Case

<insertR_0Case/>

Documentation (element)

Units: List of elements

Uninfect vectors

→ scenario → interventions → timed → intervention → uninfectVectors

<uninfectVectors/>

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

Simple larviciding intervention

→ scenario → interventions → timed → intervention → larviciding

<larviciding>
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

anopheles

Documentation (element)

Units: List of elements

Simple larviciding intervention description.

anopheles

→ scenario → interventions → timed → intervention → larviciding → anopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

Mosquito to be larvicided

mosquito=string

Mosquito to be larvicided

Proportionate reduction in emergence

effectiveness=double

Units: none Min: 0 Max: 1

Proportional reduction in emergence rate

Duration of activity

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

Mass Cohort Selection

→ scenario → interventions → timed → intervention → cohort

<cohort
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

Units: List of elements

Description of mass cohort selection.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

Health system description

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (element)

Units: List of elements

Description of health system.

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entoData

<entoData
    name=string
    mode=("2" or "4")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Attributes

Entomology dataset

name=string

Units: string

Name of entomology data

Transmission simulation mode

mode=("2" or "4")

Units: Code

Override annual EIR

annualEIR=double

Units: Infectious bites per adult per year

If set, overrides the annual EIR by scaling it to this level. If ommitted, EIR levels are as specified elsewhere.

Transmission setting (vector control not enabled)

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Units: List of elements

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Units: List of elements

Parameters of the transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <eir ... /> 
| |   <monthlyEir ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Identifier for this anopheles species

Initial guess of proportion of mosquitoes infected

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial guess of proportion of mosquitoes infectious

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Fourier approximation to pre-intervention EIR

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    b1=double
    a2=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Infectious bites per adult per day

Attributes

a0 parameter of Fourier approximation to ln(EIR)

a0=double

a0 parameter of Fourier approximation to ln(EIR)

a1 parameter of Fourier approximation to ln(EIR)

a1=double

a1 parameter of Fourier approximation to ln(EIR)

b1 parameter of Fourier approximation to ln(EIR)

b1=double

b1 parameter of Fourier approximation to ln(EIR)

a2 parameter of Fourier approximation to ln(EIR)

a2=double

a2 parameter of Fourier approximation to ln(EIR)

b2 parameter of Fourier approximation to ln(EIR)

b2=double

b2 parameter of Fourier approximation to ln(EIR)

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: radians

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

Monthly values for pre-intervention EIR

→ scenario → entoData → vector → anopheles → monthlyEir

<monthlyEir
    annualEIR=double
  >
IN THIS ORDER:
| ( <item ... /> ){12,12}
</monthlyEir>

item

Documentation (element)

Units: Infectious bites per adult per month

Attributes

Annual EIR

annualEIR=double

Units: Infectious bites per adult per year Min: 0

Scales the monthly values to give this annual innoculation rate.

Monthly pre-intervention EIR

→ scenario → entoData → vector → anopheles → monthlyEir → item

<item>
    double
</item>

Documentation (element)

Units: Inoculations per person per month

Inoculations per person per month

Vector Species

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqLaidEggsSameDayProportion=double
    mosqSeekingDuration=double
    mosqSurvivalFeedingCycleProbability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
    mosqHumanBloodIndex=double
    minInfectedThreshold=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

Duration of the resting period of the vector (days)

mosqRestDuration=int

name:Duration of the resting period of the vector (days);

Extrinsic incubation period (days)

extrinsicIncubationPeriod=int

name:Extrinsic incubation period (days)

Proportion of mosquitoes host seeking on same day as ovipositing

mosqLaidEggsSameDayProportion=double

Proportion of mosquitoes host seeking on same day as ovipositing

Duration of the host-seeking period of the vector (days)

mosqSeekingDuration=double

Duration of the host-seeking period of the vector (days)

Probability that the mosquito survives the feeding cycle

mosqSurvivalFeedingCycleProbability=double

Probability that the mosquito survives the feeding cycle

Probability that the mosquito succesfully bites chosen host

mosqProbBiting=double

Probability that the mosquito succesfully bites chosen host

Probability that the mosquito escapes host and finds a resting place after biting

mosqProbFindRestSite=double

Probability that the mosquito escapes host and finds a resting place after biting

Probability of mosquito successfully resting after finding a resting site

mosqProbResting=double

Probability of mosquito successfully resting after finding a resting site

Probability of a mosquito successfully laying eggs given that it has rested

mosqProbOvipositing=double

Probability of a mosquito successfully laying eggs given that it has rested

Human blood index

mosqHumanBloodIndex=double

The proportion of resting mosquitoes which fed on human blood during the last feed.

Min infected threshold

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
    mosqRelativeEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Identifier for this category of non-human hosts

Relative availability of nonhuman hosts of type i (to other nonhuman hosts)

mosqRelativeEntoAvailability=double

Relative availability of nonhuman hosts of type i (to other nonhuman hosts)

Probability of mosquito successfully biting host

mosqProbBiting=double

Probability of mosquito successfully biting host

Probability that the mosquito escapes host and finds a resting place after biting

mosqProbFindRestSite=double

Probability that the mosquito escapes host and finds a resting place after biting

Probability of mosquito successfully resting after finding a resting site

mosqProbResting=double

Probability of mosquito successfully resting after finding a resting site

nonHumanHosts

→ scenario → entoData → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Units: List of elements

Name of this species of non human hosts (must match up with those described per anopheles section)

number

number=double

Pharmacokinetics and pharmacodynamics

<drugDescription>
IN THIS ORDER:
| ( <drug ... /> )+
</drugDescription>

drug

Documentation (element)

Units: List of elements

Drug model parameters

Library of drug parameters

→ scenario → drugDescription → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (element)

Sequence of drug descriptions forming a library of drug parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → drugDescription → drug → PD

<PD>
IN THIS ORDER:
| ( <allele ... /> )+
</PD>

allele

PD parameters per allele

→ scenario → drugDescription → drug → PD → allele

<allele
    name=string
  >
IN THIS ORDER:
|   <initial_frequency ... /> 
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</allele>

Documentation (element)

PD parameters per allele, plus initial frequency of each allele.

Note: we assume a one-to-one correspondance of drugs to loci, hence each drug has an independent set of alleles here.

Attributes

name

name=string

Relative frequency

→ scenario → drugDescription → drug → PD → allele → initial_frequency

<initial_frequency>
    double
</initial_frequency>

Documentation (element)

Units: relative frequency Min: 0

Frequency, relative to the total frequency of all alleles for this drug/locus.

Maximal parasite killing rate

→ scenario → drugDescription → drug → PD → allele → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → drugDescription → drug → PD → allele → IC50

<IC50>
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

Slope of effect curve

→ scenario → drugDescription → drug → PD → allele → slope

<slope>
    double
</slope>

Documentation (element)

Units: no units

n — Slope of the concentration effect curve

PK

→ scenario → drugDescription → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
|   <half_life ... /> 
|   <vol_dist ... /> 
</PK>

Drug concentration considered negligible

→ scenario → drugDescription → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → drugDescription → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate (which is: ln(2) / half_life).

Volume of Distribution

→ scenario → drugDescription → drug → PK → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Model options and parameters

→ scenario → model

<model>
IN THIS ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
|   <parameters ... /> 
</model>

Documentation (element)

Units: List of elements

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

Units: List of elements

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: include/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=int
  >
IN THIS ORDER:
| [ <NonMalariaFevers ... /> ]
</clinical>

NonMalariaFevers

Documentation (type)

Units: List of elements

Description of clinical parameters.

This is related to the health-system description, but contains data which can't be changed as part of an intervention and is not restricted to treatment.

Attributes

Follow-up period during which recurrence is treated as a failure

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
|   <prNeedTreatmentNMF ... /> 
|   <prNeedTreatmentMF ... /> 
</NonMalariaFevers>

Documentation (type)

Description of non-malaria fever incidence. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: none Min: 0 Max: 1

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | NMF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentNMF

<prNeedTreatmentNMF
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentNMF>

group

Documentation (element)

Units: none Min: 0 Max: 1

Probability that a non-malaria fever needs treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites may be present).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment | MF)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatmentMF

<prNeedTreatmentMF
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatmentMF>

group

Documentation (element)

Units: none Min: 0 Max: 1

Probability that a malaria fever needs treatment with antibiotics (assuming fever is induced by malaria, although concurrent bacteria may be present).

Meaning partially overlaps with separate model for comorbidity given malaria.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

By age group data on availability of humans to mosquitoes relative to an adult.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Units: List of elements

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → model → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 25 documentation

Generated from: scenario_25.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    name=string
    wuID=int
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_25.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entoData ... /> 
| [ <drugDescription ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Units: string

Name of intervention

Work unit identifier

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Attributes

Name of demography data

name=string

Units: string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: years Min: 0 Max: 100

Maximum age of simulated humans in years.

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Percentage of human population in age group

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ cohortOnly=boolean ]
  [ firstBoutOnly=boolean ]
  [ firstTreatmentOnly=boolean ]
  [ firstInfectionOnly=boolean ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Attributes

Name of monitoring information

name=string

Units: string

Name of monitoring data

Survey only cohort

cohortOnly=boolean

Time to first episode only

firstBoutOnly=boolean

Time to first treatment only

firstTreatmentOnly=boolean

Time to first infection only

firstInfectionOnly=boolean

continuous

→ scenario → monitoring → continuous

<continuous
    period=int
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Days between reports

period=int

Units: Days Min: 1 Max: unbounded

Number of timesteps between reports.

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
  [ value=boolean ] DEFAULT VALUE true
  />

Attributes

Model options required

name=string

Options define different model structures. Option name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.

Indicator of whether option is required

value=boolean

Default value: true

Option value (true/false). Each option has a default value used if the option is not listed (usually false but sometimes true).

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time; 0 means just before start of main sim and is a valid survey-point. Reported data is either from a point-time survey (immediate data) or is collected over the previous year (data from previous timesteps-per-year period). Simulation will end immediately after last survey is taken.

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Preventative interventions

<interventions
    name=string
  >
IN THIS ORDER:
|   <descriptions ... /> 
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

Attributes

Intervention

name=string

Units: string

Name of age specific intervention

descriptions

<descriptions>
IN THIS ORDER:
| [ <MDADescription ... /> ]
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| ( <anopheles ... /> )*
</descriptions>

Documentation (element)

Descriptions applying across all uses of an intervention.

Description of MDA

→ scenario → interventions → descriptions → MDADescription

<MDADescription>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</MDADescription>

Documentation (element)

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

decisions

→ scenario → interventions → descriptions → MDADescription → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )*
</decisions>

decision

Documentation (type)

case (uncomplicated only): Returns "UC1" if there is no recent history of a malarial case, or "UC2" if there is.
result: Dependent on decision "test", this performs a parasite density test. Output is one of "none" (no test performed), "positive", "negative".

The following decisions must be described here:

test (uncomplicated only): Outputs must be "none", "microscopy" or "RDT" to describe which test the "result" decision uses.
treatment: Describes which treatment to use. Values aren't restricted but must match up with a treatment described in the corresponding "treatments" section.
hospitalisation (complicated only): none, immediate or delayed.

decision

→ scenario → interventions → descriptions → MDADescription → decisions → decision

<decision
    name=string
    depends=string
    values=string
  >
    string
</decision>

Documentation (type)

A decision describes how to choose between a set of values.

Lexically, it can contain symbols matching "[_.a-zA-Z0-9]+", round brackets: (), braces: {} and colons. Whitespace is ignored except to separate symbols.

For each BRANCH_SET each BRANCH must have the same DECISION. This DECISION must be one of the dependencies mentioned in "depends". This may be:

another decision, in which case the VALUE immediately following in brackets must correspond to one of its output values. The BRANCH_SET immediately containing this BRANCH must represent each output value of the same decision exactly once, and no parent BRANCH_SET may be for the same DECISION.
"p": this indicates a probabilistic decision. In this case the value is a probability, the sum of all values for the BRANCH_SET must be 1 and the decision must be associated directly with OUTCOMEs (not sub-TREEs).
"age": this indicates an age-test. The VALUE must have the form "a-b", indicating that this branch will be taken for individuals aged such that a <= age < b, where a,b are non-negative real numbers or the special value "inf", and a <= b. All VALUEs in the BRANCH_SET must cover all possible (non-negative real) ages, with no overlap (hence, smallest a must be 0 and greatest b must be inf).

Semantically, each OUTCOME must be one of the values associated with this decision.

Attributes

Name of decision

name=string

The name of this decision. The name must match the regular expression "[_a-zA-Z0-9]+"; that is it can only contain letters, digits and _ characters (no spaces, punctuation, etc.).

Preceding decisions

depends=string

Outcome values

values=string

A comma-separated list of outcome values this decision may have. The name of each value must be of the same form as decision names (i.e. only contain letters, digits and _ characters).

treatments

→ scenario → interventions → descriptions → MDADescription → treatments

<treatments>
IN THIS ORDER:
| ( <treatment ... /> )*
</treatments>

treatment

Documentation (type)

Units: string

A list of drug treatment tables. Each should have a name corresponding to one of the "drug" decision's values.

treatment

→ scenario → interventions → descriptions → MDADescription → treatments → treatment

<treatment
    name=string
  >
IN THIS ORDER:
|   <schedule ... /> 
| ( <modifier ... /> )*
</treatment>

Documentation (type)

A description of a base treatment schedule along with modifiers to handle delays, quality variations, etc.

Attributes

Treatment administered

name=string

Units: string

Name corresponding to one of the drug decision's output values.

schedule

→ scenario → interventions → descriptions → MDADescription → treatments → treatment → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

The base (unmodified) schedule of drugs administered for this treatment.

medicate

→ scenario → interventions → descriptions → MDADescription → treatments → treatment → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  [ duration=double ]
  />

Attributes

drug

drug=string

Units: string

Abbreviated name of drug compound

drug dose

mg=double

Units: mg

Quantity of drug compound

time of administration

hour=double

Units: hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

duration of administration

duration=double

Units: hours Min: 0

If this attribute is given, use IV administration instead of orally. Specifies the number of hours over which the dose is administered.

modifier

→ scenario → interventions → descriptions → MDADescription → treatments → treatment → modifier

<modifier
    decision=string
  >
EXACTLY ONE OF:
| ( <multiplyQty ... /> )*
| ( <delay ... /> )*
| ( <selectTimeRange ... /> )*
</modifier>

Documentation (type)

A modifier for this treatment, according to the outputs of a decision.

Attributes

decision

decision=string

Units: string

Specifies the decision that this modifier acts on.

multiplyQty

→ scenario → interventions → descriptions → MDADescription → treatments → treatment → modifier → multiplyQty

<multiplyQty
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Multiplies the quantity of active ingredients of drugs administered.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of multipliers for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0.5,1" the quantity of drug A is halved while that of B is unchanged.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

delay

→ scenario → interventions → descriptions → MDADescription → treatments → treatment → modifier → delay

<delay
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Delays administration of drugs listed in the base schedule by so many hours.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of delays (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0,6", drug A is administered as in the base schedule while drug B is administered 6 hours later than specified.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

selectTimeRange

→ scenario → interventions → descriptions → MDADescription → treatments → treatment → modifier → selectTimeRange

<selectTimeRange
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Selects which drug doses to administer according to time of administration (before times are modified by delays). Half-open interval: [x,y)

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of time-ranges (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. The time-ranges should be of the form x-y and are interpreted as the half-open interval [x,y); that is a drug listed with time t will only be administered if x <= t < y.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

vaccineDescription

→ scenario → interventions → descriptions → vaccineDescription

<vaccineDescription
    vaccineType=("PEV" or "BSV" or "TBV")
  >
IN THIS ORDER:
|   <decay ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

Type of vaccine

vaccineType=("PEV" or "BSV" or "TBV")

Units: Code

Type of vaccine

Decay of effect

→ scenario → interventions → descriptions → vaccineDescription → decay

<decay
    function=("constant" or "linear" or "exponential" or "weibull" or "hill" or "chitnis")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
  />

Documentation (element)

Specification of decay of efficacy

Documentation (type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "linear" or "exponential" or "weibull" or "hill" or "chitnis")

Units: None Min: 0 Max: 1

Determines which decay function to use. Available decay functions, for age t in years: constant: initial linear: initial * (1 - t/L) exponential: initial * exp( - t/L * log(2) ) weibull: initial * exp( -(t/L)^k * log(2) ) hill: initial / (1 + (t/L)^k) chitnis: initial * exp( k - k / (1 - (t/L)^2) ) for t less than L, 0 for t greater than or equal to L.

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Variance parameter for vaccine efficacy

→ scenario → interventions → descriptions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

initialEfficacy

→ scenario → interventions → descriptions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

iptiDescription

→ scenario → interventions → descriptions → iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → descriptions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

Age specific intervention

name=string

Units: string

Name of age specific intervention

Frequency

freq=double

Frequency of parasite genotype

ACR

ACR=double

Adequate clinical response (proportion)

Prophylactic period

proph=int

Prophylactic period

Tolerance period

tolPeriod=int

Tolerance period

atten=double

Tolerance period

anopheles

→ scenario → interventions → descriptions → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <VADescription ... /> ]
</anopheles>

Attributes

Entomological effects of interventions

mosquito=string

Description of the entomological effects of interventions

ITNDescription

→ scenario → interventions → descriptions → anopheles → ITNDescription

<ITNDescription>
IN THIS ORDER:
|   <deterrency ... /> 
</ITNDescription>

Deterrency

→ scenario → interventions → descriptions → anopheles → ITNDescription → deterrency

<deterrency
    function=("constant" or "linear" or "exponential" or "weibull" or "hill" or "chitnis")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
    initial=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of decay or survival of a parameter along with initial value.

Documentation (base type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "linear" or "exponential" or "weibull" or "hill" or "chitnis")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

Pre-prandial killing effect

→ scenario → interventions → descriptions → anopheles → ITNDescription → preprandialKillingEffect

<preprandialKillingEffect
    function=("constant" or "linear" or "exponential" or "weibull" or "hill" or "chitnis")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
    initial=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Documentation (type)

Specification of decay or survival of a parameter along with initial value.

Documentation (base type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "linear" or "exponential" or "weibull" or "hill" or "chitnis")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

Post-prandial killing effect

→ scenario → interventions → descriptions → anopheles → ITNDescription → postprandialKillingEffect

<postprandialKillingEffect
    function=("constant" or "linear" or "exponential" or "weibull" or "hill" or "chitnis")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
    initial=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Documentation (type)

Specification of decay or survival of a parameter along with initial value.

Documentation (base type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "linear" or "exponential" or "weibull" or "hill" or "chitnis")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

IRSDescription

→ scenario → interventions → descriptions → anopheles → IRSDescription

<IRSDescription>
IN THIS ORDER:
|   <deterrency ... /> 
</IRSDescription>

killing effect

→ scenario → interventions → descriptions → anopheles → IRSDescription → killingEffect

<killingEffect
    function=("constant" or "linear" or "exponential" or "weibull" or "hill" or "chitnis")
    L=double
  [ k=double ] DEFAULT VALUE 1.0
    initial=double
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Documentation (type)

Specification of decay or survival of a parameter along with initial value.

Documentation (base type)

Specification of decay or survival of a parameter.

Attributes

function

function=("constant" or "linear" or "exponential" or "weibull" or "hill" or "chitnis")

Units: None Min: 0 Max: 1

L

L=double

Units: Years Min: 0

k

k=double

Units: none Min: 0

Default value: 1.0

Shape parameter of distribution. If not specified, default value of 1 is used. Meaning depends on function; not used in some cases.

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

VADescription

→ scenario → interventions → descriptions → anopheles → VADescription

<VADescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</VADescription>

deterrency

Attributes

Name of intervention

name=string

Units: string

Name of intervention

Continuously applied interventions

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
| ( <cohort ... /> )*
</continuous>

List of age groups for vaccination

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Description of ITN deployment

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

List of age groups for IPTi

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Continuous cohort selection

→ scenario → interventions → continuous → cohort

<cohort
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

Description of continuous selection of individuals for a cohort study.

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Timed interventions

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfectionsPerThousandHosts ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <VectorAvailability ... /> ]
| [ <ipti ... /> ]
| [ <immuneSuppression ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <larviciding ... /> ]
| [ <cohort ... /> ]
</intervention>

Attributes

Time step of intervention

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
| [ <NonMalariaFevers ... /> ]
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</uncomplicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</complicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
|   <pImmediateUC ... /> 
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: days Min: 0 Max: unbounded

Maximum number of timesteps (including first of case) an individual will remember they are sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial/non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of a complicated/severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Probability of immediate UC treatment seeking

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → pImmediateUC

<pImmediateUC>
    double
</pImmediateUC>

Documentation (element)

Units: none Min: 0 Max: 1

Probability that UC treatment seeking will be done immediately when sick, on second day given that it wasn't done on first, etc.

NonMalariaFevers

→ scenario → healthSystem → EventScheduler → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <prTreatment ... /> 
|   <effectNegativeTest ... /> 
|   <effectPositiveTest ... /> 
|   <effectNeed ... /> 
|   <effectInformal ... /> 
|   <CFR ... /> 
|   <TreatmentEfficacy ... /> 
</NonMalariaFevers>

Documentation (type)

P(treatment|no diagnostic)

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → prTreatment

<prTreatment>
    double
</prTreatment>

Documentation (element)

Units: none Min: 0 Max: 1

Probability of a non-malaria fever being treated with an antibiotic given that no malaria diagnostic was used but independent of need. Symbol: P₀.

Effect of a negative test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNegativeTest

<effectNegativeTest>
    double
</effectNegativeTest>

Documentation (element)

The effect of a negative malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₁).

Effect of a positive test

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectPositiveTest

<effectPositiveTest>
    double
</effectPositiveTest>

Documentation (element)

The effect of a positive malaria diagnostic on the odds ratio of receiving antibiotics. Symbol: exp(β₂).

Effect of need

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectNeed

<effectNeed>
    double
</effectNeed>

Documentation (element)

The effect of needing antibiotic treatment on the odds ratio of receiving antibiotics. Symbol: exp(β₃).

Effect of informal provider

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → effectInformal

<effectInformal>
    double
</effectInformal>

Documentation (element)

The effect of seeking treatment from an informal provider (i.e. a provider untrained in NMF diagnosis) on the odds ratio of receiving antibiotics. Symbol: exp(β₄)

Case fatality rate

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → CFR

<CFR
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Units: none Min: 0 Max: 1

Base case fatality rate for non-malaria fevers (probability of death from a fever requiring antibiotic treatment given that no antibiotic treatment is received, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Treatment efficacy

→ scenario → healthSystem → EventScheduler → NonMalariaFevers → TreatmentEfficacy

<TreatmentEfficacy>
    double
</TreatmentEfficacy>

Documentation (element)

Units: none Min: 0 Max: 1

Probability that treatment would prevent a death (i.e. CFR is multiplied by one minus this when treatment occurs).

ImmediateOutcomes

<ImmediateOutcomes
    name=string
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
</ImmediateOutcomes>

Documentation (type)

Units: List of elements

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Case Management model

name=string

Units: string

Name of health system

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

ACT

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

QN

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

Probability that a patient with uncomplicated disease seeks official care immediately

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease self-treats

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

CFR

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients, during a severe bout.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Replacement transmission setting (vector control not enabled)

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (element)

Units: List of elements

New description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

EIRDaily

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Import infections

→ scenario → interventions → timed → intervention → importedInfectionsPerThousandHosts

<importedInfectionsPerThousandHosts>
    double
</importedInfectionsPerThousandHosts>

Documentation (element)

Units: Number per 1000 hosts Min: 0

Import infections (as if a mosquito bites a human). Imported via a Bernoulli trial per host.

Mass Drug Administration

→ scenario → interventions → timed → intervention → MDA

<MDA
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Vaccination

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

ITN deployment

→ scenario → interventions → timed → intervention → ITN

<ITN
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

IRS deployment

→ scenario → interventions → timed → intervention → IRS

<IRS
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

Units: List of elements

Description of IRS deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

Mosquito deterrent

→ scenario → interventions → timed → intervention → VectorAvailability

<VectorAvailability
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

Units: List of elements

Description of a mosquito deterrent deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

IPTi deployment

→ scenario → interventions → timed → intervention → ipti

<ipti
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

Immune suppression deployment

→ scenario → interventions → timed → intervention → immuneSuppression

<immuneSuppression
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  />

Documentation (element)

Units: List of elements

Removes all exposure-related immunity gained over time by hosts without removing infections.

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Insert R_0 case

→ scenario → interventions → timed → intervention → insertR_0Case

<insertR_0Case/>

Documentation (element)

Units: List of elements

Uninfect vectors

→ scenario → interventions → timed → intervention → uninfectVectors

<uninfectVectors/>

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

larviciding

→ scenario → interventions → timed → intervention → larviciding

<larviciding>
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

anopheles

Documentation (element)

Simple larviciding intervention description.

anopheles

→ scenario → interventions → timed → intervention → larviciding → anopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

Mosquito to be larvicided

mosquito=string

Mosquito to be larvicided

Proportionate reduction in emergence

effectiveness=double

Units: none Min: 0 Max: 1

Proportional reduction in emergence rate

Duration of activity

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

Mass Cohort Selection

→ scenario → interventions → timed → intervention → cohort

<cohort
  [ maxAge=double ] DEFAULT VALUE 100
  [ minAge=double ] DEFAULT VALUE 0
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ cumulativeWithMaxAge=double ]
  />

Documentation (element)

Units: List of elements

Description of mass cohort selection.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Default value: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Default value: 0

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort.

Cumulative deployment: maximum age

cumulativeWithMaxAge=double

Units: Years Min: 0

healthSystem

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entoData

<entoData
    name=string
    mode=("2" or "4")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Attributes

Entomology dataset

name=string

Units: string

Name of entomology data

Transmission simulation mode

mode=("2" or "4")

Units: Code

Override annual EIR

annualEIR=double

Units: Infectious bites per adult per year

If set, overrides the annual EIR by scaling it to this level. If ommitted, EIR levels are as specified elsewhere.

Transmission setting (vector control not enabled)

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Units: List of elements

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Units: List of elements

Parameters of the transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <eir ... /> 
| |   <monthlyEir ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Initial guess of proportion of mosquitoes infected

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial guess of proportion of mosquitoes infectious

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Fourier approximation to pre-intervention EIR

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    b1=double
    a2=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Infectious bites per adult per day

Attributes

a0 parameter of Fourier approximation to ln(EIR)

a0=double

a1 parameter of Fourier approximation to ln(EIR)

a1=double

b1 parameter of Fourier approximation to ln(EIR)

b1=double

a2 parameter of Fourier approximation to ln(EIR)

a2=double

b2 parameter of Fourier approximation to ln(EIR)

b2=double

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: radians

Monthly values for pre-intervention EIR

→ scenario → entoData → vector → anopheles → monthlyEir

<monthlyEir
    annualEIR=double
  >
IN THIS ORDER:
| ( <item ... /> ){12,12}
</monthlyEir>

item

Documentation (element)

Units: Infectious bites per adult per month

Attributes

Annual EIR

annualEIR=double

Units: Infectious bites per adult per year Min: 0

Scales the monthly values to give this annual innoculation rate.

Monthly pre-intervention EIR

→ scenario → entoData → vector → anopheles → monthlyEir → item

<item>
    double
</item>

Vector Species

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqLaidEggsSameDayProportion=double
    mosqSeekingDuration=double
    mosqSurvivalFeedingCycleProbability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
    mosqHumanBloodIndex=double
    minInfectedThreshold=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

Duration of the resting period of the vector (days)

mosqRestDuration=int

Extrinsic incubation period (days)

extrinsicIncubationPeriod=int

Proportion of mosquitoes host seeking on same day as ovipositing

mosqLaidEggsSameDayProportion=double

Duration of the host-seeking period of the vector (days)

mosqSeekingDuration=double

Probability that the mosquito survives the feeding cycle

mosqSurvivalFeedingCycleProbability=double

Probability that the mosquito succesfully bites chosen host

mosqProbBiting=double

Probability that the mosquito escapes host and finds a resting place after biting

mosqProbFindRestSite=double

Probability of mosquito successfully resting after finding a resting site

mosqProbResting=double

Probability of a mosquito successfully laying eggs given that it has rested

mosqProbOvipositing=double

Human blood index

mosqHumanBloodIndex=double

The proportion of resting mosquitoes which fed on human blood during the last feed.

Min infected threshold

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
    mosqRelativeEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Relative availability of nonhuman hosts of type i (to other nonhuman hosts)

mosqRelativeEntoAvailability=double

Probability of mosquito successfully biting host

mosqProbBiting=double

Probability that the mosquito escapes host and finds a resting place after biting

mosqProbFindRestSite=double

Probability of mosquito successfully resting after finding a resting site

mosqProbResting=double

nonHumanHosts

→ scenario → entoData → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Units: List of elements

Name of this species of non human hosts (must match up with those described per anopheles section)

number

number=double

Pharmacokinetics and pharmacodynamics

<drugDescription>
IN THIS ORDER:
| ( <drug ... /> )+
</drugDescription>

drug

Documentation (element)

Units: List of elements

Drug model parameters

drug

→ scenario → drugDescription → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (element)

Sequence of drug descriptions forming a library of drug parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → drugDescription → drug → PD

<PD>
IN THIS ORDER:
| ( <allele ... /> )+
</PD>

allele

allele

→ scenario → drugDescription → drug → PD → allele

<allele
    name=string
  >
IN THIS ORDER:
|   <initial_frequency ... /> 
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</allele>

Documentation (element)

PD parameters per allele, plus initial frequency of each allele.

Note: we assume a one-to-one correspondance of drugs to loci, hence each drug has an independent set of alleles here.

Attributes

name

name=string

Relative frequency

→ scenario → drugDescription → drug → PD → allele → initial_frequency

<initial_frequency>
    double
</initial_frequency>

Documentation (element)

Units: relative frequency Min: 0

Frequency, relative to the total frequency of all alleles for this drug/locus.

Maximal parasite killing rate

→ scenario → drugDescription → drug → PD → allele → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → drugDescription → drug → PD → allele → IC50

<IC50>
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

Slope of effect curve

→ scenario → drugDescription → drug → PD → allele → slope

<slope>
    double
</slope>

Documentation (element)

Units: no units

n — Slope of the concentration effect curve

PK

→ scenario → drugDescription → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
|   <half_life ... /> 
|   <vol_dist ... /> 
</PK>

Drug concentration considered negligible

→ scenario → drugDescription → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → drugDescription → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate (which is: ln(2) / half_life).

Volume of Distribution

→ scenario → drugDescription → drug → PK → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Model options and parameters

→ scenario → model

<model>
IN THIS ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
|   <parameters ... /> 
</model>

Documentation (element)

Units: List of elements

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

Units: List of elements

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: include/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=int
  >
IN THIS ORDER:
| [ <NonMalariaFevers ... /> ]
</clinical>

NonMalariaFevers

Documentation (type)

Units: List of elements

Description of clinical parameters.

This is related to the health-system description, but contains data which can't be changed as part of an intervention and is not restricted to treatment.

Attributes

Follow-up period during which recurrence is treated as a failure

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

NonMalariaFevers

→ scenario → model → clinical → NonMalariaFevers

<NonMalariaFevers>
IN THIS ORDER:
|   <incidence ... /> 
|   <prNeedTreatment ... /> 
</NonMalariaFevers>

Documentation (type)

Description of non-malaria fever incidence. Non-malaria fevers are only modelled if the NON_MALARIA_FEVERS option is used.

P(NMF)

→ scenario → model → clinical → NonMalariaFevers → incidence

<incidence
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</incidence>

group

Documentation (element)

Units: none Min: 0 Max: 1

Probability that a non-malaria fever occurs given that no concurrent malaria fever occurs.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

P(need treatment)

→ scenario → model → clinical → NonMalariaFevers → prNeedTreatment

<prNeedTreatment
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</prNeedTreatment>

group

Documentation (element)

Units: none Min: 0 Max: 1

Probability that a non-malaria fever needs treatment with antibiotics (assuming fever is not induced by malaria, although concurrent parasites are possible).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

By age group data on availability of humans to mosquitoes relative to an adult.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Units: List of elements

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → model → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 24 documentation

Generated from: scenario_24.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    name=string
    wuID=int
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_24.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entoData ... /> 
| [ <drugDescription ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Units: string

Name of intervention

Work unit identifier

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Attributes

Name of demography data

name=string

Units: string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: years Min: 0 Max: 100

Maximum age of simulated humans in years.

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Percentage of human population in age group

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ cohortOnly=boolean ]
  [ firstBoutOnly=boolean ]
  [ firstTreatmentOnly=boolean ]
  [ firstInfectionOnly=boolean ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Attributes

Name of monitoring information

name=string

Units: string

Name of monitoring data

Survey only cohort

cohortOnly=boolean

Time to first episode only

firstBoutOnly=boolean

Time to first treatment only

firstTreatmentOnly=boolean

Time to first infection only

firstInfectionOnly=boolean

continuous

→ scenario → monitoring → continuous

<continuous
    period=int
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Days between reports

period=int

Units: Days Min: 1 Max: unbounded

Number of timesteps between reports.

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
    value=boolean
  />

Attributes

Model options required

name=string

Options define different model structures. Option name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.

Indicator of whether option is required

value=boolean

Option value (true/false). Each option has a default value used if the option is not listed (usually false but sometimes true).

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time; 0 means just before start of main sim and is a valid survey-point. Reported data is either from a point-time survey (immediate data) or is collected over the previous year (data from previous timesteps-per-year period). Simulation will end immediately after last survey is taken.

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Preventative interventions

<interventions
    name=string
  >
IN THIS ORDER:
|   <descriptions ... /> 
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

Attributes

Intervention

name=string

Units: string

Name of age specific intervention

descriptions

<descriptions>
IN THIS ORDER:
| [ <MDADescription ... /> ]
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| ( <anopheles ... /> )*
</descriptions>

Documentation (element)

Descriptions applying across all uses of an intervention.

Drug dose(s) used in MDA

→ scenario → interventions → descriptions → MDADescription

<MDADescription>
IN THIS ORDER:
| [ <schedule ... /> ]
</MDADescription>

schedule

Documentation (element)

Units: List of medicate elements

Description of drug dose(s) used in a mass-drug-administration intervention.

When using the new (Event Scheduler) case management model, a treatment schedule must be present.

schedule

→ scenario → interventions → descriptions → MDADescription → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

The base (unmodified) schedule of drugs administered for this treatment.

medicate

→ scenario → interventions → descriptions → MDADescription → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  [ duration=double ]
  />

Attributes

drug

drug=string

Units: string

Abbreviated name of drug compound

drug dose

mg=double

Units: mg

Quantity of drug compound

time of administration

hour=double

Units: hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

duration of administration

duration=double

Units: hours Min: 0

If this attribute is given, use IV administration instead of orally. Specifies the number of hours over which the dose is administered.

vaccineDescription

→ scenario → interventions → descriptions → vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

Type of vaccine

vaccineType=int

Units: Code

Type of vaccine

Half life of drug effect

→ scenario → interventions → descriptions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Variance parameter for vaccine efficacy

→ scenario → interventions → descriptions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

initialEfficacy

→ scenario → interventions → descriptions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

iptiDescription

→ scenario → interventions → descriptions → iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → descriptions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

Age specific intervention

name=string

Units: string

Name of age specific intervention

Frequency

freq=double

Frequency of parasite genotype

ACR

ACR=double

Adequate clinical response (proportion)

Prophylactic period

proph=int

Prophylactic period

Tolerance period

tolPeriod=int

Tolerance period

atten=double

Tolerance period

anopheles

→ scenario → interventions → descriptions → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <VADescription ... /> ]
</anopheles>

Attributes

Entomological effects of interventions

mosquito=string

Description of the entomological effects of interventions

ITNDescription

→ scenario → interventions → descriptions → anopheles → ITNDescription

<ITNDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</ITNDescription>

Attributes

ITN effects

name=string

Units: string

Name of Insecticide Treated Net intervention

Deterrency

→ scenario → interventions → descriptions → anopheles → ITNDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability (before decay).

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

Pre-prandial killing effect

→ scenario → interventions → descriptions → anopheles → ITNDescription → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

Post-prandial killing effect

→ scenario → interventions → descriptions → anopheles → ITNDescription → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

IRSDescription

→ scenario → interventions → descriptions → anopheles → IRSDescription

<IRSDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <killingEffect ... /> 
</IRSDescription>

Attributes

name of IRS intervention

name=string

Units: string

Name of Indoor Residual Spraying intervention

Deterrency

→ scenario → interventions → descriptions → anopheles → IRSDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

killing effect

→ scenario → interventions → descriptions → anopheles → IRSDescription → killingEffect

<killingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

VADescription

→ scenario → interventions → descriptions → anopheles → VADescription

<VADescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</VADescription>

deterrency

Attributes

Name of mosquito deterrency intervention

name=string

Units: string

Name of mosquito deterrency intervention

Deterrency

→ scenario → interventions → descriptions → anopheles → VADescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

Continuously applied interventions

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
| ( <cohort ... /> )*
</continuous>

List of age groups for vaccination

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Description of ITN deployment

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

List of age groups for IPTi

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Continuous cohort selection

→ scenario → interventions → continuous → cohort

<cohort
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

Description of continuous selection of individuals for a cohort study.

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Timed interventions

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfectionsPerThousandHosts ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <VectorAvailability ... /> ]
| [ <ipti ... /> ]
| [ <immuneSuppression ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <larviciding ... /> ]
| [ <cohort ... /> ]
</intervention>

Attributes

Time step of intervention

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</uncomplicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

decisions

→ scenario → healthSystem → EventScheduler → uncomplicated → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )*
</decisions>

decision

Documentation (type)

case (uncomplicated only): Returns "UC1" if there is no recent history of a malarial case, or "UC2" if there is.
result: Dependent on decision "test", this performs a parasite density test. Output is one of "none" (no test performed), "positive", "negative".

The following decisions must be described here:

test (uncomplicated only): Outputs must be "none", "microscopy" or "RDT" to describe which test the "result" decision uses.
treatment: Describes which treatment to use. Values aren't restricted but must match up with a treatment described in the corresponding "treatments" section.
hospitalisation (complicated only): none, immediate or delayed.

decision

→ scenario → healthSystem → EventScheduler → uncomplicated → decisions → decision

<decision
    name=string
    depends=string
    values=string
  >
    string
</decision>

Documentation (type)

A decision describes how to choose between a set of values.

Lexically, it can contain symbols matching "[_.a-zA-Z0-9]+", round brackets: (), braces: {} and colons. Whitespace is ignored except to separate symbols.

For each BRANCH_SET each BRANCH must have the same DECISION. This DECISION must be one of the dependencies mentioned in "depends". This may be:

another decision, in which case the VALUE immediately following in brackets must correspond to one of its output values. The BRANCH_SET immediately containing this BRANCH must represent each output value of the same decision exactly once, and no parent BRANCH_SET may be for the same DECISION.
"p": this indicates a probabilistic decision. In this case the value is a probability, the sum of all values for the BRANCH_SET must be 1 and the decision must be associated directly with OUTCOMEs (not sub-TREEs).
"age": this indicates an age-test. The VALUE must have the form "a-b", indicating that this branch will be taken for individuals aged such that a <= age < b, where a,b are non-negative real numbers or the special value "inf", and a <= b. All VALUEs in the BRANCH_SET must cover all possible (non-negative real) ages, with no overlap (hence, smallest a must be 0 and greatest b must be inf).

Semantically, each OUTCOME must be one of the values associated with this decision.

Attributes

Name of decision

name=string

The name of this decision. The name must match the regular expression "[_a-zA-Z0-9]+"; that is it can only contain letters, digits and _ characters (no spaces, punctuation, etc.).

Preceding decisions

depends=string

Outcome values

values=string

A comma-separated list of outcome values this decision may have. The name of each value must be of the same form as decision names (i.e. only contain letters, digits and _ characters).

treatments

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments

<treatments>
IN THIS ORDER:
| ( <treatment ... /> )*
</treatments>

treatment

Documentation (type)

Units: string

A list of drug treatment tables. Each should have a name corresponding to one of the "drug" decision's values.

treatment

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment

<treatment
    name=string
  >
IN THIS ORDER:
|   <schedule ... /> 
| ( <modifier ... /> )*
</treatment>

Documentation (type)

A description of a base treatment schedule along with modifiers to handle delays, quality variations, etc.

Attributes

Treatment administered

name=string

Units: string

Name corresponding to one of the drug decision's output values.

schedule

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

The base (unmodified) schedule of drugs administered for this treatment.

modifier

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier

<modifier
    decision=string
  >
EXACTLY ONE OF:
| ( <multiplyQty ... /> )*
| ( <delay ... /> )*
| ( <selectTimeRange ... /> )*
</modifier>

Documentation (type)

A modifier for this treatment, according to the outputs of a decision.

Attributes

decision

decision=string

Units: string

Specifies the decision that this modifier acts on.

multiplyQty

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier → multiplyQty

<multiplyQty
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Multiplies the quantity of active ingredients of drugs administered.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of multipliers for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0.5,1" the quantity of drug A is halved while that of B is unchanged.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

delay

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier → delay

<delay
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Delays administration of drugs listed in the base schedule by so many hours.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of delays (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0,6", drug A is administered as in the base schedule while drug B is administered 6 hours later than specified.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

selectTimeRange

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier → selectTimeRange

<selectTimeRange
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Selects which drug doses to administer according to time of administration (before times are modified by delays). Half-open interval: [x,y)

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of time-ranges (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. The time-ranges should be of the form x-y and are interpreted as the half-open interval [x,y); that is a drug listed with time t will only be administered if x <= t < y.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</complicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
|   <pImmediateUC ... /> 
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: days Min: 0 Max: unbounded

Maximum number of timesteps (including first of case) an individual will remember they are sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial/non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of a complicated/severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Probability of immediate UC treatment seeking

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → pImmediateUC

<pImmediateUC>
    double
</pImmediateUC>

Documentation (element)

Units: none Min: 0 Max: 1

Probability that UC treatment seeking will be done immediately when sick, on second day given that it wasn't done on first, etc.

ImmediateOutcomes

<ImmediateOutcomes
    name=string
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
</ImmediateOutcomes>

Documentation (type)

Units: List of elements

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Case Management model

name=string

Units: string

Name of health system

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

ACT

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

QN

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

Probability that a patient with uncomplicated disease seeks official care immediately

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease self-treats

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

CFR

→ scenario → healthSystem → CFR

<CFR
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

age group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Documentation (element)

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Probabilities of sequelae in inpatients

<pSequelaeInpatient
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients, during a severe bout.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Replacement transmission setting (vector control not enabled)

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (element)

Units: List of elements

New description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

EIRDaily

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Infectious bites per adult per day

Attributes

Time origin of EIR sequence

origin=string

Import infections

→ scenario → interventions → timed → intervention → importedInfectionsPerThousandHosts

<importedInfectionsPerThousandHosts>
    double
</importedInfectionsPerThousandHosts>

Documentation (element)

Units: Number per 1000 hosts Min: 0

Import infections (as if a mosquito bites a human). Imported via a Bernoulli trial per host.

Mass Drug Administration

→ scenario → interventions → timed → intervention → MDA

<MDA
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

Vaccination

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

ITN deployment

→ scenario → interventions → timed → intervention → ITN

<ITN
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

IRS deployment

→ scenario → interventions → timed → intervention → IRS

<IRS
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of IRS deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

Mosquito deterrent

→ scenario → interventions → timed → intervention → VectorAvailability

<VectorAvailability
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of a mosquito deterrent deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

IPTi deployment

→ scenario → interventions → timed → intervention → ipti

<ipti
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

Immune suppression deployment

→ scenario → interventions → timed → intervention → immuneSuppression

<immuneSuppression
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Removes all exposure-related immunity gained over time by hosts without removing infections.

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

Insert R_0 case

→ scenario → interventions → timed → intervention → insertR_0Case

<insertR_0Case/>

Documentation (element)

Units: List of elements

Uninfect vectors

→ scenario → interventions → timed → intervention → uninfectVectors

<uninfectVectors/>

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

larviciding

→ scenario → interventions → timed → intervention → larviciding

<larviciding>
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

anopheles

Documentation (element)

Simple larviciding intervention description.

anopheles

→ scenario → interventions → timed → intervention → larviciding → anopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

Mosquito to be larvicided

mosquito=string

Mosquito to be larvicided

Proportionate reduction in emergence

effectiveness=double

Units: none Min: 0 Max: 1

Proportional reduction in emergence rate

Duration of activity

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

Mass Cohort Selection

→ scenario → interventions → timed → intervention → cohort

<cohort
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of mass cohort selection.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

healthSystem

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entoData

<entoData
    name=string
    mode=("2" or "4")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Attributes

Entomology dataset

name=string

Units: string

Name of entomology data

Transmission simulation mode

mode=("2" or "4")

Units: Code

Override annual EIR

annualEIR=double

Units: Infectious bites per adult per year

If set, overrides the annual EIR by scaling it to this level. If ommitted, EIR levels are as specified elsewhere.

Transmission setting (vector control not enabled)

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Units: List of elements

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Units: List of elements

Parameters of the transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <eir ... /> 
| |   <monthlyEir ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Initial guess of proportion of mosquitoes infected

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial guess of proportion of mosquitoes infectious

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Fourier approximation to pre-intervention EIR

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    b1=double
    a2=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Infectious bites per adult per day

Attributes

a0 parameter of Fourier approximation to ln(EIR)

a0=double

a1 parameter of Fourier approximation to ln(EIR)

a1=double

b1 parameter of Fourier approximation to ln(EIR)

b1=double

a2 parameter of Fourier approximation to ln(EIR)

a2=double

b2 parameter of Fourier approximation to ln(EIR)

b2=double

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: radians

Monthly values for pre-intervention EIR

→ scenario → entoData → vector → anopheles → monthlyEir

<monthlyEir
    annualEIR=double
  >
IN THIS ORDER:
| ( <item ... /> ){12,12}
</monthlyEir>

item

Documentation (element)

Units: Infectious bites per adult per month

Attributes

Annual EIR

annualEIR=double

Units: Infectious bites per adult per year Min: 0

Scales the monthly values to give this annual innoculation rate.

Monthly pre-intervention EIR

→ scenario → entoData → vector → anopheles → monthlyEir → item

<item>
    double
</item>

Vector Species

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqLaidEggsSameDayProportion=double
    mosqSeekingDuration=double
    mosqSurvivalFeedingCycleProbability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
    mosqHumanBloodIndex=double
    minInfectedThreshold=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

Duration of the resting period of the vector (days)

mosqRestDuration=int

Extrinsic incubation period (days)

extrinsicIncubationPeriod=int

Proportion of mosquitoes host seeking on same day as ovipositing

mosqLaidEggsSameDayProportion=double

Duration of the host-seeking period of the vector (days)

mosqSeekingDuration=double

Probability that the mosquito survives the feeding cycle

mosqSurvivalFeedingCycleProbability=double

Probability that the mosquito succesfully bites chosen host

mosqProbBiting=double

Probability that the mosquito escapes host and finds a resting place after biting

mosqProbFindRestSite=double

Probability of mosquito successfully resting after finding a resting site

mosqProbResting=double

Probability of a mosquito successfully laying eggs given that it has rested

mosqProbOvipositing=double

Human blood index

mosqHumanBloodIndex=double

The proportion of resting mosquitoes which fed on human blood during the last feed.

Min infected threshold

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
    mosqRelativeEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Relative availability of nonhuman hosts of type i (to other nonhuman hosts)

mosqRelativeEntoAvailability=double

Probability of mosquito successfully biting host

mosqProbBiting=double

Probability that the mosquito escapes host and finds a resting place after biting

mosqProbFindRestSite=double

Probability of mosquito successfully resting after finding a resting site

mosqProbResting=double

nonHumanHosts

→ scenario → entoData → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Units: List of elements

Name of this species of non human hosts (must match up with those described per anopheles section)

number

number=double

Pharmacokinetics and pharmacodynamics

<drugDescription>
IN THIS ORDER:
| ( <drug ... /> )+
</drugDescription>

drug

Documentation (element)

Units: List of elements

Drug model parameters

drug

→ scenario → drugDescription → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (element)

Sequence of drug descriptions forming a library of drug parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → drugDescription → drug → PD

<PD>
IN THIS ORDER:
| ( <allele ... /> )+
</PD>

allele

allele

→ scenario → drugDescription → drug → PD → allele

<allele
    name=string
  >
IN THIS ORDER:
|   <initial_frequency ... /> 
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</allele>

Documentation (element)

PD parameters per allele, plus initial frequency of each allele.

Note: we assume a one-to-one correspondance of drugs to loci, hence each drug has an independent set of alleles here.

Attributes

name

name=string

Relative frequency

→ scenario → drugDescription → drug → PD → allele → initial_frequency

<initial_frequency>
    double
</initial_frequency>

Documentation (element)

Units: relative frequency Min: 0

Frequency, relative to the total frequency of all alleles for this drug/locus.

Maximal parasite killing rate

→ scenario → drugDescription → drug → PD → allele → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → drugDescription → drug → PD → allele → IC50

<IC50>
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

Slope of effect curve

→ scenario → drugDescription → drug → PD → allele → slope

<slope>
    double
</slope>

Documentation (element)

Units: no units

n — Slope of the concentration effect curve

PK

→ scenario → drugDescription → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
|   <half_life ... /> 
|   <vol_dist ... /> 
</PK>

Drug concentration considered negligible

→ scenario → drugDescription → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → drugDescription → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate (which is: ln(2) / half_life).

Volume of Distribution

→ scenario → drugDescription → drug → PK → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Model options and parameters

→ scenario → model

<model>
IN THIS ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <human ... /> 
|   <parameters ... /> 
</model>

Documentation (element)

Units: List of elements

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

Units: List of elements

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: include/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=int
  />

Documentation (type)

Units: List of elements

Description of clinical parameters.

This is related to the health-system description, but contains data which can't be changed as part of an intervention and is not restricted to treatment.

Attributes

Follow-up period during which recurrence is treated as a failure

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

human

→ scenario → model → human

<human>
IN THIS ORDER:
|   <availabilityToMosquitoes ... /> 
| [ <weight ... /> ]
</human>

Documentation (type)

Parameters of host models.

Availability to mosquitoes

→ scenario → model → human → availabilityToMosquitoes

<availabilityToMosquitoes
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
  >
IN THIS ORDER:
| ( <group ... /> )+
</availabilityToMosquitoes>

group

Documentation (element)

Units: None Min: 0 Max: 1

By age group data on availability of humans to mosquitoes relative to an adult.

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Weight

→ scenario → model → human → weight

<weight
  [ interpolation=("none" or "linear") ] DEFAULT VALUE linear
    multStdDev=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</weight>

group

Documentation (element)

Units: kg Min: 0

By age group data on human weight (mass).

Attributes

interpolation

interpolation=("none" or "linear")

Units: none

Default value: linear

none: input values are used directly
linear: straight lines (on an age vs. value graph) are used to interpolate data points.

Standard deviation

multStdDev=double

Units: None Min: 0

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Units: List of elements

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → model → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 23 documentation

Generated from: scenario_23.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    name=string
    wuID=int
    assimMode=("0" or "1")
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_23.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entoData ... /> 
| [ <drugDescription ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Units: string

Name of intervention

Work unit identifier

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

Assimilator mode

assimMode=("0" or "1")

Units: Code

Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Attributes

Name of demography data

name=string

Units: string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: years Min: 0 Max: 100

Maximum age of simulated humans in years.

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Percentage of human population in age group

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ cohortOnly=boolean ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Attributes

Name of monitoring information

name=string

Units: string

Name of monitoring data

Survey only cohort

cohortOnly=boolean

continuous

→ scenario → monitoring → continuous

<continuous
    period=int
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Days between reports

period=int

Units: Days Min: 1 Max: unbounded

Number of timesteps between reports.

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
    value=boolean
  />

Attributes

Model options required

name=string

Options define different model structures. Option name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.

Indicator of whether option is required

value=boolean

Option value (true/false). Each option has a default value used if the option is not listed (usually false but sometimes true).

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time; 0 means just before start of main sim and is a valid survey-point. Reported data is either from a point-time survey (immediate data) or is collected over the previous year (data from previous timesteps-per-year period). Simulation will end immediately after last survey is taken.

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Preventative interventions

<interventions
    name=string
  >
IN THIS ORDER:
|   <descriptions ... /> 
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

Attributes

Intervention

name=string

Units: string

Name of age specific intervention

descriptions

<descriptions>
IN THIS ORDER:
| [ <MDADescription ... /> ]
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| ( <anopheles ... /> )*
</descriptions>

Documentation (element)

Descriptions applying across all uses of an intervention.

Drug dose(s) used in MDA

→ scenario → interventions → descriptions → MDADescription

<MDADescription>
IN THIS ORDER:
| [ <schedule ... /> ]
</MDADescription>

schedule

Documentation (element)

Units: List of medicate elements

Description of drug dose(s) used in a mass-drug-administration intervention.

When using the new (Event Scheduler) case management model, a treatment schedule must be present.

schedule

→ scenario → interventions → descriptions → MDADescription → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

The base (unmodified) schedule of drugs administered for this treatment.

medicate

→ scenario → interventions → descriptions → MDADescription → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  [ duration=double ]
  />

Attributes

drug

drug=string

Units: string

Abbreviated name of drug compound

drug dose

mg=double

Units: mg

Quantity of drug compound

time of administration

hour=double

Units: hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

duration of administration

duration=double

Units: hours Min: 0

If this attribute is given, use IV administration instead of orally. Specifies the number of hours over which the dose is administered.

vaccineDescription

→ scenario → interventions → descriptions → vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

Type of vaccine

vaccineType=int

Units: Code

Type of vaccine

Half life of drug effect

→ scenario → interventions → descriptions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Variance parameter for vaccine efficacy

→ scenario → interventions → descriptions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

initialEfficacy

→ scenario → interventions → descriptions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

iptiDescription

→ scenario → interventions → descriptions → iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → descriptions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

Age specific intervention

name=string

Units: string

Name of age specific intervention

Frequency

freq=double

Frequency of parasite genotype

ACR

ACR=double

Adequate clinical response (proportion)

Prophylactic period

proph=int

Prophylactic period

Tolerance period

tolPeriod=int

Tolerance period

atten=double

Tolerance period

anopheles

→ scenario → interventions → descriptions → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <VADescription ... /> ]
</anopheles>

Attributes

Entomological effects of interventions

mosquito=string

Description of the entomological effects of interventions

ITNDescription

→ scenario → interventions → descriptions → anopheles → ITNDescription

<ITNDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</ITNDescription>

Attributes

ITN effects

name=string

Units: string

Name of Insecticide Treated Net intervention

Deterrency

→ scenario → interventions → descriptions → anopheles → ITNDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability (before decay).

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

Pre-prandial killing effect

→ scenario → interventions → descriptions → anopheles → ITNDescription → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

Post-prandial killing effect

→ scenario → interventions → descriptions → anopheles → ITNDescription → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

IRSDescription

→ scenario → interventions → descriptions → anopheles → IRSDescription

<IRSDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <killingEffect ... /> 
</IRSDescription>

Attributes

name of IRS intervention

name=string

Units: string

Name of Indoor Residual Spraying intervention

Deterrency

→ scenario → interventions → descriptions → anopheles → IRSDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

killing effect

→ scenario → interventions → descriptions → anopheles → IRSDescription → killingEffect

<killingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

VADescription

→ scenario → interventions → descriptions → anopheles → VADescription

<VADescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</VADescription>

deterrency

Attributes

Name of mosquito deterrency intervention

name=string

Units: string

Name of mosquito deterrency intervention

Deterrency

→ scenario → interventions → descriptions → anopheles → VADescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

Continuously applied interventions

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
| ( <cohort ... /> )*
</continuous>

List of age groups for vaccination

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Description of ITN deployment

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

List of age groups for IPTi

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Continuous cohort selection

→ scenario → interventions → continuous → cohort

<cohort
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

Description of continuous selection of individuals for a cohort study.

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Timed interventions

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfectionsPerThousandHosts ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <VectorAvailability ... /> ]
| [ <ipti ... /> ]
| [ <immuneSuppression ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <larviciding ... /> ]
| [ <cohort ... /> ]
</intervention>

Attributes

Time step of intervention

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</uncomplicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

decisions

→ scenario → healthSystem → EventScheduler → uncomplicated → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )*
</decisions>

decision

Documentation (type)

case (uncomplicated only): Returns "UC1" if there is no recent history of a malarial case, or "UC2" if there is.
result: Dependent on decision "test", this performs a parasite density test. Output is one of "none" (no test performed), "positive", "negative".

The following decisions must be described here:

test (uncomplicated only): Outputs must be "none", "microscopy" or "RDT" to describe which test the "result" decision uses.
treatment: Describes which treatment to use. Values aren't restricted but must match up with a treatment described in the corresponding "treatments" section.
hospitalisation (complicated only): none, immediate or delayed.

decision

→ scenario → healthSystem → EventScheduler → uncomplicated → decisions → decision

<decision
    name=string
    depends=string
    values=string
  >
    string
</decision>

Documentation (type)

A decision describes how to choose between a set of values.

Lexically, it can contain symbols matching "[_.a-zA-Z0-9]+", round brackets: (), braces: {} and colons. Whitespace is ignored except to separate symbols.

For each BRANCH_SET each BRANCH must have the same DECISION. This DECISION must be one of the dependencies mentioned in "depends". This may be:

another decision, in which case the VALUE immediately following in brackets must correspond to one of its output values. The BRANCH_SET immediately containing this BRANCH must represent each output value of the same decision exactly once, and no parent BRANCH_SET may be for the same DECISION.
"p": this indicates a probabilistic decision. In this case the value is a probability, the sum of all values for the BRANCH_SET must be 1 and the decision must be associated directly with OUTCOMEs (not sub-TREEs).
"age": this indicates an age-test. The VALUE must have the form "a-b", indicating that this branch will be taken for individuals aged such that a <= age < b, where a,b are non-negative real numbers or the special value "inf", and a <= b. All VALUEs in the BRANCH_SET must cover all possible (non-negative real) ages, with no overlap (hence, smallest a must be 0 and greatest b must be inf).

Semantically, each OUTCOME must be one of the values associated with this decision.

Attributes

Name of decision

name=string

The name of this decision. The name must match the regular expression "[_a-zA-Z0-9]+"; that is it can only contain letters, digits and _ characters (no spaces, punctuation, etc.).

Preceding decisions

depends=string

Outcome values

values=string

A comma-separated list of outcome values this decision may have. The name of each value must be of the same form as decision names (i.e. only contain letters, digits and _ characters).

treatments

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments

<treatments>
IN THIS ORDER:
| ( <treatment ... /> )*
</treatments>

treatment

Documentation (type)

Units: string

A list of drug treatment tables. Each should have a name corresponding to one of the "drug" decision's values.

treatment

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment

<treatment
    name=string
  >
IN THIS ORDER:
|   <schedule ... /> 
| ( <modifier ... /> )*
</treatment>

Documentation (type)

A description of a base treatment schedule along with modifiers to handle delays, quality variations, etc.

Attributes

Treatment administered

name=string

Units: string

Name corresponding to one of the drug decision's output values.

schedule

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

The base (unmodified) schedule of drugs administered for this treatment.

modifier

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier

<modifier
    decision=string
  >
EXACTLY ONE OF:
| ( <multiplyQty ... /> )*
| ( <delay ... /> )*
| ( <selectTimeRange ... /> )*
</modifier>

Documentation (type)

A modifier for this treatment, according to the outputs of a decision.

Attributes

decision

decision=string

Units: string

Specifies the decision that this modifier acts on.

multiplyQty

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier → multiplyQty

<multiplyQty
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Multiplies the quantity of active ingredients of drugs administered.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of multipliers for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0.5,1" the quantity of drug A is halved while that of B is unchanged.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

delay

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier → delay

<delay
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Delays administration of drugs listed in the base schedule by so many hours.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of delays (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0,6", drug A is administered as in the base schedule while drug B is administered 6 hours later than specified.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

selectTimeRange

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier → selectTimeRange

<selectTimeRange
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Selects which drug doses to administer according to time of administration (before times are modified by delays). Half-open interval: [x,y)

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of time-ranges (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. The time-ranges should be of the form x-y and are interpreted as the half-open interval [x,y); that is a drug listed with time t will only be administered if x <= t < y.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</complicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
|   <pImmediateUC ... /> 
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: days Min: 0 Max: unbounded

Maximum number of timesteps (including first of case) an individual will remember they are sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial/non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of a complicated/severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Probability of immediate UC treatment seeking

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → pImmediateUC

<pImmediateUC>
    double
</pImmediateUC>

Documentation (element)

Units: none Min: 0 Max: 1

Probability that UC treatment seeking will be done immediately when sick, on second day given that it wasn't done on first, etc.

ImmediateOutcomes

<ImmediateOutcomes
    name=string
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
</ImmediateOutcomes>

Documentation (type)

Units: List of elements

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Case Management model

name=string

Units: string

Name of health system

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

ACT

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

QN

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

Probability that a patient with uncomplicated disease seeks official care immediately

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease self-treats

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

CFR

→ scenario → healthSystem → CFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Probabilities of sequelae in inpatients

<pSequelaeInpatient>
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients, during a severe bout.

Replacement transmission setting (vector control not enabled)

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (element)

Units: List of elements

New description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

Daily EIR

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (element)

Units: innoculations per adult per day

Sequence of EIR values. Should cover at least one whole year. Values are averaged to result in a sequence of EIR-per-timestep values, but are otherwise not smoothed.

Documentation (type)

Units: Inoculations per person per day

There are two distinct ways of inputing the transmission setting. With this option, the values of daily EIR are input separately. This is only valid for models that do not invoke vector control and is retained only for backward compatibility. When multiple values are given for a single timestep they are averaged.

Attributes

Time origin of EIR sequence

origin=string

importedInfectionsPerThousandHosts

→ scenario → interventions → timed → intervention → importedInfectionsPerThousandHosts

<importedInfectionsPerThousandHosts>
    double
</importedInfectionsPerThousandHosts>

Mass Drug Administration

→ scenario → interventions → timed → intervention → MDA

<MDA
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

Vaccination

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

ITN deployment

→ scenario → interventions → timed → intervention → ITN

<ITN
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

IRS deployment

→ scenario → interventions → timed → intervention → IRS

<IRS
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of IRS deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

Mosquito deterrent

→ scenario → interventions → timed → intervention → VectorAvailability

<VectorAvailability
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of a mosquito deterrent deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

IPTi deployment

→ scenario → interventions → timed → intervention → ipti

<ipti
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

Immune suppression deployment

→ scenario → interventions → timed → intervention → immuneSuppression

<immuneSuppression
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Removes all exposure-related immunity gained over time by hosts without removing infections.

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

Insert R_0 case

→ scenario → interventions → timed → intervention → insertR_0Case

<insertR_0Case/>

Documentation (element)

Units: List of elements

Uninfect vectors

→ scenario → interventions → timed → intervention → uninfectVectors

<uninfectVectors/>

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

larviciding

→ scenario → interventions → timed → intervention → larviciding

<larviciding>
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

anopheles

Documentation (element)

Simple larviciding intervention description.

anopheles

→ scenario → interventions → timed → intervention → larviciding → anopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

Mosquito to be larvicided

mosquito=string

Mosquito to be larvicided

Proportionate reduction in emergence

effectiveness=double

Units: none Min: 0 Max: 1

Proportional reduction in emergence rate

Duration of activity

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

Mass Cohort Selection

→ scenario → interventions → timed → intervention → cohort

<cohort
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of mass cohort selection.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

healthSystem

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entoData

<entoData
    name=string
    mode=("2" or "4")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Attributes

Entomology dataset

name=string

Units: string

Name of entomology data

Transmission simulation mode

mode=("2" or "4")

Units: Code

Override annual EIR

annualEIR=double

Units: Infectious bites per person/adult per year

If set, overrides the annual EIR by scaling it to this level. If ommitted, EIR levels are as specified elsewhere.

Transmission setting (vector control not enabled)

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Units: List of elements

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Units: List of elements

Parameters of the transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <eir ... /> 
| |   <monthlyEir ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Initial guess of proportion of mosquitoes infected

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial guess of proportion of mosquitoes infectious

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Fourier approximation to pre-intervention EIR

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    b1=double
    a2=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Inoculations per person per day

Attributes

a0 parameter of Fourier approximation to ln(EIR)

a0=double

a1 parameter of Fourier approximation to ln(EIR)

a1=double

b1 parameter of Fourier approximation to ln(EIR)

b1=double

a2 parameter of Fourier approximation to ln(EIR)

a2=double

b2 parameter of Fourier approximation to ln(EIR)

b2=double

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: radians

Monthly values for pre-intervention EIR

→ scenario → entoData → vector → anopheles → monthlyEir

<monthlyEir
    annualEIR=double
  >
IN THIS ORDER:
| ( <item ... /> ){12,12}
</monthlyEir>

item

Documentation (element)

Units: Inoculations per person per month

Attributes

Annual EIR

annualEIR=double

Units: Innoculations per person per year Min: 0

Scales the monthly values to give this annual innoculation rate.

Monthly pre-intervention EIR

→ scenario → entoData → vector → anopheles → monthlyEir → item

<item>
    double
</item>

Vector Species

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqLaidEggsSameDayProportion=double
    mosqSeekingDuration=double
    mosqSurvivalFeedingCycleProbability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
    mosqHumanBloodIndex=double
    minInfectedThreshold=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

Duration of the resting period of the vector (days)

mosqRestDuration=int

Extrinsic incubation period (days)

extrinsicIncubationPeriod=int

Proportion of mosquitoes host seeking on same day as ovipositing

mosqLaidEggsSameDayProportion=double

Duration of the host-seeking period of the vector (days)

mosqSeekingDuration=double

Probability that the mosquito survives the feeding cycle

mosqSurvivalFeedingCycleProbability=double

Probability that the mosquito succesfully bites chosen host

mosqProbBiting=double

Probability that the mosquito escapes host and finds a resting place after biting

mosqProbFindRestSite=double

Probability of mosquito successfully resting after finding a resting site

mosqProbResting=double

Probability of a mosquito successfully laying eggs given that it has rested

mosqProbOvipositing=double

Human blood index

mosqHumanBloodIndex=double

The proportion of resting mosquitoes which fed on human blood during the last feed.

Min infected threshold

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
    mosqRelativeEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Relative availability of nonhuman hosts of type i (to other nonhuman hosts)

mosqRelativeEntoAvailability=double

Probability of mosquito successfully biting host

mosqProbBiting=double

Probability that the mosquito escapes host and finds a resting place after biting

mosqProbFindRestSite=double

Probability of mosquito successfully resting after finding a resting site

mosqProbResting=double

nonHumanHosts

→ scenario → entoData → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Units: List of elements

Name of this species of non human hosts (must match up with those described per anopheles section)

number

number=double

Pharmacokinetics and pharmacodynamics

<drugDescription>
IN THIS ORDER:
| ( <drug ... /> )+
</drugDescription>

drug

Documentation (element)

Units: List of elements

Drug model parameters

drug

→ scenario → drugDescription → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
| [ <IV ... /> ]
</drug>

Documentation (element)

Sequence of drug descriptions forming a library of drug parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → drugDescription → drug → PD

<PD>
IN THIS ORDER:
| ( <allele ... /> )+
</PD>

allele

allele

→ scenario → drugDescription → drug → PD → allele

<allele
    name=string
  >
IN THIS ORDER:
|   <initial_frequency ... /> 
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</allele>

Documentation (element)

PD parameters per allele, plus initial frequency of each allele.

Note: we assume a one-to-one correspondance of drugs to loci, hence each drug has an independent set of alleles here.

Attributes

name

name=string

Relative frequency

→ scenario → drugDescription → drug → PD → allele → initial_frequency

<initial_frequency>
    double
</initial_frequency>

Documentation (element)

Units: relative frequency Min: 0

Frequency, relative to the total frequency of all alleles for this drug/locus.

Maximal parasite killing rate

→ scenario → drugDescription → drug → PD → allele → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → drugDescription → drug → PD → allele → IC50

<IC50>
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

Slope of effect curve

→ scenario → drugDescription → drug → PD → allele → slope

<slope>
    double
</slope>

Documentation (element)

Units: no units

n — Slope of the concentration effect curve

PK

→ scenario → drugDescription → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
|   <half_life ... /> 
|   <vol_dist ... /> 
</PK>

Drug concentration considered negligible

→ scenario → drugDescription → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → drugDescription → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate (which is: ln(2) / half_life).

Volume of Distribution

→ scenario → drugDescription → drug → PK → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

IV

→ scenario → drugDescription → drug → IV

<IV>
IN THIS ORDER:
|   <half_life ... /> 
|   <vol_dist ... /> 
</IV>

drug half-life

→ scenario → drugDescription → drug → IV → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate (which is: ln(2) / half_life).

Volume of Distribution

→ scenario → drugDescription → drug → IV → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Model options and parameters

→ scenario → model

<model>
IN THIS ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <parameters ... /> 
</model>

Documentation (element)

Units: List of elements

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

Units: List of elements

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: include/util/ModelOptions.h and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=int
  />

Documentation (type)

Units: List of elements

Description of clinical parameters.

This is related to the health-system description, but contains data which can't be changed as part of an intervention and is not restricted to treatment.

Attributes

Follow-up period during which recurrence is treated as a failure

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Units: List of elements

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → model → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 22 documentation

Generated from: scenario_22.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    name=string
    wuID=int
    assimMode=("0" or "1")
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_22.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entoData ... /> 
| [ <drugDescription ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Units: string

Name of intervention

Work unit identifier

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

Assimilator mode

assimMode=("0" or "1")

Units: Code

Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Attributes

Name of demography data

name=string

Units: string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: years Min: 0 Max: 100

Maximum age of simulated humans in years.

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Percentage of human population in age group

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ cohortOnly=boolean ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Attributes

Name of monitoring information

name=string

Units: string

Name of monitoring data

Survey only cohort

cohortOnly=boolean

continuous

→ scenario → monitoring → continuous

<continuous
    period=int
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Days between reports

period=int

Units: Days Min: 1 Max: unbounded

Number of timesteps between reports.

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
    value=boolean
  />

Attributes

Model options required

name=string

Options define different model structures. Option name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.

Indicator of whether option is required

value=boolean

Option value (true/false). Each option has a default value used if the option is not listed (usually false but sometimes true).

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time; 0 means just before start of main sim and is a valid survey-point. Reported data is either from a point-time survey (immediate data) or is collected over the previous year (data from previous timesteps-per-year period). Simulation will end immediately after last survey is taken.

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Preventative interventions

<interventions
    name=string
  >
IN THIS ORDER:
|   <descriptions ... /> 
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

Attributes

Intervention

name=string

Units: string

Name of age specific intervention

descriptions

<descriptions>
IN THIS ORDER:
| [ <MDADescription ... /> ]
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| ( <anopheles ... /> )*
</descriptions>

Documentation (element)

Descriptions applying across all uses of an intervention.

Drug dose(s) used in MDA

→ scenario → interventions → descriptions → MDADescription

<MDADescription>
IN THIS ORDER:
| [ <schedule ... /> ]
</MDADescription>

schedule

Documentation (element)

Units: List of medicate elements

Description of drug dose(s) used in a mass-drug-administration intervention.

When using the new (Event Scheduler) case management model, a treatment schedule must be present.

schedule

→ scenario → interventions → descriptions → MDADescription → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

The base (unmodified) schedule of drugs administered for this treatment.

medicate

→ scenario → interventions → descriptions → MDADescription → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  />

Attributes

drug

drug=string

Units: string

Abbreviated name of drug compound

drug dose

mg=double

Units: mg

Quantity of drug compound

time of administration

hour=double

Units: hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

vaccineDescription

→ scenario → interventions → descriptions → vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

Type of vaccine

vaccineType=int

Units: Code

Type of vaccine

Half life of drug effect

→ scenario → interventions → descriptions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Variance parameter for vaccine efficacy

→ scenario → interventions → descriptions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

initialEfficacy

→ scenario → interventions → descriptions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

iptiDescription

→ scenario → interventions → descriptions → iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → descriptions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

Age specific intervention

name=string

Units: string

Name of age specific intervention

Frequency

freq=double

Frequency of parasite genotype

ACR

ACR=double

Adequate clinical response (proportion)

Prophylactic period

proph=int

Prophylactic period

Tolerance period

tolPeriod=int

Tolerance period

atten=double

Tolerance period

anopheles

→ scenario → interventions → descriptions → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <VADescription ... /> ]
</anopheles>

Attributes

Entomological effects of interventions

mosquito=string

Description of the entomological effects of interventions

ITNDescription

→ scenario → interventions → descriptions → anopheles → ITNDescription

<ITNDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</ITNDescription>

Attributes

ITN effects

name=string

Units: string

Name of Insecticide Treated Net intervention

Deterrency

→ scenario → interventions → descriptions → anopheles → ITNDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability (before decay).

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

Pre-prandial killing effect

→ scenario → interventions → descriptions → anopheles → ITNDescription → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

Post-prandial killing effect

→ scenario → interventions → descriptions → anopheles → ITNDescription → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

IRSDescription

→ scenario → interventions → descriptions → anopheles → IRSDescription

<IRSDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <killingEffect ... /> 
</IRSDescription>

Attributes

name of IRS intervention

name=string

Units: string

Name of Indoor Residual Spraying intervention

Deterrency

→ scenario → interventions → descriptions → anopheles → IRSDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

killing effect

→ scenario → interventions → descriptions → anopheles → IRSDescription → killingEffect

<killingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

VADescription

→ scenario → interventions → descriptions → anopheles → VADescription

<VADescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</VADescription>

deterrency

Attributes

Name of mosquito deterrency intervention

name=string

Units: string

Name of mosquito deterrency intervention

Deterrency

→ scenario → interventions → descriptions → anopheles → VADescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

Continuously applied interventions

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
| ( <cohort ... /> )*
</continuous>

List of age groups for vaccination

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Description of ITN deployment

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

List of age groups for IPTi

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Continuous cohort selection

→ scenario → interventions → continuous → cohort

<cohort
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

Description of continuous selection of individuals for a cohort study.

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Timed interventions

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfectionsPerThousandHosts ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <VectorAvailability ... /> ]
| [ <ipti ... /> ]
| [ <immuneSuppression ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <larviciding ... /> ]
| [ <cohort ... /> ]
</intervention>

Attributes

Time step of intervention

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</uncomplicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

decisions

→ scenario → healthSystem → EventScheduler → uncomplicated → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )*
</decisions>

decision

Documentation (type)

case (uncomplicated only): Returns "UC1" if there is no recent history of a malarial case, or "UC2" if there is.
result: Dependent on decision "test", this performs a parasite density test. Output is one of "none" (no test performed), "positive", "negative".

The following decisions must be described here:

test (uncomplicated only): Outputs must be "none", "microscopy" or "RDT" to describe which test the "result" decision uses.
treatment: Describes which treatment to use. Values aren't restricted but must match up with a treatment described in the corresponding "treatments" section.
hospitalisation (complicated only): none, immediate or delayed.

decision

→ scenario → healthSystem → EventScheduler → uncomplicated → decisions → decision

<decision
    name=string
    depends=string
    values=string
  >
    string
</decision>

Documentation (type)

A decision describes how to choose between a set of values.

Lexically, it can contain symbols matching "[_.a-zA-Z0-9]+", round brackets: (), braces: {} and colons. Whitespace is ignored except to separate symbols.

For each BRANCH_SET each BRANCH must have the same DECISION. This DECISION must be one of the dependencies mentioned in "depends". This may be:

another decision, in which case the VALUE immediately following in brackets must correspond to one of its output values. The BRANCH_SET immediately containing this BRANCH must represent each output value of the same decision exactly once, and no parent BRANCH_SET may be for the same DECISION.
"p": this indicates a probabilistic decision. In this case the value is a probability, the sum of all values for the BRANCH_SET must be 1 and the decision must be associated directly with OUTCOMEs (not sub-TREEs).
"age": this indicates an age-test. The VALUE must have the form "a-b", indicating that this branch will be taken for individuals aged such that a <= age < b, where a,b are non-negative real numbers or the special value "inf", and a <= b. All VALUEs in the BRANCH_SET must cover all possible (non-negative real) ages, with no overlap (hence, smallest a must be 0 and greatest b must be inf).

Semantically, each OUTCOME must be one of the values associated with this decision.

Attributes

Name of decision

name=string

The name of this decision. The name must match the regular expression "[_a-zA-Z0-9]+"; that is it can only contain letters, digits and _ characters (no spaces, punctuation, etc.).

Preceding decisions

depends=string

Outcome values

values=string

A comma-separated list of outcome values this decision may have. The name of each value must be of the same form as decision names (i.e. only contain letters, digits and _ characters).

treatments

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments

<treatments>
IN THIS ORDER:
| ( <treatment ... /> )*
</treatments>

treatment

Documentation (type)

Units: string

A list of drug treatment tables. Each should have a name corresponding to one of the "drug" decision's values.

treatment

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment

<treatment
    name=string
  >
IN THIS ORDER:
|   <schedule ... /> 
| ( <modifier ... /> )*
</treatment>

Documentation (type)

A description of a base treatment schedule along with modifiers to handle delays, quality variations, etc.

Attributes

Treatment administered

name=string

Units: string

Name corresponding to one of the drug decision's output values.

schedule

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

The base (unmodified) schedule of drugs administered for this treatment.

modifier

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier

<modifier
    decision=string
  >
EXACTLY ONE OF:
| ( <multiplyQty ... /> )*
| ( <delay ... /> )*
| ( <selectTimeRange ... /> )*
</modifier>

Documentation (type)

A modifier for this treatment, according to the outputs of a decision.

Attributes

decision

decision=string

Units: string

Specifies the decision that this modifier acts on.

multiplyQty

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier → multiplyQty

<multiplyQty
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Multiplies the quantity of active ingredients of drugs administered.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of multipliers for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0.5,1" the quantity of drug A is halved while that of B is unchanged.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

delay

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier → delay

<delay
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Delays administration of drugs listed in the base schedule by so many hours.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of delays (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0,6", drug A is administered as in the base schedule while drug B is administered 6 hours later than specified.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

selectTimeRange

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier → selectTimeRange

<selectTimeRange
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Selects which drug doses to administer according to time of administration (before times are modified by delays). Half-open interval: [x,y)

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of time-ranges (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. The time-ranges should be of the form x-y and are interpreted as the half-open interval [x,y); that is a drug listed with time t will only be administered if x <= t < y.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</complicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
|   <pImmediateUC ... /> 
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: days Min: 0 Max: unbounded

Maximum number of timesteps (including first of case) an individual will remember they are sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial/non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of a complicated/severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Probability of immediate UC treatment seeking

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → pImmediateUC

<pImmediateUC>
    double
</pImmediateUC>

Documentation (element)

Units: none Min: 0 Max: 1

Probability that UC treatment seeking will be done immediately when sick, on second day given that it wasn't done on first, etc.

ImmediateOutcomes

<ImmediateOutcomes
    name=string
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
</ImmediateOutcomes>

Documentation (type)

Units: List of elements

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Case Management model

name=string

Units: string

Name of health system

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

ACT

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

QN

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

Probability that a patient with uncomplicated disease seeks official care immediately

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease self-treats

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

CFR

→ scenario → healthSystem → CFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Probabilities of sequelae in inpatients

<pSequelaeInpatient>
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients, during a severe bout.

Replacement transmission setting (vector control not enabled)

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (element)

Units: List of elements

New description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

Daily EIR

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (element)

Units: innoculations per adult per day

Sequence of EIR values. Should cover at least one whole year. Values are averaged to result in a sequence of EIR-per-timestep values, but are otherwise not smoothed.

Documentation (type)

Units: Inoculations per person per day

Attributes

Time origin of EIR sequence

origin=string

importedInfectionsPerThousandHosts

→ scenario → interventions → timed → intervention → importedInfectionsPerThousandHosts

<importedInfectionsPerThousandHosts>
    double
</importedInfectionsPerThousandHosts>

Mass Drug Administration

→ scenario → interventions → timed → intervention → MDA

<MDA
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

Vaccination

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

ITN deployment

→ scenario → interventions → timed → intervention → ITN

<ITN
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

IRS deployment

→ scenario → interventions → timed → intervention → IRS

<IRS
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of IRS deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

Mosquito deterrent

→ scenario → interventions → timed → intervention → VectorAvailability

<VectorAvailability
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of a mosquito deterrent deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

IPTi deployment

→ scenario → interventions → timed → intervention → ipti

<ipti
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

Immune suppression deployment

→ scenario → interventions → timed → intervention → immuneSuppression

<immuneSuppression
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Removes all exposure-related immunity gained over time by hosts without removing infections.

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

Insert R_0 case

→ scenario → interventions → timed → intervention → insertR_0Case

<insertR_0Case/>

Documentation (element)

Units: List of elements

Uninfect vectors

→ scenario → interventions → timed → intervention → uninfectVectors

<uninfectVectors/>

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

larviciding

→ scenario → interventions → timed → intervention → larviciding

<larviciding>
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

anopheles

Documentation (element)

Simple larviciding intervention description.

anopheles

→ scenario → interventions → timed → intervention → larviciding → anopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

Mosquito to be larvicided

mosquito=string

Mosquito to be larvicided

Proportionate reduction in emergence

effectiveness=double

Units: none Min: 0 Max: 1

Proportional reduction in emergence rate

Duration of activity

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

Mass Cohort Selection

→ scenario → interventions → timed → intervention → cohort

<cohort
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of mass cohort selection.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

healthSystem

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entoData

<entoData
    name=string
    mode=("2" or "4")
  [ annualEIR=double ]
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Attributes

Entomology dataset

name=string

Units: string

Name of entomology data

Transmission simulation mode

mode=("2" or "4")

Units: Code

Override annual EIR

annualEIR=double

Units: Infectious bites per person/adult per year

If set, overrides the annual EIR by scaling it to this level. If ommitted, EIR levels are as specified elsewhere.

Transmission setting (vector control not enabled)

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Units: List of elements

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Units: List of elements

Parameters of the transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <eir ... /> 
| |   <monthlyEir ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Initial guess of proportion of mosquitoes infected

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial guess of proportion of mosquitoes infectious

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Fourier approximation to pre-intervention EIR

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    b1=double
    a2=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Inoculations per person per day

Attributes

a0 parameter of Fourier approximation to ln(EIR)

a0=double

a1 parameter of Fourier approximation to ln(EIR)

a1=double

b1 parameter of Fourier approximation to ln(EIR)

b1=double

a2 parameter of Fourier approximation to ln(EIR)

a2=double

b2 parameter of Fourier approximation to ln(EIR)

b2=double

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Units: radians

Monthly values for pre-intervention EIR

→ scenario → entoData → vector → anopheles → monthlyEir

<monthlyEir
    annualEIR=double
  >
IN THIS ORDER:
| ( <item ... /> ){12,12}
</monthlyEir>

item

Documentation (element)

Units: Inoculations per person per month

Attributes

Annual EIR

annualEIR=double

Units: Innoculations per person per year Min: 0

Scales the monthly values to give this annual innoculation rate.

Monthly pre-intervention EIR

→ scenario → entoData → vector → anopheles → monthlyEir → item

<item>
    double
</item>

Vector Species

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqLaidEggsSameDayProportion=double
    mosqSeekingDuration=double
    mosqSurvivalFeedingCycleProbability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
    mosqHumanBloodIndex=double
    minInfectedThreshold=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

Duration of the resting period of the vector (days)

mosqRestDuration=int

Extrinsic incubation period (days)

extrinsicIncubationPeriod=int

Proportion of mosquitoes host seeking on same day as ovipositing

mosqLaidEggsSameDayProportion=double

Duration of the host-seeking period of the vector (days)

mosqSeekingDuration=double

Probability that the mosquito survives the feeding cycle

mosqSurvivalFeedingCycleProbability=double

Probability that the mosquito succesfully bites chosen host

mosqProbBiting=double

Probability that the mosquito escapes host and finds a resting place after biting

mosqProbFindRestSite=double

Probability of mosquito successfully resting after finding a resting site

mosqProbResting=double

Probability of a mosquito successfully laying eggs given that it has rested

mosqProbOvipositing=double

Human blood index

mosqHumanBloodIndex=double

The proportion of resting mosquitoes which fed on human blood during the last feed.

Min infected threshold

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
    mosqRelativeEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Relative availability of nonhuman hosts of type i (to other nonhuman hosts)

mosqRelativeEntoAvailability=double

Probability of mosquito successfully biting host

mosqProbBiting=double

Probability that the mosquito escapes host and finds a resting place after biting

mosqProbFindRestSite=double

Probability of mosquito successfully resting after finding a resting site

mosqProbResting=double

nonHumanHosts

→ scenario → entoData → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Units: List of elements

Name of this species of non human hosts (must match up with those described per anopheles section)

number

number=double

Pharmacokinetics and pharmacodynamics

<drugDescription>
IN THIS ORDER:
| ( <drug ... /> )+
</drugDescription>

drug

Documentation (element)

Units: List of elements

Drug model parameters

drug

→ scenario → drugDescription → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (element)

Sequence of drug descriptions forming a library of drug parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → drugDescription → drug → PD

<PD>
IN THIS ORDER:
| ( <allele ... /> )+
</PD>

allele

allele

→ scenario → drugDescription → drug → PD → allele

<allele
    name=string
  >
IN THIS ORDER:
|   <initial_frequency ... /> 
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</allele>

Documentation (element)

PD parameters per allele, plus initial frequency of each allele.

Note: we assume a one-to-one correspondance of drugs to loci, hence each drug has an independent set of alleles here.

Attributes

name

name=string

Relative frequency

→ scenario → drugDescription → drug → PD → allele → initial_frequency

<initial_frequency>
    double
</initial_frequency>

Documentation (element)

Units: relative frequency Min: 0

Frequency, relative to the total frequency of all alleles for this drug/locus.

Maximal parasite killing rate

→ scenario → drugDescription → drug → PD → allele → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → drugDescription → drug → PD → allele → IC50

<IC50>
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

Slope of effect curve

→ scenario → drugDescription → drug → PD → allele → slope

<slope>
    double
</slope>

Documentation (element)

Units: no units

n — Slope of the concentration effect curve

PK

→ scenario → drugDescription → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
|   <half_life ... /> 
|   <vol_dist ... /> 
</PK>

Drug concentration considered negligible

→ scenario → drugDescription → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → drugDescription → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate (which is: ln(2) / half_life).

Volume of Distribution

→ scenario → drugDescription → drug → PK → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Model options and parameters

→ scenario → model

<model>
IN THIS ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <parameters ... /> 
</model>

Documentation (element)

Units: List of elements

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

Units: List of elements

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: include/util/ModelOptions.hpp and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=int
  />

Documentation (type)

Units: List of elements

Description of clinical parameters.

This is related to the health-system description, but contains data which can't be changed as part of an intervention and is not restricted to treatment.

Attributes

Follow-up period during which recurrence is treated as a failure

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Units: List of elements

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → model → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 21 documentation

Generated from: scenario_21.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    name=string
    wuID=int
    assimMode=("0" or "1")
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_21.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entoData ... /> 
| [ <drugDescription ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Units: string

Name of intervention

Work unit identifier

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

Assimilator mode

assimMode=("0" or "1")

Units: Code

Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Attributes

Name of demography data

name=string

Units: string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Number Min: 0 Max: 100

Maximum age of simulated humans

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Percentage of human population in age group

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  [ cohortOnly=boolean ]
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Attributes

Name of monitoring information

name=string

Units: string

Name of monitoring data

Survey only cohort

cohortOnly=boolean

continuous

→ scenario → monitoring → continuous

<continuous
    period=int
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Days between reports

period=int

Units: Days Min: 1 Max: unbounded

Number of timesteps between reports.

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
    value=boolean
  />

Attributes

Model options required

name=string

Options define different model structures. Option name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.

Indicator of whether option is required

value=boolean

Option value (true/false). Each option has a default value used if the option is not listed (usually false but sometimes true).

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
  >
IN THIS ORDER:
| ( <surveyTime ... /> )+
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time; 0 means just before start of main sim and is a valid survey-point. Reported data is either from a point-time survey (immediate data) or is collected over the previous year (data from previous timesteps-per-year period). Simulation will end immediately after last survey is taken.

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Preventative interventions

<interventions
    name=string
  >
IN THIS ORDER:
|   <descriptions ... /> 
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

Attributes

Intervention

name=string

Units: string

Name of age specific intervention

descriptions

<descriptions>
IN THIS ORDER:
| [ <MDADescription ... /> ]
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| ( <anopheles ... /> )*
</descriptions>

Documentation (element)

Descriptions applying across all uses of an intervention.

Drug dose(s) used in MDA

→ scenario → interventions → descriptions → MDADescription

<MDADescription>
IN THIS ORDER:
| [ <schedule ... /> ]
</MDADescription>

schedule

Documentation (element)

Units: List of medicate elements

Description of drug dose(s) used in a mass-drug-administration intervention.

When using the new (Event Scheduler) case management model, a treatment schedule must be present.

schedule

→ scenario → interventions → descriptions → MDADescription → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

The base (unmodified) schedule of drugs administered for this treatment.

medicate

→ scenario → interventions → descriptions → MDADescription → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  />

Attributes

drug

drug=string

Units: string

Abbreviated name of drug compound

drug dose

mg=double

Units: mg

Quantity of drug compound

time of administration

hour=double

Units: hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

vaccineDescription

→ scenario → interventions → descriptions → vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

Type of vaccine

vaccineType=int

Units: Code

Type of vaccine

Half life of drug effect

→ scenario → interventions → descriptions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Variance parameter for vaccine efficacy

→ scenario → interventions → descriptions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

initialEfficacy

→ scenario → interventions → descriptions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

iptiDescription

→ scenario → interventions → descriptions → iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → descriptions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

Age specific intervention

name=string

Units: string

Name of age specific intervention

Frequency

freq=double

Frequency of parasite genotype

ACR

ACR=double

Adequate clinical response (proportion)

Prophylactic period

proph=int

Prophylactic period

Tolerance period

tolPeriod=int

Tolerance period

atten=double

Tolerance period

anopheles

→ scenario → interventions → descriptions → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <VADescription ... /> ]
</anopheles>

Attributes

Entomological effects of interventions

mosquito=string

Description of the entomological effects of interventions

ITNDescription

→ scenario → interventions → descriptions → anopheles → ITNDescription

<ITNDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</ITNDescription>

Attributes

ITN effects

name=string

Units: string

Name of Insecticide Treated Net intervention

Deterrency

→ scenario → interventions → descriptions → anopheles → ITNDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability (before decay).

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

Pre-prandial killing effect

→ scenario → interventions → descriptions → anopheles → ITNDescription → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

Post-prandial killing effect

→ scenario → interventions → descriptions → anopheles → ITNDescription → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

IRSDescription

→ scenario → interventions → descriptions → anopheles → IRSDescription

<IRSDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <killingEffect ... /> 
</IRSDescription>

Attributes

name of IRS intervention

name=string

Units: string

Name of Indoor Residual Spraying intervention

Deterrency

→ scenario → interventions → descriptions → anopheles → IRSDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

killing effect

→ scenario → interventions → descriptions → anopheles → IRSDescription → killingEffect

<killingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

VADescription

→ scenario → interventions → descriptions → anopheles → VADescription

<VADescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</VADescription>

deterrency

Attributes

Name of mosquito deterrency intervention

name=string

Units: string

Name of mosquito deterrency intervention

Deterrency

→ scenario → interventions → descriptions → anopheles → VADescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

Continuously applied interventions

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
| ( <cohort ... /> )*
</continuous>

List of age groups for vaccination

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Description of ITN deployment

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

List of age groups for IPTi

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Continuous cohort selection

→ scenario → interventions → continuous → cohort

<cohort
    targetAgeYrs=double
    coverage=double
  [ cohort=boolean ] DEFAULT VALUE false
  [ begin=int ] DEFAULT VALUE 0
  [ end=int ] DEFAULT VALUE 2147483647
  />

Documentation (element)

Units: List of elements

Description of continuous selection of individuals for a cohort study.

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Default value: false

Restrict distribution to chosen cohort (default: false).

First timestep active

begin=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 0

First timestep (from 0 at the beginning of the intervention period) this item is active. Defaults to 0.

End timestep

end=int

Units: Timesteps Min: 0 Max: 2147483647

Default value: 2147483647

End of the period during which the intervention is active (to be exact, the first timestep of the intervention period at which the item becomes inactive). Defaults to 2147483647.

Timed interventions

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfectionsPerThousandHosts ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <VectorAvailability ... /> ]
| [ <ipti ... /> ]
| [ <immuneSuppression ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <larviciding ... /> ]
| [ <cohort ... /> ]
</intervention>

Attributes

Time step of intervention

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</uncomplicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

decisions

→ scenario → healthSystem → EventScheduler → uncomplicated → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )*
</decisions>

decision

Documentation (type)

case (uncomplicated only): Returns "UC1" if there is no recent history of a malarial case, or "UC2" if there is.
result: Dependent on decision "test", this performs a parasite density test. Output is one of "none" (no test performed), "positive", "negative".

The following decisions must be described here:

test (uncomplicated only): Outputs must be "none", "microscopy" or "RDT" to describe which test the "result" decision uses.
treatment: Describes which treatment to use. Values aren't restricted but must match up with a treatment described in the corresponding "treatments" section.
hospitalisation (complicated only): none, immediate or delayed.

decision

→ scenario → healthSystem → EventScheduler → uncomplicated → decisions → decision

<decision
    name=string
    depends=string
    values=string
  >
    string
</decision>

Documentation (type)

A decision describes how to choose between a set of values.

Lexically, it can contain symbols matching "[_.a-zA-Z0-9]+", round brackets: (), braces: {} and colons. Whitespace is ignored except to separate symbols.

For each BRANCH_SET each BRANCH must have the same DECISION. This DECISION must be one of the dependencies mentioned in "depends". This may be:

another decision, in which case the VALUE immediately following in brackets must correspond to one of its output values. The BRANCH_SET immediately containing this BRANCH must represent each output value of the same decision exactly once, and no parent BRANCH_SET may be for the same DECISION.
"p": this indicates a probabilistic decision. In this case the value is a probability, the sum of all values for the BRANCH_SET must be 1 and the decision must be associated directly with OUTCOMEs (not sub-TREEs).
"age": this indicates an age-test. The VALUE must have the form "a-b", indicating that this branch will be taken for individuals aged such that a <= age < b, where a,b are non-negative real numbers or the special value "inf", and a <= b. All VALUEs in the BRANCH_SET must cover all possible (non-negative real) ages, with no overlap (hence, smallest a must be 0 and greatest b must be inf).

Semantically, each OUTCOME must be one of the values associated with this decision.

Attributes

Name of decision

name=string

The name of this decision. The name must match the regular expression "[_a-zA-Z0-9]+"; that is it can only contain letters, digits and _ characters (no spaces, punctuation, etc.).

Preceding decisions

depends=string

Outcome values

values=string

A comma-separated list of outcome values this decision may have. The name of each value must be of the same form as decision names (i.e. only contain letters, digits and _ characters).

treatments

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments

<treatments>
IN THIS ORDER:
| ( <treatment ... /> )*
</treatments>

treatment

Documentation (type)

Units: string

A list of drug treatment tables. Each should have a name corresponding to one of the "drug" decision's values.

treatment

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment

<treatment
    name=string
  >
IN THIS ORDER:
|   <schedule ... /> 
| ( <modifier ... /> )*
</treatment>

Documentation (type)

A description of a base treatment schedule along with modifiers to handle delays, quality variations, etc.

Attributes

Treatment administered

name=string

Units: string

Name corresponding to one of the drug decision's output values.

schedule

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

The base (unmodified) schedule of drugs administered for this treatment.

modifier

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier

<modifier
    decision=string
  >
EXACTLY ONE OF:
| ( <multiplyQty ... /> )*
| ( <delay ... /> )*
| ( <selectTimeRange ... /> )*
</modifier>

Documentation (type)

A modifier for this treatment, according to the outputs of a decision.

Attributes

decision

decision=string

Units: string

Specifies the decision that this modifier acts on.

multiplyQty

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier → multiplyQty

<multiplyQty
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Multiplies the quantity of active ingredients of drugs administered.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of multipliers for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0.5,1" the quantity of drug A is halved while that of B is unchanged.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

delay

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier → delay

<delay
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Delays administration of drugs listed in the base schedule by so many hours.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of delays (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0,6", drug A is administered as in the base schedule while drug B is administered 6 hours later than specified.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

selectTimeRange

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier → selectTimeRange

<selectTimeRange
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Selects which drug doses to administer according to time of administration (before times are modified by delays). Half-open interval: [x,y)

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of time-ranges (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. The time-ranges should be of the form x-y and are interpreted as the half-open interval [x,y); that is a drug listed with time t will only be administered if x <= t < y.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</complicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
|   <pImmediateUC ... /> 
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: days Min: 0 Max: unbounded

Maximum number of timesteps (including first of case) an individual will remember they are sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial/non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of a complicated/severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Probability of immediate UC treatment seeking

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → pImmediateUC

<pImmediateUC>
    double
</pImmediateUC>

Documentation (element)

Units: none Min: 0 Max: 1

Probability that UC treatment seeking will be done immediately when sick, on second day given that it wasn't done on first, etc.

ImmediateOutcomes

<ImmediateOutcomes
    name=string
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
</ImmediateOutcomes>

Documentation (type)

Units: List of elements

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Case Management model

name=string

Units: string

Name of health system

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

ACT

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

QN

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

Probability that a patient with uncomplicated disease seeks official care immediately

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease self-treats

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

CFR

→ scenario → healthSystem → CFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Probabilities of sequelae in inpatients

<pSequelaeInpatient>
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients, during a severe bout.

Replacement transmission setting (vector control not enabled)

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (element)

Units: List of elements

New description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

EIRDaily

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Inoculations per person per day

Attributes

Time origin of EIR sequence

origin=string

importedInfectionsPerThousandHosts

→ scenario → interventions → timed → intervention → importedInfectionsPerThousandHosts

<importedInfectionsPerThousandHosts>
    double
</importedInfectionsPerThousandHosts>

Mass Drug Administration

→ scenario → interventions → timed → intervention → MDA

<MDA
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

Vaccination

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

ITN deployment

→ scenario → interventions → timed → intervention → ITN

<ITN
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

IRS deployment

→ scenario → interventions → timed → intervention → IRS

<IRS
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of IRS deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

Mosquito deterrent

→ scenario → interventions → timed → intervention → VectorAvailability

<VectorAvailability
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of a mosquito deterrent deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

IPTi deployment

→ scenario → interventions → timed → intervention → ipti

<ipti
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

Immune suppression deployment

→ scenario → interventions → timed → intervention → immuneSuppression

<immuneSuppression
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Removes all exposure-related immunity gained over time by hosts without removing infections.

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

Insert R_0 case

→ scenario → interventions → timed → intervention → insertR_0Case

<insertR_0Case/>

Documentation (element)

Units: List of elements

Uninfect vectors

→ scenario → interventions → timed → intervention → uninfectVectors

<uninfectVectors/>

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

larviciding

→ scenario → interventions → timed → intervention → larviciding

<larviciding>
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

anopheles

Documentation (element)

Simple larviciding intervention description.

anopheles

→ scenario → interventions → timed → intervention → larviciding → anopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

Mosquito to be larvicided

mosquito=string

Mosquito to be larvicided

Proportionate reduction in emergence

effectiveness=double

Units: none Min: 0 Max: 1

Proportional reduction in emergence rate

Duration of activity

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

Mass Cohort Selection

→ scenario → interventions → timed → intervention → cohort

<cohort
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  [ cohort=boolean ]
  />

Documentation (element)

Units: List of elements

Description of mass cohort selection.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Cohort only

cohort=boolean

Units: Proportion Min: 0 Max: 1

Restrict distribution to chosen cohort.

healthSystem

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entoData

<entoData
    name=string
    mode=("2" or "4")
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Attributes

Entomology dataset

name=string

Units: string

Name of entomology data

Transmission simulation mode

mode=("2" or "4")

Units: Code

Transmission setting (vector control not enabled)

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Units: List of elements

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Units: List of elements

Parameters of the transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <eir ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Initial guess of proportion of mosquitoes infected

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial guess of proportion of mosquitoes infectious

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Fourier approximation to pre-intervention EIR

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    b1=double
    a2=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Inoculations per person per day

Description of target entomological inoculation rate, used to calculate the vector emergence rate. An EIR array is generated from the exponent of the inverse discrete fourier transform of these parameters.

Attributes

a0 parameter of Fourier approximation to ln(EIR)

a0=double

a1 parameter of Fourier approximation to ln(EIR)

a1=double

b1 parameter of Fourier approximation to ln(EIR)

b1=double

a2 parameter of Fourier approximation to ln(EIR)

a2=double

b2 parameter of Fourier approximation to ln(EIR)

b2=double

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Vector Species

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqLaidEggsSameDayProportion=double
    mosqSeekingDuration=double
    mosqSurvivalFeedingCycleProbability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
    mosqHumanBloodIndex=double
    minInfectedThreshold=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

Duration of the resting period of the vector (days)

mosqRestDuration=int

Extrinsic incubation period (days)

extrinsicIncubationPeriod=int

Proportion of mosquitoes host seeking on same day as ovipositing

mosqLaidEggsSameDayProportion=double

Duration of the host-seeking period of the vector (days)

mosqSeekingDuration=double

Probability that the mosquito survives the feeding cycle

mosqSurvivalFeedingCycleProbability=double

Probability that the mosquito succesfully bites chosen host

mosqProbBiting=double

Probability that the mosquito escapes host and finds a resting place after biting

mosqProbFindRestSite=double

Probability of mosquito successfully resting after finding a resting site

mosqProbResting=double

Probability of a mosquito successfully laying eggs given that it has rested

mosqProbOvipositing=double

Human blood index

mosqHumanBloodIndex=double

The proportion of resting mosquitoes which fed on human blood during the last feed.

Min infected threshold

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
    mosqRelativeEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Relative availability of nonhuman hosts of type i (to other nonhuman hosts)

mosqRelativeEntoAvailability=double

Probability of mosquito successfully biting host

mosqProbBiting=double

Probability that the mosquito escapes host and finds a resting place after biting

mosqProbFindRestSite=double

Probability of mosquito successfully resting after finding a resting site

mosqProbResting=double

nonHumanHosts

→ scenario → entoData → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Units: List of elements

Name of this species of non human hosts (must match up with those described per anopheles section)

number

number=double

Pharmacokinetics and pharmacodynamics

<drugDescription>
IN THIS ORDER:
| ( <drug ... /> )+
</drugDescription>

drug

Documentation (element)

Units: List of elements

Drug model parameters

drug

→ scenario → drugDescription → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (element)

Sequence of drug descriptions forming a library of drug parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → drugDescription → drug → PD

<PD>
IN THIS ORDER:
| ( <allele ... /> )+
</PD>

allele

allele

→ scenario → drugDescription → drug → PD → allele

<allele
    name=string
  >
IN THIS ORDER:
|   <initial_frequency ... /> 
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</allele>

Documentation (element)

PD parameters per allele, plus initial frequency of each allele.

Note: we assume a one-to-one correspondance of drugs to loci, hence each drug has an independent set of alleles here.

Attributes

name

name=string

Relative frequency

→ scenario → drugDescription → drug → PD → allele → initial_frequency

<initial_frequency>
    double
</initial_frequency>

Documentation (element)

Units: relative frequency Min: 0

Frequency, relative to the total frequency of all alleles for this drug/locus.

Maximal parasite killing rate

→ scenario → drugDescription → drug → PD → allele → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → drugDescription → drug → PD → allele → IC50

<IC50>
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

Slope of effect curve

→ scenario → drugDescription → drug → PD → allele → slope

<slope>
    double
</slope>

Documentation (element)

Units: no units

n — Slope of the concentration effect curve

PK

→ scenario → drugDescription → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
|   <half_life ... /> 
|   <vol_dist ... /> 
</PK>

Drug concentration considered negligible

→ scenario → drugDescription → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → drugDescription → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate (which is: ln(2) / half_life).

Volume of Distribution

→ scenario → drugDescription → drug → PK → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Model options and parameters

→ scenario → model

<model>
IN THIS ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <parameters ... /> 
</model>

Documentation (element)

Units: List of elements

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

Units: List of elements

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: include/util/ModelOptions.hpp and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=int
  />

Documentation (type)

Units: List of elements

Description of clinical parameters.

This is related to the health-system description, but contains data which can't be changed as part of an intervention and is not restricted to treatment.

Attributes

Follow-up period during which recurrence is treated as a failure

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Units: List of elements

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → model → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 20 documentation

Generated from: scenario_20.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    name=string
    wuID=int
    assimMode=("0" or "1")
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_20.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entoData ... /> 
| [ <drugDescription ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Units: string

Name of intervention

Work unit identifier

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

Assimilator mode

assimMode=("0" or "1")

Units: Code

Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Attributes

Name of demography data

name=string

Units: string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Number Min: 0 Max: 100

Maximum age of simulated humans

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Percentage of human population in age group

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Attributes

name of monitoring information

name=string

Units: string

Name of monitoring data

continuous

→ scenario → monitoring → continuous

<continuous
    period=int
  [ duringInit=boolean ]
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Days between reports

period=int

Units: Days Min: 1 Max: unbounded

Number of timesteps between reports.

During initialization

duringInit=boolean

Units: Days Min: 1 Max: unbounded

option

→ scenario → monitoring → continuous → option

<option
    name=string
    value=boolean
  />

Attributes

Model options required

name=string

Options define different model structures. Option name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.

Indicator of whether option is required

value=boolean

Option value (true/false). Each option has a default value used if the option is not listed (usually false but sometimes true).

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
  >
IN THIS ORDER:
|   <surveyTime ... /> 
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time; 0 means just before start of main sim and is a valid survey-point. Reported data is either from a point-time survey (immediate data) or is collected over the previous year (data from previous timesteps-per-year period). Simulation will end immediately after last survey is taken.

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Preventative interventions

<interventions
    name=string
  >
IN THIS ORDER:
| [ <MDADescription ... /> ]
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| ( <anopheles ... /> )*
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

Attributes

Intervention

name=string

Units: string

Name of age specific intervention

Drug dose(s) used in MDA

<MDADescription>
IN THIS ORDER:
| [ <schedule ... /> ]
</MDADescription>

schedule

Documentation (element)

Units: List of medicate elements

Description of drug dose(s) used in a mass-drug-administration intervention.

When using the new (Event Scheduler) case management model, a treatment schedule must be present.

schedule

→ scenario → interventions → MDADescription → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

The base (unmodified) schedule of drugs administered for this treatment.

medicate

→ scenario → interventions → MDADescription → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  />

Attributes

drug

drug=string

Units: string

Abbreviated name of drug compound

drug dose

mg=double

Units: mg

Quantity of drug compound

time of administration

hour=double

Units: hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

Type of vaccine

vaccineType=int

Units: Code

Type of vaccine

Half life of drug effect

→ scenario → interventions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Variance parameter for vaccine efficacy

→ scenario → interventions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

initialEfficacy

→ scenario → interventions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

Age specific intervention

name=string

Units: string

Name of age specific intervention

Frequency

freq=double

Frequency of parasite genotype

ACR

ACR=double

Adequate clinical response (proportion)

Prophylactic period

proph=int

Prophylactic period

Tolerance period

tolPeriod=int

Tolerance period

atten=double

Tolerance period

anopheles

→ scenario → interventions → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <VADescription ... /> ]
</anopheles>

Attributes

Entomological effects of interventions

mosquito=string

Description of the entomological effects of interventions

ITNDescription

→ scenario → interventions → anopheles → ITNDescription

<ITNDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</ITNDescription>

Attributes

ITN effects

name=string

Units: string

Name of Insecticide Treated Net intervention

Deterrency

→ scenario → interventions → anopheles → ITNDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability (before decay).

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

Pre-prandial killing effect

→ scenario → interventions → anopheles → ITNDescription → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

Post-prandial killing effect

→ scenario → interventions → anopheles → ITNDescription → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

IRSDescription

→ scenario → interventions → anopheles → IRSDescription

<IRSDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <killingEffect ... /> 
</IRSDescription>

Attributes

name of IRS intervention

name=string

Units: string

Name of Indoor Residual Spraying intervention

Deterrency

→ scenario → interventions → anopheles → IRSDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

killing effect

→ scenario → interventions → anopheles → IRSDescription → killingEffect

<killingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

VADescription

→ scenario → interventions → anopheles → VADescription

<VADescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</VADescription>

deterrency

Attributes

Name of mosquito deterrency intervention

name=string

Units: string

Name of mosquito deterrency intervention

Deterrency

→ scenario → interventions → anopheles → VADescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

Continuously applied interventions

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
</continuous>

List of age groups for vaccination

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Description of ITN deployment

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

List of age groups for IPTi

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Timed interventions

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfectionsPerThousandHosts ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <VectorAvailability ... /> ]
| [ <ipti ... /> ]
| [ <immuneSuppression ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <larviciding ... /> ]
</intervention>

Attributes

Time step of intervention

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</uncomplicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

decisions

→ scenario → healthSystem → EventScheduler → uncomplicated → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )*
</decisions>

decision

Documentation (type)

case (uncomplicated only): Returns "UC1" if there is no recent history of a malarial case, or "UC2" if there is.
result: Dependent on decision "test", this performs a parasite density test. Output is one of "none" (no test performed), "positive", "negative".

The following decisions must be described here:

test (uncomplicated only): Outputs must be "none", "microscopy" or "RDT" to describe which test the "result" decision uses.
treatment: Describes which treatment to use. Values aren't restricted but must match up with a treatment described in the corresponding "treatments" section.
hospitalisation (complicated only): none, immediate or delayed.

decision

→ scenario → healthSystem → EventScheduler → uncomplicated → decisions → decision

<decision
    name=string
    depends=string
    values=string
  >
    string
</decision>

Documentation (type)

A decision describes how to choose between a set of values.

Lexically, it can contain symbols matching "[_.a-zA-Z0-9]+", round brackets: (), braces: {} and colons. Whitespace is ignored except to separate symbols.

For each BRANCH_SET each BRANCH must have the same DECISION. This DECISION must be one of the dependencies mentioned in "depends". This may be:

another decision, in which case the VALUE immediately following in brackets must correspond to one of its output values. The BRANCH_SET immediately containing this BRANCH must represent each output value of the same decision exactly once, and no parent BRANCH_SET may be for the same DECISION.
"p": this indicates a probabilistic decision. In this case the value is a probability, the sum of all values for the BRANCH_SET must be 1 and the decision must be associated directly with OUTCOMEs (not sub-TREEs).
"age": this indicates an age-test. The VALUE must have the form "a-b", indicating that this branch will be taken for individuals aged such that a <= age < b, where a,b are non-negative real numbers or the special value "inf", and a <= b. All VALUEs in the BRANCH_SET must cover all possible (non-negative real) ages, with no overlap (hence, smallest a must be 0 and greatest b must be inf).

Semantically, each OUTCOME must be one of the values associated with this decision.

Attributes

Name of decision

name=string

The name of this decision. The name must match the regular expression "[_a-zA-Z0-9]+"; that is it can only contain letters, digits and _ characters (no spaces, punctuation, etc.).

Preceding decisions

depends=string

Outcome values

values=string

A comma-separated list of outcome values this decision may have. The name of each value must be of the same form as decision names (i.e. only contain letters, digits and _ characters).

treatments

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments

<treatments>
IN THIS ORDER:
| ( <treatment ... /> )*
</treatments>

treatment

Documentation (type)

Units: string

A list of drug treatment tables. Each should have a name corresponding to one of the "drug" decision's values.

treatment

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment

<treatment
    name=string
  >
IN THIS ORDER:
|   <schedule ... /> 
| ( <modifier ... /> )*
</treatment>

Documentation (type)

A description of a base treatment schedule along with modifiers to handle delays, quality variations, etc.

Attributes

Treatment administered

name=string

Units: string

Name corresponding to one of the drug decision's output values.

schedule

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

The base (unmodified) schedule of drugs administered for this treatment.

modifier

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier

<modifier
    decision=string
  >
EXACTLY ONE OF:
| ( <multiplyQty ... /> )*
| ( <delay ... /> )*
| ( <selectTimeRange ... /> )*
</modifier>

Documentation (type)

A modifier for this treatment, according to the outputs of a decision.

Attributes

decision

decision=string

Units: string

Specifies the decision that this modifier acts on.

multiplyQty

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier → multiplyQty

<multiplyQty
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Multiplies the quantity of active ingredients of drugs administered.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of multipliers for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0.5,1" the quantity of drug A is halved while that of B is unchanged.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

delay

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier → delay

<delay
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Delays administration of drugs listed in the base schedule by so many hours.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of delays (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0,6", drug A is administered as in the base schedule while drug B is administered 6 hours later than specified.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

selectTimeRange

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier → selectTimeRange

<selectTimeRange
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Selects which drug doses to administer according to time of administration (before times are modified by delays). Half-open interval: [x,y)

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of time-ranges (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. The time-ranges should be of the form x-y and are interpreted as the half-open interval [x,y); that is a drug listed with time t will only be administered if x <= t < y.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</complicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
|   <pImmediateUC ... /> 
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: days Min: 0 Max: unbounded

Maximum number of timesteps (including first of case) an individual will remember they are sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial/non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of a complicated/severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Probability of immediate UC treatment seeking

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → pImmediateUC

<pImmediateUC>
    double
</pImmediateUC>

Documentation (element)

Units: none Min: 0 Max: 1

Probability that UC treatment seeking will be done immediately when sick, on second day given that it wasn't done on first, etc.

ImmediateOutcomes

<ImmediateOutcomes
    name=string
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
</ImmediateOutcomes>

Documentation (type)

Units: List of elements

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Case Management model

name=string

Units: string

Name of health system

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

ACT

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

QN

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

Probability that a patient with uncomplicated disease seeks official care immediately

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease self-treats

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

CFR

→ scenario → healthSystem → CFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

Documentation (element)

Case fatality rate (probability of an inpatient fatality from a bout of severe malaria, per age-group).

group

→ scenario → healthSystem → CFR → group

<group
    value=double
    lowerbound=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Probabilities of sequelae in inpatients

<pSequelaeInpatient>
IN THIS ORDER:
| ( <group ... /> )+
</pSequelaeInpatient>

group

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients, during a severe bout.

Replacement transmission setting (vector control not enabled)

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (element)

Units: List of elements

New description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

EIRDaily

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Inoculations per person per day

Attributes

Time origin of EIR sequence

origin=string

importedInfectionsPerThousandHosts

→ scenario → interventions → timed → intervention → importedInfectionsPerThousandHosts

<importedInfectionsPerThousandHosts>
    double
</importedInfectionsPerThousandHosts>

Mass Drug Administration

→ scenario → interventions → timed → intervention → MDA

<MDA
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Vaccination

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN deployment

→ scenario → interventions → timed → intervention → ITN

<ITN
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IRS deployment

→ scenario → interventions → timed → intervention → IRS

<IRS
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of IRS deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Mosquito deterrent

→ scenario → interventions → timed → intervention → VectorAvailability

<VectorAvailability
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of a mosquito deterrent deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IPTi deployment

→ scenario → interventions → timed → intervention → ipti

<ipti
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Immune suppression deployment

→ scenario → interventions → timed → intervention → immuneSuppression

<immuneSuppression
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Removes all exposure-related immunity gained over time by hosts without removing infections.

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Insert R_0 case

→ scenario → interventions → timed → intervention → insertR_0Case

<insertR_0Case/>

Documentation (element)

Units: List of elements

Used to simulate R_0. First, infections should be eliminated, immunity removed, and the population given an effective transmission- blocking vaccine (not done by this intervention). Then this intervention may be used to: pick one human, infect him, and remove transmission-blocking vaccine effect on this human. Thus only this one human will be a source of infections in an unprotected population.

Uninfect vectors

→ scenario → interventions → timed → intervention → uninfectVectors

<uninfectVectors/>

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

larviciding

→ scenario → interventions → timed → intervention → larviciding

<larviciding>
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

anopheles

Documentation (element)

Simple larviciding intervention description.

anopheles

→ scenario → interventions → timed → intervention → larviciding → anopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

Mosquito to be larvicided

mosquito=string

Mosquito to be larvicided

Proportionate reduction in emergence

effectiveness=double

Units: none Min: 0 Max: 1

Proportional reduction in emergence rate

Duration of activity

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

healthSystem

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
|   <pSequelaeInpatient ... /> 
</healthSystem>

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entoData

<entoData
    name=string
    mode=("2" or "4")
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Attributes

Entomology dataset

name=string

Units: string

Name of entomology data

Transmission simulation mode

mode=("2" or "4")

Units: Code

Transmission setting (vector control not enabled)

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Units: List of elements

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Units: List of elements

Parameters of the transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <eir ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

Identifier for this anopheles species

mosquito=string

Initial guess of proportion of mosquitoes infected

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial guess of proportion of mosquitoes infectious

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Fourier approximation to pre-intervention EIR

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    b1=double
    a2=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Inoculations per person per day

Attributes

a0 parameter of Fourier approximation to ln(EIR)

a0=double

a1 parameter of Fourier approximation to ln(EIR)

a1=double

b1 parameter of Fourier approximation to ln(EIR)

b1=double

a2 parameter of Fourier approximation to ln(EIR)

a2=double

b2 parameter of Fourier approximation to ln(EIR)

b2=double

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Vector Species

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqLaidEggsSameDayProportion=double
    mosqSeekingDuration=double
    mosqSurvivalFeedingCycleProbability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
    mosqHumanBloodIndex=double
    minInfectedThreshold=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

Duration of the resting period of the vector (days)

mosqRestDuration=int

Extrinsic incubation period (days)

extrinsicIncubationPeriod=int

Proportion of mosquitoes host seeking on same day as ovipositing

mosqLaidEggsSameDayProportion=double

Duration of the host-seeking period of the vector (days)

mosqSeekingDuration=double

Probability that the mosquito survives the feeding cycle

mosqSurvivalFeedingCycleProbability=double

Probability that the mosquito succesfully bites chosen host

mosqProbBiting=double

Probability that the mosquito escapes host and finds a resting place after biting

mosqProbFindRestSite=double

Probability of mosquito successfully resting after finding a resting site

mosqProbResting=double

Probability of a mosquito successfully laying eggs given that it has rested

mosqProbOvipositing=double

Human blood index

mosqHumanBloodIndex=double

The proportion of resting mosquitoes which fed on human blood during the last feed.

Min infected threshold

minInfectedThreshold=double

Min: 0

If less than this many mosquitoes remain infected, transmission is interrupted.

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
    mosqRelativeEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

Identifier for this category of non-human hosts

name=string

Relative availability of nonhuman hosts of type i (to other nonhuman hosts)

mosqRelativeEntoAvailability=double

Probability of mosquito successfully biting host

mosqProbBiting=double

Probability that the mosquito escapes host and finds a resting place after biting

mosqProbFindRestSite=double

Probability of mosquito successfully resting after finding a resting site

mosqProbResting=double

nonHumanHosts

→ scenario → entoData → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Units: List of elements

Name of this species of non human hosts (must match up with those described per anopheles section)

number

number=double

Pharmacokinetics and pharmacodynamics

<drugDescription>
IN THIS ORDER:
| ( <drug ... /> )+
</drugDescription>

drug

Documentation (element)

Units: List of elements

Drug model parameters

drug

→ scenario → drugDescription → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (element)

Sequence of drug descriptions forming a library of drug parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → drugDescription → drug → PD

<PD>
IN THIS ORDER:
| ( <allele ... /> )+
</PD>

allele

allele

→ scenario → drugDescription → drug → PD → allele

<allele
    name=string
  >
IN THIS ORDER:
|   <initial_frequency ... /> 
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</allele>

Documentation (element)

PD parameters per allele, plus initial frequency of each allele.

Note: we assume a one-to-one correspondance of drugs to loci, hence each drug has an independent set of alleles here.

Attributes

name

name=string

Relative frequency

→ scenario → drugDescription → drug → PD → allele → initial_frequency

<initial_frequency>
    double
</initial_frequency>

Documentation (element)

Units: relative frequency Min: 0

Frequency, relative to the total frequency of all alleles for this drug/locus.

Maximal parasite killing rate

→ scenario → drugDescription → drug → PD → allele → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → drugDescription → drug → PD → allele → IC50

<IC50>
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

Slope of effect curve

→ scenario → drugDescription → drug → PD → allele → slope

<slope>
    double
</slope>

Documentation (element)

Units: no units

n — Slope of the concentration effect curve

PK

→ scenario → drugDescription → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
|   <half_life ... /> 
|   <vol_dist ... /> 
</PK>

Drug concentration considered negligible

→ scenario → drugDescription → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → drugDescription → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate (which is: ln(2) / half_life).

Volume of Distribution

→ scenario → drugDescription → drug → PK → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Model options and parameters

→ scenario → model

<model>
IN THIS ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <parameters ... /> 
</model>

Documentation (element)

Units: List of elements

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

Units: List of elements

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: include/util/ModelOptions.hpp and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=int
  />

Documentation (type)

Units: List of elements

Description of clinical parameters.

This is related to the health-system description, but contains data which can't be changed as part of an intervention and is not restricted to treatment.

Attributes

Follow-up period during which recurrence is treated as a failure

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Units: List of elements

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → model → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 19 documentation

Generated from: scenario_19.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    name=string
    wuID=int
    assimMode=("0" or "1")
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_19.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entoData ... /> 
| [ <drugDescription ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Units: string

Name of intervention

Work unit identifier

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

Assimilator mode

assimMode=("0" or "1")

Units: Code

Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Attributes

Name of demography data

name=string

Units: string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Number Min: 0 Max: 100

Maximum age of simulated humans

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Percentage of human population in age group

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  >
IN THIS ORDER:
| [ <continuous ... /> ]
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Attributes

name of monitoring information

name=string

Units: string

Name of monitoring data

continuous

→ scenario → monitoring → continuous

<continuous
    period=int
  >
IN THIS ORDER:
| ( <option ... /> )*
</continuous>

option

Attributes

Days between reports

period=int

Units: Days Min: 1 Max: unbounded

Number of days between reports.

option

→ scenario → monitoring → continuous → option

<option
    name=string
    value=boolean
  />

Attributes

Model options required

name=string

Options define different model structures. Option name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.

Indicator of whether option is required

value=boolean

Option value (true/false). Each option has a default value used if the option is not listed (usually false but sometimes true).

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
  >
IN THIS ORDER:
|   <surveyTime ... /> 
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time; 0 means just before start of main sim and is a valid survey-point. Reported data is either from a point-time survey (immediate data) or is collected over the previous year (data from previous timesteps-per-year period). Simulation will end immediately after last survey is taken.

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Preventative interventions

<interventions
    name=string
  >
IN THIS ORDER:
| [ <MDADescription ... /> ]
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| ( <anopheles ... /> )*
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

Attributes

Intervention

name=string

Units: string

Name of age specific intervention

Drug dose(s) used in MDA

<MDADescription>
IN THIS ORDER:
| [ <schedule ... /> ]
</MDADescription>

schedule

Documentation (element)

Units: List of medicate elements

Description of drug dose(s) used in a mass-drug-administration intervention.

When using the new (Event Scheduler) case management model, a treatment schedule must be present.

schedule

→ scenario → interventions → MDADescription → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

The base (unmodified) schedule of drugs administered for this treatment.

medicate

→ scenario → interventions → MDADescription → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  />

Attributes

drug

drug=string

Units: string

Abbreviated name of drug compound

drug dose (TODO is this correct?)

mg=double

Units: mg

Quantity of drug compound

time of administration

hour=double

Units: hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

Type of vaccine

vaccineType=int

Units: Code

Type of vaccine

Half life of drug effect

→ scenario → interventions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Variance parameter for vaccine efficacy

→ scenario → interventions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

initialEfficacy

→ scenario → interventions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

Age specific intervention

name=string

Units: string

Name of age specific intervention

Frequency

freq=double

Frequency of parasite genotype

ACR

ACR=double

Adequate clinical response (proportion)

Prophylactic period

proph=int

Prophylactic period

Tolerance period

tolPeriod=int

Tolerance period

atten=double

Tolerance period

anopheles

→ scenario → interventions → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <VADescription ... /> ]
</anopheles>

Attributes

Entomological effects of interventions

mosquito=string

Description of the entomological effects of interventions

ITNDescription

→ scenario → interventions → anopheles → ITNDescription

<ITNDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</ITNDescription>

Attributes

ITN effects

name=string

Units: string

Name of Insecticide Treated Net intervention

Deterrency

→ scenario → interventions → anopheles → ITNDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability (before decay).

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

Pre-prandial killing effect

→ scenario → interventions → anopheles → ITNDescription → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

Post-prandial killing effect

→ scenario → interventions → anopheles → ITNDescription → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

IRSDescription

→ scenario → interventions → anopheles → IRSDescription

<IRSDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <killingEffect ... /> 
</IRSDescription>

Attributes

name of IRS intervention

name=string

Units: string

Name of Indoor Residual Spraying intervention

Deterrency

→ scenario → interventions → anopheles → IRSDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

killing effect

→ scenario → interventions → anopheles → IRSDescription → killingEffect

<killingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

VADescription

→ scenario → interventions → anopheles → VADescription

<VADescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</VADescription>

deterrency

Attributes

Name of mosquito deterrency intervention

name=string

Units: string

Name of mosquito deterrency intervention

Deterrency

→ scenario → interventions → anopheles → VADescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

Continuously applied interventions

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
</continuous>

List of age groups for vaccination

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Description of ITN deployment

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

List of age groups for IPTi

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Timed interventions

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfectionsPerThousandHosts ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <VectorAvailability ... /> ]
| [ <ipti ... /> ]
| [ <immuneSuppression ... /> ]
| [ <insertR_0Case ... /> ]
| [ <uninfectVectors ... /> ]
| [ <larviciding ... /> ]
</intervention>

Attributes

Time step of intervention

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</uncomplicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

decisions

→ scenario → healthSystem → EventScheduler → uncomplicated → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )*
</decisions>

decision

Documentation (type)

age5Test: tests the patient's age and returns "under5" or "over5".
case (uncomplicated only): Returns "UC1" if there is no recent history of a malarial case, or "UC2" if there is.
result (uncomplicated only): Dependent on decision "test", this performs a parasite density test. Output is one of "none" (no test performed), "positive", "negative".

The following decisions must be described here:

test (uncomplicated only): Outputs must be "none", "microscopy" or "RDT" to describe which test the "result" decision uses.
treatment: Describes which treatment to use. Values aren't restricted but must match up with a treatment described in the corresponding "treatments" section.

decision

→ scenario → healthSystem → EventScheduler → uncomplicated → decisions → decision

<decision
    name=string
    depends=string
    values=string
  >
    string
</decision>

Documentation (type)

A decision describes how to choose between a set of values.

Lexically, it can contain symbols matching "[_.a-zA-Z0-9]+", round brackets: (), braces: {} and colons. Whitespace is ignored except to separate symbols.

For each BRANCH_SET each BRANCH must have the same DECISION. This DECISION must be one of the dependencies mentioned in "depends". This may be:

another decision, in which case the VALUE immediately following in brackets must correspond to one of its output values. The BRANCH_SET immediately containing this BRANCH must represent each output value of the same decision exactly once, and no parent BRANCH_SET may be for the same DECISION.
"p": this indicates a probabilistic decision. In this case the value is a probability, the sum of all values for the BRANCH_SET must be 1 and the decision must be associated directly with OUTCOMEs (not sub-TREEs).
"age": this indicates an age-test. The VALUE must have the form "a-b", indicating that this branch will be taken for individuals aged such that a <= age < b, where a,b are non-negative real numbers or the special value "inf", and a <= b. All VALUEs in the BRANCH_SET must cover all possible (non-negative real) ages, with no overlap (hence, smallest a must be 0 and greatest b must be inf).

Semantically, each OUTCOME must be one of the values associated with this decision.

Attributes

Name of decision

name=string

The name of this decision. The name must match the regular expression "[_a-zA-Z0-9]+"; that is it can only contain letters, digits and _ characters (no spaces, punctuation, etc.).

Preceding decisions

depends=string

Outcome values

values=string

A comma-separated list of outcome values this decision may have. The name of each value must be of the same form as decision names (i.e. only contain letters, digits and _ characters).

treatments

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments

<treatments>
IN THIS ORDER:
| ( <treatment ... /> )*
</treatments>

treatment

Documentation (type)

Units: string

A list of drug treatment tables. Each should have a name corresponding to one of the "drug" decision's values.

treatment

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment

<treatment
    name=string
  >
IN THIS ORDER:
|   <schedule ... /> 
| ( <modifier ... /> )*
</treatment>

Documentation (type)

A description of a base treatment schedule along with modifiers to handle delays, quality variations, etc.

Attributes

Treatment administered

name=string

Units: string

Name corresponding to one of the drug decision's output values.

schedule

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

The base (unmodified) schedule of drugs administered for this treatment.

modifier

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier

<modifier
    decision=string
  >
EXACTLY ONE OF:
| ( <multiplyQty ... /> )*
| ( <delay ... /> )*
| ( <selectTimeRange ... /> )*
</modifier>

Documentation (type)

A modifier for this treatment, according to the outputs of a decision.

Attributes

decision

decision=string

Units: string

Specifies the decision that this modifier acts on.

multiplyQty

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier → multiplyQty

<multiplyQty
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Multiplies the quantity of active ingredients of drugs administered.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of multipliers for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0.5,1" the quantity of drug A is halved while that of B is unchanged.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

delay

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier → delay

<delay
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Delays administration of drugs listed in the base schedule by so many hours.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of delays (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0,6", drug A is administered as in the base schedule while drug B is administered 6 hours later than specified.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

selectTimeRange

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier → selectTimeRange

<selectTimeRange
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Selects which drug doses to administer according to time of administration (before times are modified by delays).

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of time-ranges (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. The time-ranges should be of the form x-y and are interpreted as the half-open interval [x,y); that is a drug listed with time t will only be administered if x <= t < y.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</complicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
|   <pImmediateUC ... /> 
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: days Min: 0 Max: unbounded

Maximum number of timesteps (including first of case) an individual will remember they are sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial/non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of a complicated/severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Probability of immediate UC treatment seeking

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → pImmediateUC

<pImmediateUC>
    double
</pImmediateUC>

Documentation (element)

Units: none Min: 0 Max: 1

Probability that UC treatment seeking will be done immediately when sick, on second day given that it wasn't done on first, etc.

ImmediateOutcomes

<ImmediateOutcomes
    name=string
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
</ImmediateOutcomes>

Documentation (type)

Units: List of elements

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Case Management model

name=string

Units: string

Name of health system

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

ACT

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

QN

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

Probability that a patient with uncomplicated disease seeks official care immediately

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease self-treats

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probabilities of sequelae in inpatients

→ scenario → healthSystem → ImmediateOutcomes → pSequelaeInpatient

<pSequelaeInpatient>
IN THIS ORDER:
| ( <item ... /> )+
</pSequelaeInpatient>

item

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients.

Note: previously these ranges were silently remapped. To prevent unexpected differences, there must be two groups, with maxAgeYrs bounds 5 and 99 respectively.

item

→ scenario → healthSystem → ImmediateOutcomes → pSequelaeInpatient → item

<item
    value=double
    maxAgeYrs=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Upper bound

maxAgeYrs=double

Units: Years Min: 0 Max: 100

Upper bound of age group

CFR

→ scenario → healthSystem → CFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

group

→ scenario → healthSystem → CFR → group

<group
    cfr=double
    lowerbound=double
  />

Attributes

Case fatality rate

cfr=double

Units: Proportion Min: 0 Max: 1

Case fatality rate

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Replacement transmission setting (vector control not enabled)

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (element)

Units: List of elements

New description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

EIRDaily

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Inoculations per person per day

Attributes

Time origin of EIR sequence

origin=string

importedInfectionsPerThousandHosts

→ scenario → interventions → timed → intervention → importedInfectionsPerThousandHosts

<importedInfectionsPerThousandHosts>
    double
</importedInfectionsPerThousandHosts>

Mass Drug Administration

→ scenario → interventions → timed → intervention → MDA

<MDA
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Vaccination

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN deployment

→ scenario → interventions → timed → intervention → ITN

<ITN
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IRS deployment

→ scenario → interventions → timed → intervention → IRS

<IRS
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of IRS deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Mosquito deterrent

→ scenario → interventions → timed → intervention → VectorAvailability

<VectorAvailability
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of a mosquito deterrent deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IPTi deployment

→ scenario → interventions → timed → intervention → ipti

<ipti
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Immune suppression deployment

→ scenario → interventions → timed → intervention → immuneSuppression

<immuneSuppression
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Removes all exposure-related immunity gained over time by hosts without removing infections.

Hypothetical, but potentially useful to simulate scenarios with unprotected humans.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Insert R_0 case

→ scenario → interventions → timed → intervention → insertR_0Case

<insertR_0Case/>

Documentation (element)

Units: List of elements

Used to simulate R_0. First, infections should be eliminated, immunity removed, and the population given an effective transmission- blocking vaccine (not done by this intervention). Then this intervention may be used to: pick one human, infect him, and remove transmission-blocking vaccine effect on this human. Thus only this one human will be a source of infections in an unprotected population.

Uninfect vectors

→ scenario → interventions → timed → intervention → uninfectVectors

<uninfectVectors/>

Documentation (element)

Units: List of elements

Hypothetical, but potentially useful to simulate a setting starting from no infections, but with enough mosquitoes to reach a set equilibrium of exposure.

larviciding

→ scenario → interventions → timed → intervention → larviciding

<larviciding>
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

anopheles

Documentation (element)

Simple larviciding intervention description.

anopheles

→ scenario → interventions → timed → intervention → larviciding → anopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

Mosquito to be larvicided

mosquito=string

Mosquito to be larvicided

Proportionate reduction in emergence

effectiveness=double

Units: none Min: 0 Max: 1

Proportional reduction in emergence rate

Duration of activity

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

healthSystem

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
</healthSystem>

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entoData

<entoData
    name=string
    mode=("2" or "4")
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Attributes

Entomology dataset

name=string

Units: string

Name of entomology data

Transmission simulation mode

mode=("2" or "4")

Units: Code

Transmission setting (vector control not enabled)

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Units: List of elements

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Units: List of elements

Parameters of the transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <eir ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

(TODO- Nakul to assign description)

mosquito=string

Initial guess of proportion of mosquitoes infected

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial guess of proportion of mosquitoes infectious

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Fourier approximation to pre-intervention EIR

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    b1=double
    a2=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Inoculations per person per day

Attributes

a0 parameter of Fourier approximation to ln(EIR)

a0=double

a1 parameter of Fourier approximation to ln(EIR)

a1=double

b1 parameter of Fourier approximation to ln(EIR)

b1=double

a2 parameter of Fourier approximation to ln(EIR)

a2=double

b2 parameter of Fourier approximation to ln(EIR)

b2=double

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Vector Species

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqLaidEggsSameDayProportion=double
    mosqSeekingDuration=double
    mosqSurvivalFeedingCycleProbability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
    mosqHumanBloodIndex=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

Duration of the resting period of the vector (days)

mosqRestDuration=int

Extrinsic incubation period (days)

extrinsicIncubationPeriod=int

Proportion of mosquitoes host seeking on same day as ovipositing

mosqLaidEggsSameDayProportion=double

Duration of the host-seeking period of the vector (days)

mosqSeekingDuration=double

Probability that the mosquito survives the feeding cycle

mosqSurvivalFeedingCycleProbability=double

Probability that the mosquito survives biting (TODO- check description)

mosqProbBiting=double

Probability that the mosquito finds a resting place

mosqProbFindRestSite=double

Probability that the mosquito survives resting (TODO- check description)

mosqProbResting=double

Probability that the mosquito survives oviposition (TODO- check description)

mosqProbOvipositing=double

Human blood index

mosqHumanBloodIndex=double

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
    mosqRelativeEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

(TODO- Nakul to assign description)

name=string

(TODO- Nakul to assign description)

mosqRelativeEntoAvailability=double

(TODO- Nakul to assign description)

mosqProbBiting=double

(TODO- Nakul to assign description)

mosqProbFindRestSite=double

(TODO- Nakul to assign description)

mosqProbResting=double

nonHumanHosts

→ scenario → entoData → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Units: List of elements

Name of this species of non human hosts (must match up with those described per anopheles section)

number

number=double

Pharmacokinetics and pharmacodynamics

<drugDescription>
IN THIS ORDER:
| ( <drug ... /> )+
</drugDescription>

drug

Documentation (element)

Units: List of elements

Drug model parameters

drug

→ scenario → drugDescription → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (element)

Sequence of drug descriptions forming a library of drug parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → drugDescription → drug → PD

<PD>
IN THIS ORDER:
| ( <allele ... /> )+
</PD>

allele

allele

→ scenario → drugDescription → drug → PD → allele

<allele
    name=string
  >
IN THIS ORDER:
|   <initial_frequency ... /> 
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</allele>

Documentation (element)

PD parameters per allele, plus initial frequency of each allele.

Note: we assume a one-to-one correspondance of drugs to loci, hence each drug has an independent set of alleles here.

Attributes

name

name=string

Relative frequency

→ scenario → drugDescription → drug → PD → allele → initial_frequency

<initial_frequency>
    double
</initial_frequency>

Documentation (element)

Units: relative frequency Min: 0

Frequency, relative to the total frequency of all alleles for this drug/locus.

Maximal parasite killing rate

→ scenario → drugDescription → drug → PD → allele → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → drugDescription → drug → PD → allele → IC50

<IC50>
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

Slope of effect curve

→ scenario → drugDescription → drug → PD → allele → slope

<slope>
    double
</slope>

Documentation (element)

Units: no units

n — Slope of the concentration effect curve

PK

→ scenario → drugDescription → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
|   <half_life ... /> 
|   <vol_dist ... /> 
</PK>

Drug concentration considered negligible

→ scenario → drugDescription → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → drugDescription → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate (which is: ln(2) / half_life).

Volume of Distribution

→ scenario → drugDescription → drug → PK → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Model options and parameters

→ scenario → model

<model>
IN THIS ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <parameters ... /> 
</model>

Documentation (element)

Units: List of elements

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

Units: List of elements

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: include/util/ModelOptions.hpp and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=int
  />

Documentation (type)

Units: List of elements

Description of clinical parameters.

This is related to the health-system description, but contains data which can't be changed as part of an intervention and is not restricted to treatment.

Attributes

Follow-up period during which recurrence is treated as a failure

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Units: List of elements

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

Pre-erythrocytic latent period

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → model → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 18 documentation

Generated from: scenario_18.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

Scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    name=string
    wuID=int
    assimMode=("0" or "1")
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_18.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entoData ... /> 
| [ <drugDescription ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

Version of the xml schema

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

Reference number of the analysis

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

Name of intervention

name=string

Units: string

Name of intervention

Work unit identifier

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

Assimilator mode

assimMode=("0" or "1")

Units: Code

Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)

Human age distribution

→ scenario → demography

<demography
    name=string
    popSize=int
    maximumAgeYrs=double
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Attributes

Name of demography data

name=string

Units: string

Name of demography data

Population size

popSize=int

Units: Count Min: 1 Max: 100000

Population size

Maximum age of simulated humans

maximumAgeYrs=double

Units: Number Min: 0 Max: 100

Maximum age of simulated humans

Growth rate of human population

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population. (we should be able to implement this with non-zero values)

Age groups

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

Percentage in age group

poppercent=double

Percentage of human population in age group

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Measures to be reported

→ scenario → monitoring

<monitoring
    name=string
  >
IN THIS ORDER:
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Attributes

name of monitoring information

name=string

Units: string

Name of monitoring data

Name of quantity

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

option

→ scenario → monitoring → SurveyOptions → option

<option
    name=string
    value=boolean
  />

Attributes

Model options required

name=string

Options define different model structures. Option name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.

Indicator of whether option is required

value=boolean

Option value (true/false). Each option has a default value (may be true or false) which is used if the option is not listed.

Survey times (time steps)

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
  >
IN THIS ORDER:
|   <surveyTime ... /> 
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

Detection limit for parasitaemia

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

Survey time

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time; 0 means just before start of main sim and is a valid survey-point. Reported data is either from a point-time survey (immediate data) or is collected over the previous year (data from previous timesteps-per-year period). Simulation will end immediately after last survey is taken.

Age groups

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lower bound of age group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upper bound of age group

upperbound=double

Units: Years Min: 0 Max: 100

Upper bound of age group

Preventative interventions

<interventions
    name=string
  >
IN THIS ORDER:
| [ <MDADescription ... /> ]
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| ( <anopheles ... /> )*
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

Attributes

Intervention

name=string

Units: string

Name of age specific intervention

Drug dose(s) used in MDA

<MDADescription>
IN THIS ORDER:
| [ <schedule ... /> ]
</MDADescription>

schedule

Documentation (element)

Units: List of medicate elements

Description of drug dose(s) used in a mass-drug-administration intervention.

When using the new (Event Scheduler) case management model, a treatment schedule must be present.

schedule

→ scenario → interventions → MDADescription → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

The base (unmodified) schedule of drugs administered for this treatment.

medicate

→ scenario → interventions → MDADescription → schedule → medicate

<medicate
    drug=string
    mg=double
    hour=double
  />

Attributes

drug

drug=string

Units: string

Abbreviated name of drug compound

drug dose (TODO is this correct?)

mg=double

Units: mg

Quantity of drug compound

time of administration

hour=double

Units: hours Min: 0

Number of hours past start of timestep this drug dose is administered at (first dose should be at hour 0).

vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

Type of vaccine

vaccineType=int

Units: Code

Type of vaccine

Half life of drug effect

→ scenario → interventions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Variance parameter for vaccine efficacy

→ scenario → interventions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

initialEfficacy

→ scenario → interventions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

Age specific intervention

name=string

Units: string

Name of age specific intervention

Frequency

freq=double

Frequency of parasite genotype

ACR

ACR=double

Adequate clinical response (proportion)

Prophylactic period

proph=int

Prophylactic period

Tolerance period

tolPeriod=int

Tolerance period

atten=double

Tolerance period

anopheles

→ scenario → interventions → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <VADescription ... /> ]
</anopheles>

Attributes

Entomological effects of interventions

mosquito=string

Description of the entomological effects of interventions

ITNDescription

→ scenario → interventions → anopheles → ITNDescription

<ITNDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</ITNDescription>

Attributes

ITN effects

name=string

Units: string

Name of Insecticide Treated Net intervention

Deterrency

→ scenario → interventions → anopheles → ITNDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability (before decay).

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

Pre-prandial killing effect

→ scenario → interventions → anopheles → ITNDescription → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

Post-prandial killing effect

→ scenario → interventions → anopheles → ITNDescription → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

IRSDescription

→ scenario → interventions → anopheles → IRSDescription

<IRSDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <killingEffect ... /> 
</IRSDescription>

Attributes

name of IRS intervention

name=string

Units: string

Name of Indoor Residual Spraying intervention

Deterrency

→ scenario → interventions → anopheles → IRSDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

killing effect

→ scenario → interventions → anopheles → IRSDescription → killingEffect

<killingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

VADescription

→ scenario → interventions → anopheles → VADescription

<VADescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</VADescription>

deterrency

Attributes

Name of mosquito deterrency intervention

name=string

Units: string

Name of mosquito deterrency intervention

Deterrency

→ scenario → interventions → anopheles → VADescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

Initial proportion

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

half-life

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibull k parameter

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

Continuously applied interventions

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
</continuous>

List of age groups for vaccination

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Description of ITN deployment

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

List of age groups for IPTi

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

Target age

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

Proportion covered

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Timed interventions

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <importedInfectionsPerThousandHosts ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <VectorAvailability ... /> ]
| [ <ipti ... /> ]
| [ <larviciding ... /> ]
</intervention>

Attributes

Time step of intervention

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <uncomplicated ... /> 
|   <complicated ... /> 
|   <ClinicalOutcomes ... /> 
</EventScheduler>

uncomplicated

→ scenario → healthSystem → EventScheduler → uncomplicated

<uncomplicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</uncomplicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

decisions

→ scenario → healthSystem → EventScheduler → uncomplicated → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )*
</decisions>

decision

Documentation (type)

age5Test: tests the patient's age and returns "under5" or "over5".
case (uncomplicated only): Returns "UC1" if there is no recent history of a malarial case, or "UC2" if there is.
result (uncomplicated only): Dependent on decision "test", this performs a parasite density test. Output is one of "none" (no test performed), "positive", "negative".

The following decisions must be described here:

test (uncomplicated only): Outputs must be "none", "microscopy" or "RDT" to describe which test the "result" decision uses.
treatment: Describes which treatment to use. Values aren't restricted but must match up with a treatment described in the corresponding "treatments" section.

decision

→ scenario → healthSystem → EventScheduler → uncomplicated → decisions → decision

<decision
    name=string
    depends=string
    values=string
  >
    string
</decision>

Documentation (type)

A decision describes how to choose between a set of values.

Lexically, it can contain symbols matching "[_.a-zA-Z0-9]+", round brackets: (), braces: {} and colons. Whitespace is ignored except to separate symbols.

For each BRANCH_SET each BRANCH must have the same DECISION. This DECISION must be one of the dependencies mentioned in "depends". This may be:

another decision, in which case the VALUE immediately following in brackets must correspond to one of its output values. The BRANCH_SET immediately containing this BRANCH must represent each output value of the same decision exactly once, and no parent BRANCH_SET may be for the same DECISION.
"p": this indicates a probabilistic decision. In this case the value is a probability, the sum of all values for the BRANCH_SET must be 1 and the decision must be associated directly with OUTCOMEs (not sub-TREEs).
"age": this indicates an age-test. The VALUE must have the form "a-b", indicating that this branch will be taken for individuals aged such that a <= age < b, where a,b are non-negative real numbers or the special value "inf", and a <= b. All VALUEs in the BRANCH_SET must cover all possible (non-negative real) ages, with no overlap (hence, smallest a must be 0 and greatest b must be inf).

Semantically, each OUTCOME must be one of the values associated with this decision.

Attributes

Name of decision

name=string

The name of this decision. The name must match the regular expression "[_a-zA-Z0-9]+"; that is it can only contain letters, digits and _ characters (no spaces, punctuation, etc.).

Preceding decisions

depends=string

Outcome values

values=string

A comma-separated list of outcome values this decision may have. The name of each value must be of the same form as decision names (i.e. only contain letters, digits and _ characters).

treatments

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments

<treatments>
IN THIS ORDER:
| ( <treatment ... /> )*
</treatments>

treatment

Documentation (type)

Units: string

A list of drug treatment tables. Each should have a name corresponding to one of the "drug" decision's values.

treatment

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment

<treatment
    name=string
  >
IN THIS ORDER:
|   <schedule ... /> 
| ( <modifier ... /> )*
</treatment>

Documentation (type)

A description of a base treatment schedule along with modifiers to handle delays, quality variations, etc.

Attributes

Treatment administered

name=string

Units: string

Name corresponding to one of the drug decision's output values.

schedule

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → schedule

<schedule>
IN THIS ORDER:
| ( <medicate ... /> )*
</schedule>

medicate

Documentation (type)

The base (unmodified) schedule of drugs administered for this treatment.

modifier

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier

<modifier
    decision=string
  >
EXACTLY ONE OF:
| ( <multiplyQty ... /> )*
| ( <delay ... /> )*
| ( <selectTimeRange ... /> )*
</modifier>

Documentation (type)

A modifier for this treatment, according to the outputs of a decision.

Attributes

decision

decision=string

Units: string

Specifies the decision that this modifier acts on.

multiplyQty

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier → multiplyQty

<multiplyQty
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Multiplies the quantity of active ingredients of drugs administered.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of multipliers for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0.5,1" the quantity of drug A is halved while that of B is unchanged.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

delay

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier → delay

<delay
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Delays administration of drugs listed in the base schedule by so many hours.

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of delays (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. E.g. with drugs="A,B" and content "0,6", drug A is administered as in the base schedule while drug B is administered 6 hours later than specified.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

selectTimeRange

→ scenario → healthSystem → EventScheduler → uncomplicated → treatments → treatment → modifier → selectTimeRange

<selectTimeRange
    value=string
    effect=string
  [ affectsCost=boolean ]
  />

Documentation (element)

Selects which drug doses to administer according to time of administration (before times are modified by delays).

The "drugs" attribute is a comma-separated list of all active ingredients administered in the base schedule (each must be listed once) and the content of this element is a comma- separated list of time-ranges (in hours) for each active ingredient, listed in the same order as in the "drugs" attribute. The time-ranges should be of the form x-y and are interpreted as the half-open interval [x,y); that is a drug listed with time t will only be administered if x <= t < y.

Attributes

value of decision

value=string

Units: string

Specifies a value of the decision to act on.

List of drugs affected

effect=string

Units: string

Comma-separated list of the effect the modifier has on each drug, in the form DRUG1(EFFECT1),DRUG2(EFFECT2), etc.

Affects cost?

affectsCost=boolean

Units: none

Does this affect the cost? If false, the effective drug usage (w.r.t. cost) is unaffected by this modifier; if true it is. Defaults to true (if omitted). Is meaningless for delays.

complicated

→ scenario → healthSystem → EventScheduler → complicated

<complicated>
IN THIS ORDER:
|   <decisions ... /> 
|   <treatments ... /> 
</complicated>

Documentation (type)

Units: List of elements

A set of decisions and a set of treatments.

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes>
IN THIS ORDER:
|   <maxUCSeekingMemory ... /> 
|   <uncomplicatedCaseDuration ... /> 
|   <complicatedCaseDuration ... /> 
|   <complicatedRiskDuration ... /> 
|   <pImmediateUC ... /> 
|   <propDeathsFirstDay ... /> 
|   <communityOddsMultiplier ... /> 
</ClinicalOutcomes>

Documentation (type)

Description of base parameters of the clinical model.

Max UC treatment-seeking memory

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → maxUCSeekingMemory

<maxUCSeekingMemory>
    int
</maxUCSeekingMemory>

Documentation (element)

Units: days Min: 0 Max: unbounded

Maximum number of timesteps (including first of case) an individual will remember they are sick before resetting.

Uncomplicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → uncomplicatedCaseDuration

<uncomplicatedCaseDuration>
    int
</uncomplicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of an uncomplicated case of malarial/non-malarial sickness (from treatment seeking until return to life-as-usual). Usually 3.

Complicated case duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedCaseDuration

<complicatedCaseDuration>
    int
</complicatedCaseDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Fixed length of a complicated/severe case of malaria (from treatment seeking until return to life-as-usual).

Complicated risk duration

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → complicatedRiskDuration

<complicatedRiskDuration>
    int
</complicatedRiskDuration>

Documentation (element)

Units: days Min: 1 Max: unbounded

Number of days for which humans are at risk of death during a severe or complicated case of malaria. Cannot be greater than the duration of a complicated case or less than 1 day.

Probability of immediate UC treatment seeking

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → pImmediateUC

<pImmediateUC>
    double
</pImmediateUC>

Documentation (element)

Units: none Min: 0 Max: 1

Probability that UC treatment seeking will be done immediately when sick, on second day given that it wasn't done on first, etc.

Proportion of direct deaths on first day

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → propDeathsFirstDay

<propDeathsFirstDay>
    double
</propDeathsFirstDay>

Documentation (element)

Units: none Min: 0 Max: 1

Proportion of direct deaths from severe malaria or a complication which happen on the day of entry to the health system.

Community odds of death multiplier

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → communityOddsMultiplier

<communityOddsMultiplier>
    double
</communityOddsMultiplier>

Documentation (element)

Units: none Min: 0 Max: unbounded

Multiplies the odds of dying in a community case, where the base (hospital) probability of death comes from other inputs.

ImmediateOutcomes

<ImmediateOutcomes
    name=string
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
</ImmediateOutcomes>

Documentation (type)

Units: List of elements

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

Case Management model

name=string

Units: string

Name of health system

Description of drug regimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

First line drug

firstLine=string

Units: Drug code

Code for first line drug

Second line drug

secondLine=string

Units: Drug code

Code for second line drug

Drug use for treating inpatients

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

Initial cure rate

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

Chloroquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Sulphadoxine-pyrimethamine/Amodiaquine

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

ACT

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

Input parameter value

value=double

A double-precision floating-point value.

QN

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

Input parameter value

value=double

A double-precision floating-point value.

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Adherence to treatment

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

Effectiveness of treatment in non-adherent patients

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

Probability that a patient with uncomplicated disease seeks official care immediately

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with uncomplicated disease self-treats

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a recurring patient seeks official care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probability that a patient with severe disease obtains appropriate care

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease obtains appropriate care

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Probabilities of sequelae in inpatients

→ scenario → healthSystem → ImmediateOutcomes → pSequelaeInpatient

<pSequelaeInpatient>
IN THIS ORDER:
| ( <item ... /> )+
</pSequelaeInpatient>

item

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients.

Note: previously these ranges were silently remapped. To prevent unexpected differences, there must be two groups, with maxAgeYrs bounds 5 and 99 respectively.

item

→ scenario → healthSystem → ImmediateOutcomes → pSequelaeInpatient → item

<item
    value=double
    maxAgeYrs=double
  />

Attributes

Input parameter value

value=double

A double-precision floating-point value.

Upper bound

maxAgeYrs=double

Units: Years Min: 0 Max: 100

Upper bound of age group

CFR

→ scenario → healthSystem → CFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

group

→ scenario → healthSystem → CFR → group

<group
    cfr=double
    lowerbound=double
  />

Attributes

Case fatality rate

cfr=double

Units: Proportion Min: 0 Max: 1

Case fatality rate

Lower bound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

Replacement transmission setting (vector control not enabled)

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (element)

Units: List of elements

New description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

EIRDaily

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Inoculations per person per day

Attributes

Time origin of EIR sequence

origin=string

importedInfectionsPerThousandHosts

→ scenario → interventions → timed → intervention → importedInfectionsPerThousandHosts

<importedInfectionsPerThousandHosts>
    double
</importedInfectionsPerThousandHosts>

Mass Drug Administration

→ scenario → interventions → timed → intervention → MDA

<MDA
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community.

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Vaccination

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN deployment

→ scenario → interventions → timed → intervention → ITN

<ITN
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IRS deployment

→ scenario → interventions → timed → intervention → IRS

<IRS
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of IRS deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

Mosquito deterrent

→ scenario → interventions → timed → intervention → VectorAvailability

<VectorAvailability
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of a mosquito deterrent deployment in the community

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IPTi deployment

→ scenario → interventions → timed → intervention → ipti

<ipti
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

Maximum age of eligible individuals

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

Minimum age of eligible individuals

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

Coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

larviciding

→ scenario → interventions → timed → intervention → larviciding

<larviciding>
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

anopheles

Documentation (element)

Simple larviciding intervention description.

anopheles

→ scenario → interventions → timed → intervention → larviciding → anopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

Mosquito to be larvicided

mosquito=string

Mosquito to be larvicided

Proportionate reduction in emergence

effectiveness=double

Units: none Min: 0 Max: 1

Proportional reduction in emergence rate

Duration of activity

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

healthSystem

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
</healthSystem>

Documentation (type)

Units: List of elements

Description of case management system, used to specify the initial model or a replacement (an intervention). Encompasses case management data and some other data required to derive case outcomes.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

Transmission and vector bionomics

→ scenario → entoData

<entoData
    name=string
    mode=("2" or "3" or "4")
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Attributes

Entomology dataset

name=string

Units: string

Name of entomology data

Transmission simulation mode

mode=("2" or "3" or "4")

Units: Code

Transmission simulation mode

Transmission setting (vector control not enabled)

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (element)

Units: List of elements

Description of transmission setting for models without vector control interventions (included for backward compatibility)

Attributes

Duration of sporogony (days)

eipDuration=int

The duration of sporogony in days

Transmission setting (vector control enabled)

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Units: List of elements

Parameters of the transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <eir ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Documentation (type)

Description of input EIR for one specific vector species in terms of a Fourier approximation to the ln of the EIR during the burn in period

Attributes

(TODO- Nakul to assign description)

mosquito=string

Initial guess of proportion of mosquitoes infected

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

Initial guess of proportion of mosquitoes infectious

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

Fourier approximation to pre-intervention EIR

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    b1=double
    a2=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Inoculations per person per day

Attributes

a0 parameter of Fourier approximation to ln(EIR)

a0=double

a1 parameter of Fourier approximation to ln(EIR)

a1=double

b1 parameter of Fourier approximation to ln(EIR)

b1=double

a2 parameter of Fourier approximation to ln(EIR)

a2=double

b2 parameter of Fourier approximation to ln(EIR)

b2=double

Rotation angle defining the origin of the Fourier approximation to ln (EIR)

EIRRotateAngle=double

Vector Species

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqLaidEggsSameDayProportion=double
    mosqSeekingDuration=double
    mosqSurvivalFeedingCycleProbability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
    mosqHumanBloodIndex=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

Duration of the resting period of the vector (days)

mosqRestDuration=int

Extrinsic incubation period (days)

extrinsicIncubationPeriod=int

Proportion of mosquitoes host seeking on same day as ovipositing

mosqLaidEggsSameDayProportion=double

Duration of the host-seeking period of the vector (days)

mosqSeekingDuration=double

Probability that the mosquito survives the feeding cycle

mosqSurvivalFeedingCycleProbability=double

Probability that the mosquito survives biting (TODO- check description)

mosqProbBiting=double

Probability that the mosquito finds a resting place

mosqProbFindRestSite=double

Probability that the mosquito survives resting (TODO- check description)

mosqProbResting=double

Probability that the mosquito survives oviposition (TODO- check description)

mosqProbOvipositing=double

Human blood index

mosqHumanBloodIndex=double

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
    mosqRelativeEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

(TODO- Nakul to assign description)

name=string

(TODO- Nakul to assign description)

mosqRelativeEntoAvailability=double

(TODO- Nakul to assign description)

mosqProbBiting=double

(TODO- Nakul to assign description)

mosqProbFindRestSite=double

(TODO- Nakul to assign description)

mosqProbResting=double

nonHumanHosts

→ scenario → entoData → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

Species of alternative host

name=string

Units: List of elements

Name of this species of non human hosts (must match up with those described per anopheles section)

number

number=double

Pharmacokinetics and pharmacodynamics

<drugDescription>
IN THIS ORDER:
| ( <drug ... /> )+
</drugDescription>

drug

Documentation (element)

Units: List of elements

Drug model parameters

drug

→ scenario → drugDescription → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (element)

Sequence of drug descriptions forming a library of drug parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → drugDescription → drug → PD

<PD>
IN THIS ORDER:
| ( <allele ... /> )+
</PD>

allele

allele

→ scenario → drugDescription → drug → PD → allele

<allele
    name=string
  >
IN THIS ORDER:
|   <initial_frequency ... /> 
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</allele>

Documentation (element)

PD parameters per allele, plus initial frequency of each allele.

Note: we assume a one-to-one correspondance of drugs to loci, hence each drug has an independent set of alleles here.

Attributes

name

name=string

Relative frequency

→ scenario → drugDescription → drug → PD → allele → initial_frequency

<initial_frequency>
    double
</initial_frequency>

Documentation (element)

Units: relative frequency Min: 0

Frequency, relative to the total frequency of all alleles for this drug/locus.

Maximal parasite killing rate

→ scenario → drugDescription → drug → PD → allele → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → drugDescription → drug → PD → allele → IC50

<IC50>
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

Slope of effect curve

→ scenario → drugDescription → drug → PD → allele → slope

<slope>
    double
</slope>

Documentation (element)

Units: no units

n — Slope of the concentration effect curve

PK

→ scenario → drugDescription → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
|   <half_life ... /> 
|   <vol_dist ... /> 
</PK>

Drug concentration considered negligible

→ scenario → drugDescription → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

drug half-life

→ scenario → drugDescription → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimination rate (which is: ln(2) / half_life).

Volume of Distribution

→ scenario → drugDescription → drug → PK → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

Model options and parameters

→ scenario → model

<model>
IN THIS ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <parameters ... /> 
</model>

Documentation (element)

Units: List of elements

Encapsulation of all parameters which describe the model according to which fitting is done.

Model Options

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

Units: List of elements

All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: include/util/ModelOptions.hpp and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=int
  />

Documentation (type)

Units: List of elements

Description of clinical parameters.

This is related to the health-system description, but contains data which can't be changed as part of an intervention and is not restricted to treatment.

Attributes

Follow-up period during which recurrence is treated as a failure

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

Parameters of the model of epidemiology

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    delta=double
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Units: List of elements

Parameters of the epidemiological model

Attributes

Simulation step

interval=int

Units: Days

Simulation step

Random number seed

iseed=int

Units: Number

Seed for RNG

delta

delta=double

Units: ? Redundant

this no longer seems to be used

Pre-erythrocytic latent period

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → model → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

Name of parameter

name=string

Units: string

Name of parameter

Parameter number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

Parameter value

value=double

Units: Number Min: 0

Parameter value

Sampling indicator

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 17 documentation

Generated from: scenario_17.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    maximumAgeYrs=double
    name=string
    popSize=int
    wuID=int
    assimMode=("0" or "1")
    mode=("2" or "3" or "4")
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_17.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entoData ... /> 
| [ <drugDescription ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

schemaVersion

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

analysisNo

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

maximumAgeYrs

maximumAgeYrs=double

Units: Number Min: 0 Max: 100

Maximum age of simulated humans

name

name=string

Units: string

Name of intervention

popSize

popSize=int

Units: Count Min: 1 Max: 100000

Population size

wuID

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

assimMode

assimMode=("0" or "1")

Units: Code

Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)

mode

mode=("2" or "3" or "4")

Units: Code

Transmission simulation mode

demography

→ scenario → demography

<demography
    name=string
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Documentation (type)

Units: List of elements

Description of demography

Attributes

name

name=string

Units: string

Name of demography data

growthRate

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population.

ageGroup

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

poppercent

poppercent=double

upperbound

upperbound=double

monitoring

→ scenario → monitoring

<monitoring
    name=string
  >
IN THIS ORDER:
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Documentation (type)

Units: List of elements

Description of surveys

Attributes

name

name=string

Units: string

Name of monitoring data

SurveyOptions

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

option

→ scenario → monitoring → SurveyOptions → option

<option
    name=string
    value=boolean
  />

Attributes

name

name=string

Option name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.

value

value=boolean

Option value (true/false). Each option has a default value (may be true or false) which is used if the option is not listed.

surveys

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
  >
IN THIS ORDER:
|   <surveyTime ... /> 
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

detectionLimit

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

surveyTime

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time; 0 means just before start of main sim and is a valid survey-point. Reported data is either from a point-time survey (immediate data) or is collected over the previous year (data from previous timesteps-per-year period). Simulation will end immediately after last survey is taken.

ageGroup

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upperbound

upperbound=double

interventions

<interventions
    name=string
  >
IN THIS ORDER:
| [ <MDADescription ... /> ]
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| ( <anopheles ... /> )*
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

List of interventions

Documentation (type)

Units: List of elements

List of interventions

Attributes

name

name=string

Units: string

Name of age specific intervention

MDADescription

<MDADescription>
IN THIS ORDER:
| ( <medicate ... /> )*
</MDADescription>

medicate

Documentation (element)

Units: List of medicate elements

Description of drug dose(s) used in a mass-drug-administration intervention.

medicate

→ scenario → interventions → MDADescription → medicate

<medicate
    name=string
    qty=double
    time=double
  />

Attributes

name

name=string

Units: string

Abbreviated name of drug compound

qty

qty=double

Units: mg

Quantity of drug compound

time

time=double

Units: hours Min: 0

Number of hours past start of timestep the drug is medicated at (usually 0).

vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

vaccineType

vaccineType=int

Units: Code

Type of vaccine

halfLifeYrs

→ scenario → interventions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

value

value=double

TODO

efficacyB

→ scenario → interventions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

value

value=double

TODO

initialEfficacy

→ scenario → interventions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

value

value=double

TODO

iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

name

name=string

Units: string

Name of age specific intervention

freq

freq=double

ACR

ACR=double

proph

proph=int

tolPeriod

tolPeriod=int

atten

atten=double

anopheles

→ scenario → interventions → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <VADescription ... /> ]
</anopheles>

Attributes

mosquito

mosquito=string

ITNDescription

→ scenario → interventions → anopheles → ITNDescription

<ITNDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</ITNDescription>

Attributes

name

name=string

Units: string

Name of Insecticide Treated Net intervention

deterrency

→ scenario → interventions → anopheles → ITNDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability (before decay).

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

preprandialKillingEffect

→ scenario → interventions → anopheles → ITNDescription → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

postprandialKillingEffect

→ scenario → interventions → anopheles → ITNDescription → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

IRSDescription

→ scenario → interventions → anopheles → IRSDescription

<IRSDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <killingEffect ... /> 
</IRSDescription>

Attributes

name

name=string

Units: string

Name of Indoor Residual Spraying intervention

deterrency

→ scenario → interventions → anopheles → IRSDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

killingEffect

→ scenario → interventions → anopheles → IRSDescription → killingEffect

<killingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

VADescription

→ scenario → interventions → anopheles → VADescription

<VADescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</VADescription>

deterrency

Attributes

name

name=string

Units: string

Name of mosquito deterrency intervention

deterrency

→ scenario → interventions → anopheles → VADescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

continuous

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
</continuous>

vaccine

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

timed

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <VectorAvailability ... /> ]
| [ <ipti ... /> ]
| [ <larviciding ... /> ]
</intervention>

Attributes

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Generic description of health system, used to specify the default or a replacement-as-intervention.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <CaseManagementTree ... /> 
|   <ClinicalOutcomes ... /> 
</EventScheduler>

CaseManagementTree

→ scenario → healthSystem → EventScheduler → CaseManagementTree

<CaseManagementTree
    mask=int
  >
IN THIS ORDER:
| ( <CM_pBranchSet ... /> )*
| ( <CM_leaf ... /> )+
</CaseManagementTree>

Documentation (element)

Units: List of elements

Partial description of the case management tree. The tree consists of: Probability branches: map an ID to another ID (the outcome) stochastically. Test branches: map an ID with a special flag to another ID; these are hard-coded. Leaf nodes: these map an ID to a list of drug medications.

Test branches are used if a flag requests a test (currently only RESULT_DETERMINE for parasite tests). Otherwise a probability or leaf branch is used by masking the current ID with mask (attribute for this element).

Attributes

mask

mask=int

Units: None Min: 0 Max: 0xFFFFFFFF

Value used to mask decision ids before selecting a branch/leaf.

CM_pBranchSet

→ scenario → healthSystem → EventScheduler → CaseManagementTree → CM_pBranchSet

<CM_pBranchSet
    ID=int
  >
IN THIS ORDER:
| ( <CM_pBranch ... /> )+
</CM_pBranchSet>

CM_pBranch

Documentation (element)

A probability branch node: contains a list of outcome nodes along with probabilities, which link to another probability/test branch or leaf node.

Attributes

ID

ID=int

Units: ID

Decision identifier.

CM_pBranch

→ scenario → healthSystem → EventScheduler → CaseManagementTree → CM_pBranchSet → CM_pBranch

<CM_pBranch
    outcome=int
    p=double
  />

Attributes

outcome

outcome=int

ID of next probability/test branch or leaf node.

p

p=double

Units: Proportion Min: 0 Max: 1

Probability of this outcome

CM_leaf

→ scenario → healthSystem → EventScheduler → CaseManagementTree → CM_leaf

<CM_leaf
    ID=int
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</CM_leaf>

medicate

Documentation (element)

End points of the case management tree, listing treatments.

Attributes

ID

ID=int

Units: ID

Decision identifier.

medicate

→ scenario → healthSystem → EventScheduler → CaseManagementTree → CM_leaf → medicate

<medicate
    name=string
    qty=double
    time=double
  />

Attributes

name

name=string

Units: string

Abbreviated name of drug compound

qty

qty=double

Units: mg

Quantity of drug compound

time

time=double

Units: hours Min: 0

Number of hours past start of timestep the drug is medicated at (usually 0).

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes
    severeMask=int
  >
IN THIS ORDER:
| ( <outcomes ... /> )+
</ClinicalOutcomes>

outcomes

Documentation (element)

Tables describing the probability of death and the expected length of hospital stay.

The ID looked up in each table is the final outcome ID of the case-management tree binary or-ed with the mask given here.

Attributes

severeMask

severeMask=int

Units: None Min: 0 Max: 0xFFFFFFFF

Value used to mask the final ID from the case-management tree before looking up values here.

outcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → outcomes

<outcomes
    ID=int
    pDeath=double
    hospitalizationDaysDeath=int
    hospitalizationDaysRecover=int
  />

Documentation (element)

Parameters for a path through the case-management tree (i.e. table row).

Attributes

ID

ID=int

pDeath

pDeath=double

Units: None Min: 0 Max: 1

The probability of death. This probability is applied once-only for each case, irrespective of the branch (thus entries with p=0 for UC cases are probably needed).

hospitalizationDaysDeath

hospitalizationDaysDeath=int

Units: Days Min: 0

The median length of stay in hospital, given the patient dies directly from this event. (Use median rather than a distribution because data should be more reliable and the effect of heterogeneity should be small.)

hospitalizationDaysRecover

hospitalizationDaysRecover=int

Units: Days Min: 0

The median length of stay in hospital, given the patient recovers from this event. (Use median rather than a distribution because data should be more reliable and the effect of heterogeneity should be small.)

ImmediateOutcomes

<ImmediateOutcomes
    name=string
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
</ImmediateOutcomes>

Documentation (type)

Units: List of elements

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

name

name=string

Units: string

Name of health system

drugRegimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

firstLine

firstLine=string

Units: Drug code

Code for first line drug

secondLine

secondLine=string

Units: Drug code

Code for second line drug

inpatient

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

initialACR

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

CQ

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

value

value=double

TODO

SP

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

value

value=double

TODO

AQ

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

value

value=double

TODO

SPAQ

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

value

value=double

TODO

ACT

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

value

value=double

TODO

QN

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

value

value=double

TODO

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

value

value=double

TODO

compliance

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

nonCompliersEffective

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

pSeekOfficialCareUncomplicated1

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSelfTreatUncomplicated

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

value

value=double

TODO

pSeekOfficialCareUncomplicated2

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSeekOfficialCareSevere

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease seeks official care

Attributes

value

value=double

TODO

pSequelaeInpatient

→ scenario → healthSystem → ImmediateOutcomes → pSequelaeInpatient

<pSequelaeInpatient>
IN THIS ORDER:
| ( <item ... /> )+
</pSequelaeInpatient>

item

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients.

Note: previously these ranges were silently remapped. To prevent unexpected differences, there must be two groups, with maxAgeYrs bounds 5 and 99 respectively.

item

→ scenario → healthSystem → ImmediateOutcomes → pSequelaeInpatient → item

<item
    value=double
    maxAgeYrs=double
  />

Attributes

value

value=double

TODO

maxAgeYrs

maxAgeYrs=double

Units: Years Min: 0 Max: 100

Upper bound of age group

CFR

→ scenario → healthSystem → CFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

group

→ scenario → healthSystem → CFR → group

<group
    cfr=double
    lowerbound=double
  />

Attributes

cfr

cfr=double

Units: Proportion Min: 0 Max: 1

Case fatality rate

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

changeEIR

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

EIRDaily

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Innoculations per person per day

Value of daily EIR; when multiple values are given for a single timestep they are averaged.

Attributes

origin

origin=string

MDA

→ scenario → interventions → timed → intervention → MDA

<MDA
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community.

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

vaccinate

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → timed → intervention → ITN

<ITN
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IRS

→ scenario → interventions → timed → intervention → IRS

<IRS
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of IRS deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

VectorAvailability

→ scenario → interventions → timed → intervention → VectorAvailability

<VectorAvailability
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of a mosquito detterent deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → timed → intervention → ipti

<ipti
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

larviciding

→ scenario → interventions → timed → intervention → larviciding

<larviciding>
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

anopheles

Documentation (element)

Simple larviciding intervention description.

anopheles

→ scenario → interventions → timed → intervention → larviciding → anopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

mosquito

mosquito=string

effectiveness

effectiveness=double

Units: none Min: 0 Max: 1

Proportion to reduce emergence rates by.

duration

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

healthSystem

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
</healthSystem>

Documentation (type)

Units: List of elements

Generic description of health system, used to specify the default or a replacement-as-intervention.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

entoData

→ scenario → entoData

<entoData
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Documentation (type)

Units: List of elements

Data for entomodel

Attributes

name

name=string

Units: string

Name of entomology data

nonVector

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

vector

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters for the vector transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <eir ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Attributes

mosquito

mosquito=string

propInfected

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

propInfectious

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

eir

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    b1=double
    a2=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Innoculations per person per day

Attributes

a0

a0=double

a1

a1=double

b1

b1=double

a2

a2=double

b2

b2=double

EIRRotateAngle

EIRRotateAngle=double

mosq

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqLaidEggsSameDayProportion=double
    mosqSeekingDuration=double
    mosqSurvivalFeedingCycleProbability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
    mosqHumanBloodIndex=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

mosqRestDuration

mosqRestDuration=int

extrinsicIncubationPeriod

extrinsicIncubationPeriod=int

mosqLaidEggsSameDayProportion

mosqLaidEggsSameDayProportion=double

mosqSeekingDuration

mosqSeekingDuration=double

mosqSurvivalFeedingCycleProbability

mosqSurvivalFeedingCycleProbability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

mosqProbOvipositing

mosqProbOvipositing=double

mosqHumanBloodIndex

mosqHumanBloodIndex=double

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
    mosqRelativeEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

name

name=string

mosqRelativeEntoAvailability

mosqRelativeEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

nonHumanHosts

→ scenario → entoData → vector → nonHumanHosts

<nonHumanHosts
    name=string
    number=double
  />

Attributes

name

name=string

Units: List of elements

Name of this species of non human hosts (must match up with those described per anopheles section)

number

number=double

drugDescription

<drugDescription>
IN THIS ORDER:
| ( <drug ... /> )+
</drugDescription>

drug

Documentation (element)

Units: List of elements

Drug model parameters

drug

→ scenario → drugDescription → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (element)

Sequence of drug descriptions forming a library of drug parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → drugDescription → drug → PD

<PD>
IN THIS ORDER:
| ( <allele ... /> )+
</PD>

allele

allele

→ scenario → drugDescription → drug → PD → allele

<allele
    name=string
  >
IN THIS ORDER:
|   <initial_frequency ... /> 
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</allele>

Documentation (element)

PD parameters per allele, plus initial frequency of each allele.

Note: we assume a one-to-one correspondance of drugs to loci, hence each drug has an independent set of alleles here.

Attributes

name

name=string

initial_frequency

→ scenario → drugDescription → drug → PD → allele → initial_frequency

<initial_frequency>
    double
</initial_frequency>

Documentation (element)

Units: relative frequency Min: 0

Frequency, relative to the total frequency of all alleles for this drug/locus.

max_killing_rate

→ scenario → drugDescription → drug → PD → allele → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → drugDescription → drug → PD → allele → IC50

<IC50>
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

slope

→ scenario → drugDescription → drug → PD → allele → slope

<slope>
    double
</slope>

Documentation (element)

Units: no units

n — Slope of the concentration effect curve

PK

→ scenario → drugDescription → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
|   <half_life ... /> 
|   <vol_dist ... /> 
</PK>

negligible_concentration

→ scenario → drugDescription → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

half_life

→ scenario → drugDescription → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimintation rate (which is: ln(2) / half_life).

vol_dist

→ scenario → drugDescription → drug → PK → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

model

→ scenario → model

<model>
IN THIS ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

ModelOptions

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).

The list of recognised options can be found in the code at: include/util/ModelOptions.hpp and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=int
  />

Documentation (type)

Units: List of elements

Description of clinical parameters.

This is related to the health-system description, but contains data which can't be changed as part of an intervention and is not restricted to treatment.

Attributes

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

parameters

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    delta=double
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Units: List of elements

Parameters for mathematical model

Documentation (type)

Units: List of elements

Parameter vector

Attributes

interval

interval=int

Units: Days

Simulation step

iseed

iseed=int

Units: Number

Seed for RNG

delta

delta=double

Units: ? Redundant

this no longer seems to be used

latentp

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → model → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

name

name=string

Units: string

Name of parameter

number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

value

value=double

Units: Number Min: 0

Parameter value

include

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 16 documentation

Generated from: scenario_16.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    maximumAgeYrs=double
    name=string
    popSize=int
    wuID=int
    assimMode=("0" or "1")
    mode=("2" or "3" or "4")
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_16.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
|   <healthSystem ... /> 
|   <entoData ... /> 
| [ <drugDescription ... /> ]
|   <model ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

schemaVersion

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

analysisNo

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

maximumAgeYrs

maximumAgeYrs=double

Units: Number Min: 0 Max: 100

Maximum age of simulated humans

name

name=string

Units: string

Name of intervention

popSize

popSize=int

Units: Count Min: 1 Max: 100000

Population size

wuID

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

assimMode

assimMode=("0" or "1")

Units: Code

Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)

mode

mode=("2" or "3" or "4")

Units: Code

Transmission simulation mode

demography

→ scenario → demography

<demography
    name=string
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Documentation (type)

Units: List of elements

Description of demography

Attributes

name

name=string

Units: string

Name of demography data

growthRate

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population.

ageGroup

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

poppercent

poppercent=double

upperbound

upperbound=double

monitoring

→ scenario → monitoring

<monitoring
    name=string
  >
IN THIS ORDER:
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Documentation (type)

Units: List of elements

Description of surveys

Attributes

name

name=string

Units: string

Name of monitoring data

SurveyOptions

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

option

→ scenario → monitoring → SurveyOptions → option

<option
    name=string
    value=boolean
  />

Attributes

name

name=string

Option name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.

value

value=boolean

Option value (true/false). Each option has a default value (may be true or false) which is used if the option is not listed.

surveys

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
  >
IN THIS ORDER:
|   <surveyTime ... /> 
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

detectionLimit

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

surveyTime

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time; 0 means just before start of main sim and is a valid survey-point. Reported data is either from a point-time survey (immediate data) or is collected over the previous year (data from previous timesteps-per-year period). Simulation will end immediately after last survey is taken.

ageGroup

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upperbound

upperbound=double

interventions

<interventions
    name=string
  >
IN THIS ORDER:
| [ <MDADescription ... /> ]
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| ( <anopheles ... /> )*
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

List of interventions

Documentation (type)

Units: List of elements

List of interventions

Attributes

name

name=string

Units: string

Name of age specific intervention

MDADescription

<MDADescription>
IN THIS ORDER:
| ( <medicate ... /> )*
</MDADescription>

medicate

Documentation (element)

Units: List of medicate elements

Description of drug dose(s) used in a mass-drug-administration intervention.

medicate

→ scenario → interventions → MDADescription → medicate

<medicate
    name=string
    qty=double
    time=double
  />

Attributes

name

name=string

Units: string

Abbreviated name of drug compound

qty

qty=double

Units: mg

Quantity of drug compound

time

time=double

Units: hours Min: 0

Number of hours past start of timestep the drug is medicated at (usually 0).

vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

vaccineType

vaccineType=int

Units: Code

Type of vaccine

halfLifeYrs

→ scenario → interventions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

value

value=double

TODO

efficacyB

→ scenario → interventions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

value

value=double

TODO

initialEfficacy

→ scenario → interventions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

value

value=double

TODO

iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

name

name=string

Units: string

Name of age specific intervention

freq

freq=double

ACR

ACR=double

proph

proph=int

tolPeriod

tolPeriod=int

atten

atten=double

anopheles

→ scenario → interventions → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <VADescription ... /> ]
</anopheles>

Attributes

mosquito

mosquito=string

ITNDescription

→ scenario → interventions → anopheles → ITNDescription

<ITNDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</ITNDescription>

Attributes

name

name=string

Units: string

Name of Insecticide Treated Net intervention

deterrency

→ scenario → interventions → anopheles → ITNDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability (before decay).

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

preprandialKillingEffect

→ scenario → interventions → anopheles → ITNDescription → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

postprandialKillingEffect

→ scenario → interventions → anopheles → ITNDescription → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

IRSDescription

→ scenario → interventions → anopheles → IRSDescription

<IRSDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <killingEffect ... /> 
</IRSDescription>

Attributes

name

name=string

Units: string

Name of Indoor Residual Spraying intervention

deterrency

→ scenario → interventions → anopheles → IRSDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

killingEffect

→ scenario → interventions → anopheles → IRSDescription → killingEffect

<killingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

VADescription

→ scenario → interventions → anopheles → VADescription

<VADescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</VADescription>

deterrency

Attributes

name

name=string

Units: string

Name of mosquito deterrency intervention

deterrency

→ scenario → interventions → anopheles → VADescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

continuous

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
</continuous>

vaccine

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

timed

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <VectorAvailability ... /> ]
| [ <ipti ... /> ]
| [ <larviciding ... /> ]
</intervention>

Attributes

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Generic description of health system, used to specify the default or a replacement-as-intervention.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <CaseManagementTree ... /> 
|   <ClinicalOutcomes ... /> 
</EventScheduler>

CaseManagementTree

→ scenario → healthSystem → EventScheduler → CaseManagementTree

<CaseManagementTree
    mask=int
  >
IN THIS ORDER:
| ( <CM_pBranchSet ... /> )*
| ( <CM_leaf ... /> )+
</CaseManagementTree>

Documentation (element)

Units: List of elements

Attributes

mask

mask=int

Units: None Min: 0 Max: 0xFFFFFFFF

Value used to mask decision ids before selecting a branch/leaf.

CM_pBranchSet

→ scenario → healthSystem → EventScheduler → CaseManagementTree → CM_pBranchSet

<CM_pBranchSet
    ID=int
  >
IN THIS ORDER:
| ( <CM_pBranch ... /> )+
</CM_pBranchSet>

CM_pBranch

Documentation (element)

A probability branch node: contains a list of outcome nodes along with probabilities, which link to another probability/test branch or leaf node.

Attributes

ID

ID=int

Units: ID

Decision identifier.

CM_pBranch

→ scenario → healthSystem → EventScheduler → CaseManagementTree → CM_pBranchSet → CM_pBranch

<CM_pBranch
    outcome=int
    p=double
  />

Attributes

outcome

outcome=int

ID of next probability/test branch or leaf node.

p

p=double

Units: Proportion Min: 0 Max: 1

Probability of this outcome

CM_leaf

→ scenario → healthSystem → EventScheduler → CaseManagementTree → CM_leaf

<CM_leaf
    ID=int
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</CM_leaf>

medicate

Documentation (element)

End points of the case management tree, listing treatments.

Attributes

ID

ID=int

Units: ID

Decision identifier.

medicate

→ scenario → healthSystem → EventScheduler → CaseManagementTree → CM_leaf → medicate

<medicate
    name=string
    qty=double
    time=double
  />

Attributes

name

name=string

Units: string

Abbreviated name of drug compound

qty

qty=double

Units: mg

Quantity of drug compound

time

time=double

Units: hours Min: 0

Number of hours past start of timestep the drug is medicated at (usually 0).

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes
    severeMask=int
  >
IN THIS ORDER:
| ( <outcomes ... /> )+
</ClinicalOutcomes>

outcomes

Documentation (element)

Tables describing the probability of death and the expected length of hospital stay.

The ID looked up in each table is the final outcome ID of the case-management tree binary or-ed with the mask given here.

Attributes

severeMask

severeMask=int

Units: None Min: 0 Max: 0xFFFFFFFF

Value used to mask the final ID from the case-management tree before looking up values here.

outcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → outcomes

<outcomes
    ID=int
    pDeath=double
    hospitalizationDaysDeath=int
    hospitalizationDaysRecover=int
  />

Documentation (element)

Parameters for a path through the case-management tree (i.e. table row).

Attributes

ID

ID=int

pDeath

pDeath=double

Units: None Min: 0 Max: 1

The probability of death. This probability is applied once-only for each case, irrespective of the branch (thus entries with p=0 for UC cases are probably needed).

hospitalizationDaysDeath

hospitalizationDaysDeath=int

Units: Days Min: 0

hospitalizationDaysRecover

hospitalizationDaysRecover=int

Units: Days Min: 0

ImmediateOutcomes

<ImmediateOutcomes
    name=string
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
</ImmediateOutcomes>

Documentation (type)

Units: List of elements

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

name

name=string

Units: string

Name of health system

drugRegimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

firstLine

firstLine=string

Units: Drug code

Code for first line drug

secondLine

secondLine=string

Units: Drug code

Code for second line drug

inpatient

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

initialACR

→ scenario → healthSystem → ImmediateOutcomes → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

CQ

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

value

value=double

TODO

SP

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

value

value=double

TODO

AQ

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

value

value=double

TODO

SPAQ

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

value

value=double

TODO

ACT

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

value

value=double

TODO

QN

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

value

value=double

TODO

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

value

value=double

TODO

compliance

→ scenario → healthSystem → ImmediateOutcomes → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

nonCompliersEffective

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

pSeekOfficialCareUncomplicated1

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSelfTreatUncomplicated

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

value

value=double

TODO

pSeekOfficialCareUncomplicated2

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSeekOfficialCareSevere

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease seeks official care

Attributes

value

value=double

TODO

pSequelaeInpatient

→ scenario → healthSystem → ImmediateOutcomes → pSequelaeInpatient

<pSequelaeInpatient>
IN THIS ORDER:
| ( <item ... /> )+
</pSequelaeInpatient>

item

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients.

Note: previously these ranges were silently remapped. To prevent unexpected differences, there must be two groups, with maxAgeYrs bounds 5 and 99 respectively.

item

→ scenario → healthSystem → ImmediateOutcomes → pSequelaeInpatient → item

<item
    value=double
    maxAgeYrs=double
  />

Attributes

value

value=double

TODO

maxAgeYrs

maxAgeYrs=double

Units: Years Min: 0 Max: 100

Upper bound of age group

CFR

→ scenario → healthSystem → CFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

group

→ scenario → healthSystem → CFR → group

<group
    cfr=double
    lowerbound=double
  />

Attributes

cfr

cfr=double

Units: Proportion Min: 0 Max: 1

Case fatality rate

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

changeEIR

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

EIRDaily

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Innoculations per person per day

Value of daily EIR; when multiple values are given for a single timestep they are averaged.

Attributes

origin

origin=string

MDA

→ scenario → interventions → timed → intervention → MDA

<MDA
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community.

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

vaccinate

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → timed → intervention → ITN

<ITN
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IRS

→ scenario → interventions → timed → intervention → IRS

<IRS
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of IRS deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

VectorAvailability

→ scenario → interventions → timed → intervention → VectorAvailability

<VectorAvailability
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of a mosquito detterent deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → timed → intervention → ipti

<ipti
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

larviciding

→ scenario → interventions → timed → intervention → larviciding

<larviciding>
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

anopheles

Documentation (element)

Simple larviciding intervention description.

anopheles

→ scenario → interventions → timed → intervention → larviciding → anopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

mosquito

mosquito=string

effectiveness

effectiveness=double

Units: none Min: 0 Max: 1

Proportion to reduce emergence rates by.

duration

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

healthSystem

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
</healthSystem>

Documentation (type)

Units: List of elements

Generic description of health system, used to specify the default or a replacement-as-intervention.

Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.

entoData

→ scenario → entoData

<entoData
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Documentation (type)

Units: List of elements

Data for entomodel

Attributes

name

name=string

Units: string

Name of entomology data

nonVector

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

vector

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
</vector>

anopheles

Documentation (element)

Parameters for the vector transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <eir ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Attributes

mosquito

mosquito=string

propInfected

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

propInfectious

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

eir

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    b1=double
    a2=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Innoculations per person per day

Attributes

a0

a0=double

a1

a1=double

b1

b1=double

a2

a2=double

b2

b2=double

EIRRotateAngle

EIRRotateAngle=double

mosq

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqSeekingDeathRate=double
    mosqSeekingDuration=double
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

mosqRestDuration

mosqRestDuration=int

extrinsicIncubationPeriod

extrinsicIncubationPeriod=int

mosqSeekingDeathRate

mosqSeekingDeathRate=double

mosqSeekingDuration

mosqSeekingDuration=double

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

mosqProbOvipositing

mosqProbOvipositing=double

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

name

name=string

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

drugDescription

<drugDescription>
IN THIS ORDER:
| ( <drug ... /> )+
</drugDescription>

drug

Documentation (element)

Units: List of elements

Drug model parameters

drug

→ scenario → drugDescription → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (element)

Sequence of drug descriptions forming a library of drug parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → drugDescription → drug → PD

<PD>
IN THIS ORDER:
| ( <allele ... /> )+
</PD>

allele

allele

→ scenario → drugDescription → drug → PD → allele

<allele
    name=string
  >
IN THIS ORDER:
|   <initial_frequency ... /> 
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</allele>

Documentation (element)

PD parameters per allele, plus initial frequency of each allele.

Note: we assume a one-to-one correspondance of drugs to loci, hence each drug has an independent set of alleles here.

Attributes

name

name=string

initial_frequency

→ scenario → drugDescription → drug → PD → allele → initial_frequency

<initial_frequency>
    double
</initial_frequency>

Documentation (element)

Units: relative frequency Min: 0

Frequency, relative to the total frequency of all alleles for this drug/locus.

max_killing_rate

→ scenario → drugDescription → drug → PD → allele → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → drugDescription → drug → PD → allele → IC50

<IC50>
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

slope

→ scenario → drugDescription → drug → PD → allele → slope

<slope>
    double
</slope>

Documentation (element)

Units: no units

n — Slope of the concentration effect curve

PK

→ scenario → drugDescription → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
|   <half_life ... /> 
|   <vol_dist ... /> 
</PK>

negligible_concentration

→ scenario → drugDescription → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

half_life

→ scenario → drugDescription → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimintation rate (which is: ln(2) / half_life).

vol_dist

→ scenario → drugDescription → drug → PK → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

model

→ scenario → model

<model>
IN THIS ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

ModelOptions

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).

The list of recognised options can be found in the code at: include/util/ModelOptions.hpp and should also be in the wiki.

clinical

→ scenario → model → clinical

<clinical
    healthSystemMemory=int
  />

Documentation (type)

Units: List of elements

Description of clinical parameters.

This is related to the health-system description, but contains data which can't be changed as part of an intervention and is not restricted to treatment.

Attributes

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

parameters

→ scenario → model → parameters

<parameters
    interval=int
    iseed=int
    delta=double
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Units: List of elements

Parameters for mathematical model

Documentation (type)

Units: List of elements

Parameter vector

Attributes

interval

interval=int

Units: Days

Simulation step

iseed

iseed=int

Units: Number

Seed for RNG

delta

delta=double

Units: ? Redundant

this no longer seems to be used

latentp

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → model → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

name

name=string

Units: string

Name of parameter

number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

value

value=double

Units: Number Min: 0

Parameter value

include

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 15 documentation

Generated from: scenario_15.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    maximumAgeYrs=double
    name=string
    popSize=int
    wuID=int
    assimMode=("0" or "1")
    mode=("2" or "3" or "4")
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_15.xsd"
  >
IN THIS ORDER:
|   <ModelOptions ... /> 
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <healthSystem ... /> 
|   <entoData ... /> 
| [ <drugDescription ... /> ]
|   <parameters ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

schemaVersion

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

analysisNo

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

maximumAgeYrs

maximumAgeYrs=double

Units: Number Min: 0 Max: 100

Maximum age of simulated humans

name

name=string

Units: string

Name of intervention

popSize

popSize=int

Units: Count Min: 1 Max: 100000

Population size

wuID

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

assimMode

assimMode=("0" or "1")

Units: Code

Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)

mode

mode=("2" or "3" or "4")

Units: Code

Transmission simulation mode

ModelOptions

→ scenario → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).

The list of recognised options can be found in the code at: include/util/ModelOptions.hpp and should also be in the wiki.

option

→ scenario → ModelOptions → option

<option
    name=string
    value=boolean
  />

Attributes

name

name=string

Option name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.

value

value=boolean

Option value (true/false). Each option has a default value (may be true or false) which is used if the option is not listed.

demography

→ scenario → demography

<demography
    name=string
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Documentation (type)

Units: List of elements

Description of demography

Attributes

name

name=string

Units: string

Name of demography data

growthRate

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population.

ageGroup

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

poppercent

poppercent=double

upperbound

upperbound=double

monitoring

→ scenario → monitoring

<monitoring
    name=string
  >
IN THIS ORDER:
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Documentation (type)

Units: List of elements

Description of surveys

Attributes

name

name=string

Units: string

Name of monitoring data

SurveyOptions

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

surveys

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
  >
IN THIS ORDER:
|   <surveyTime ... /> 
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

detectionLimit

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

surveyTime

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time; 0 means just before start of main sim and is a valid survey-point. Reported data is either from a point-time survey (immediate data) or is collected over the previous year (data from previous timesteps-per-year period). Simulation will end immediately after last survey is taken.

ageGroup

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upperbound

upperbound=double

interventions

<interventions
    name=string
  >
IN THIS ORDER:
| [ <MDADescription ... /> ]
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| ( <anopheles ... /> )*
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

List of interventions

Documentation (type)

Units: List of elements

List of interventions

Attributes

name

name=string

Units: string

Name of age specific intervention

MDADescription

<MDADescription>
IN THIS ORDER:
| ( <medicate ... /> )*
</MDADescription>

medicate

Documentation (element)

Units: List of medicate elements

Description of drug dose(s) used in a mass-drug-administration intervention.

medicate

→ scenario → interventions → MDADescription → medicate

<medicate
    name=string
    qty=double
    time=double
  />

Attributes

name

name=string

Units: string

Abbreviated name of drug compound

qty

qty=double

Units: mg

Quantity of drug compound

time

time=double

Units: hours Min: 0

Number of hours past start of timestep the drug is medicated at (usually 0).

vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

vaccineType

vaccineType=int

Units: Code

Type of vaccine

halfLifeYrs

→ scenario → interventions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

value

value=double

TODO

efficacyB

→ scenario → interventions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

value

value=double

TODO

initialEfficacy

→ scenario → interventions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

value

value=double

TODO

iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

name

name=string

Units: string

Name of age specific intervention

freq

freq=double

ACR

ACR=double

proph

proph=int

tolPeriod

tolPeriod=int

atten

atten=double

anopheles

→ scenario → interventions → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <VADescription ... /> ]
</anopheles>

Attributes

mosquito

mosquito=string

ITNDescription

→ scenario → interventions → anopheles → ITNDescription

<ITNDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</ITNDescription>

Attributes

name

name=string

Units: string

Name of Insecticide Treated Net intervention

deterrency

→ scenario → interventions → anopheles → ITNDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability (before decay).

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

preprandialKillingEffect

→ scenario → interventions → anopheles → ITNDescription → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

postprandialKillingEffect

→ scenario → interventions → anopheles → ITNDescription → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

IRSDescription

→ scenario → interventions → anopheles → IRSDescription

<IRSDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <killingEffect ... /> 
</IRSDescription>

Attributes

name

name=string

Units: string

Name of Indoor Residual Spraying intervention

deterrency

→ scenario → interventions → anopheles → IRSDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

killingEffect

→ scenario → interventions → anopheles → IRSDescription → killingEffect

<killingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

VADescription

→ scenario → interventions → anopheles → VADescription

<VADescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</VADescription>

deterrency

Attributes

name

name=string

Units: string

Name of mosquito deterrency intervention

deterrency

→ scenario → interventions → anopheles → VADescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

continuous

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
</continuous>

vaccine

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

timed

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <VectorAvailability ... /> ]
| [ <ipti ... /> ]
| [ <larviciding ... /> ]
</intervention>

Attributes

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

drugRegimen

→ scenario → healthSystem → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

firstLine

firstLine=string

Units: Drug code

Code for first line drug

secondLine

secondLine=string

Units: Drug code

Code for second line drug

inpatient

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

initialACR

→ scenario → healthSystem → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

CQ

→ scenario → healthSystem → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

value

value=double

TODO

SP

→ scenario → healthSystem → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

value

value=double

TODO

AQ

→ scenario → healthSystem → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

value

value=double

TODO

SPAQ

→ scenario → healthSystem → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

value

value=double

TODO

ACT

→ scenario → healthSystem → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

value

value=double

TODO

QN

→ scenario → healthSystem → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

value

value=double

TODO

selfTreatment

→ scenario → healthSystem → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

value

value=double

TODO

compliance

→ scenario → healthSystem → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

pSeekOfficialCareUncomplicated1

→ scenario → healthSystem → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSelfTreatUncomplicated

→ scenario → healthSystem → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

value

value=double

TODO

pSeekOfficialCareUncomplicated2

→ scenario → healthSystem → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSeekOfficialCareSevere

→ scenario → healthSystem → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease seeks official care

Attributes

value

value=double

TODO

pSequelaeInpatient

<pSequelaeInpatient>
IN THIS ORDER:
| ( <item ... /> )+
</pSequelaeInpatient>

item

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients.

Note: previously these ranges were silently remapped. To prevent unexpected differences, there must be two groups, with maxAgeYrs bounds 5 and 99 respectively.

item

→ scenario → healthSystem → pSequelaeInpatient → item

<item
    value=double
    maxAgeYrs=double
  />

Attributes

value

value=double

TODO

maxAgeYrs

maxAgeYrs=double

Units: Years Min: 0 Max: 100

Upper bound of age group

CFR

→ scenario → healthSystem → CFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

group

→ scenario → healthSystem → CFR → group

<group
    cfr=double
    lowerbound=double
  />

Attributes

cfr

cfr=double

Units: Proportion Min: 0 Max: 1

Case fatality rate

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

changeEIR

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

EIRDaily

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Innoculations per person per day

Value of daily EIR; when multiple values are given for a single timestep they are averaged.

Attributes

origin

origin=string

MDA

→ scenario → interventions → timed → intervention → MDA

<MDA
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community.

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

vaccinate

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → timed → intervention → ITN

<ITN
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IRS

→ scenario → interventions → timed → intervention → IRS

<IRS
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of IRS deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

VectorAvailability

→ scenario → interventions → timed → intervention → VectorAvailability

<VectorAvailability
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of a mosquito detterent deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → timed → intervention → ipti

<ipti
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

larviciding

→ scenario → interventions → timed → intervention → larviciding

<larviciding>
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

anopheles

Documentation (element)

Simple larviciding intervention description.

anopheles

→ scenario → interventions → timed → intervention → larviciding → anopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

mosquito

mosquito=string

effectiveness

effectiveness=double

Units: none Min: 0 Max: 1

Proportion to reduce emergence rates by.

duration

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

EventScheduler

<EventScheduler
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <CaseManagementTree ... /> 
|   <ClinicalOutcomes ... /> 
</EventScheduler>

Documentation (element)

Units: List of elements

Description of case management and clinical events.

Attributes

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

CaseManagementTree

<CaseManagementTree
    mask=int
  >
IN THIS ORDER:
| ( <CM_pBranchSet ... /> )*
| ( <CM_leaf ... /> )+
</CaseManagementTree>

Documentation (element)

Units: List of elements

Attributes

mask

mask=int

Units: None Min: 0 Max: 0xFFFFFFFF

Value used to mask decision ids before selecting a branch/leaf.

CM_pBranchSet

→ scenario → EventScheduler → CaseManagementTree → CM_pBranchSet

<CM_pBranchSet
    ID=int
  >
IN THIS ORDER:
| ( <CM_pBranch ... /> )+
</CM_pBranchSet>

CM_pBranch

Documentation (element)

A probability branch node: contains a list of outcome nodes along with probabilities, which link to another probability/test branch or leaf node.

Attributes

ID

ID=int

Units: ID

Decision identifier.

CM_pBranch

→ scenario → EventScheduler → CaseManagementTree → CM_pBranchSet → CM_pBranch

<CM_pBranch
    outcome=int
    p=double
  />

Attributes

outcome

outcome=int

ID of next probability/test branch or leaf node.

p

p=double

Units: Proportion Min: 0 Max: 1

Probability of this outcome

CM_leaf

→ scenario → EventScheduler → CaseManagementTree → CM_leaf

<CM_leaf
    ID=int
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</CM_leaf>

medicate

Documentation (element)

End points of the case management tree, listing treatments.

Attributes

ID

ID=int

Units: ID

Decision identifier.

medicate

→ scenario → EventScheduler → CaseManagementTree → CM_leaf → medicate

<medicate
    name=string
    qty=double
    time=double
  />

Attributes

name

name=string

Units: string

Abbreviated name of drug compound

qty

qty=double

Units: mg

Quantity of drug compound

time

time=double

Units: hours Min: 0

Number of hours past start of timestep the drug is medicated at (usually 0).

ClinicalOutcomes

→ scenario → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes
    severeMask=int
  >
IN THIS ORDER:
| ( <outcomes ... /> )+
</ClinicalOutcomes>

outcomes

Documentation (element)

Tables describing the probability of death and the expected length of hospital stay.

The ID looked up in each table is the final outcome ID of the case-management tree binary or-ed with the mask given here.

Attributes

severeMask

severeMask=int

Units: None Min: 0 Max: 0xFFFFFFFF

Value used to mask the final ID from the case-management tree before looking up values here.

outcomes

→ scenario → EventScheduler → ClinicalOutcomes → outcomes

<outcomes
    ID=int
    pDeath=double
    hospitalizationDaysDeath=int
    hospitalizationDaysRecover=int
  />

Documentation (element)

Parameters for a path through the case-management tree (i.e. table row).

Attributes

ID

ID=int

pDeath

pDeath=double

Units: None Min: 0 Max: 1

The probability of death. This probability is applied once-only for each case, irrespective of the branch (thus entries with p=0 for UC cases are probably needed).

hospitalizationDaysDeath

hospitalizationDaysDeath=int

Units: Days Min: 0

hospitalizationDaysRecover

hospitalizationDaysRecover=int

Units: Days Min: 0

healthSystem

→ scenario → healthSystem

<healthSystem
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</healthSystem>

Documentation (element)

Units: List of elements

Description of (old) health system model.

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

entoData

→ scenario → entoData

<entoData
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Documentation (type)

Units: List of elements

Data for entomodel

Attributes

name

name=string

Units: string

Name of entomology data

nonVector

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

vector

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
</vector>

anopheles

Documentation (element)

Parameters for the vector transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <eir ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Attributes

mosquito

mosquito=string

propInfected

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

propInfectious

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

eir

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    b1=double
    a2=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Innoculations per person per day

Attributes

a0

a0=double

a1

a1=double

b1

b1=double

a2

a2=double

b2

b2=double

EIRRotateAngle

EIRRotateAngle=double

mosq

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqSeekingDeathRate=double
    mosqSeekingDuration=double
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

mosqRestDuration

mosqRestDuration=int

extrinsicIncubationPeriod

extrinsicIncubationPeriod=int

mosqSeekingDeathRate

mosqSeekingDeathRate=double

mosqSeekingDuration

mosqSeekingDuration=double

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

mosqProbOvipositing

mosqProbOvipositing=double

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

name

name=string

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

drugDescription

<drugDescription>
IN THIS ORDER:
| ( <drug ... /> )+
</drugDescription>

drug

Documentation (element)

Units: List of elements

Drug model parameters

drug

→ scenario → drugDescription → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (element)

Sequence of drug descriptions forming a library of drug parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → drugDescription → drug → PD

<PD>
IN THIS ORDER:
| ( <allele ... /> )+
</PD>

allele

allele

→ scenario → drugDescription → drug → PD → allele

<allele
    name=string
  >
IN THIS ORDER:
|   <initial_frequency ... /> 
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</allele>

Documentation (element)

PD parameters per allele, plus initial frequency of each allele.

Note: we assume a one-to-one correspondance of drugs to loci, hence each drug has an independent set of alleles here.

Attributes

name

name=string

initial_frequency

→ scenario → drugDescription → drug → PD → allele → initial_frequency

<initial_frequency>
    double
</initial_frequency>

Documentation (element)

Units: relative frequency Min: 0

Frequency, relative to the total frequency of all alleles for this drug/locus.

max_killing_rate

→ scenario → drugDescription → drug → PD → allele → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → drugDescription → drug → PD → allele → IC50

<IC50>
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

slope

→ scenario → drugDescription → drug → PD → allele → slope

<slope>
    double
</slope>

Documentation (element)

Units: no units

n — Slope of the concentration effect curve

PK

→ scenario → drugDescription → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
|   <half_life ... /> 
|   <vol_dist ... /> 
</PK>

negligible_concentration

→ scenario → drugDescription → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

half_life

→ scenario → drugDescription → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimintation rate (which is: ln(2) / half_life).

vol_dist

→ scenario → drugDescription → drug → PK → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

parameters

→ scenario → parameters

<parameters
    interval=int
    iseed=int
    delta=double
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Units: List of elements

Parameters for mathematical model

Documentation (type)

Units: List of elements

Parameter vector

Attributes

interval

interval=int

Units: Days

Simulation step

iseed

iseed=int

Units: Number

Seed for RNG

delta

delta=double

Units: ? Redundant

this no longer seems to be used

latentp

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

name

name=string

Units: string

Name of parameter

number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

value

value=double

Units: Number Min: 0

Parameter value

include

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 14 documentation

Generated from: scenario_14.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    maximumAgeYrs=double
    name=string
    popSize=int
    wuID=int
    assimMode=("0" or "1")
    mode=("2" or "3" or "4")
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_14.xsd"
  >
IN THIS ORDER:
|   <ModelOptions ... /> 
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <healthSystem ... /> 
|   <entoData ... /> 
| [ <drugDescription ... /> ]
|   <parameters ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

schemaVersion

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

analysisNo

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

maximumAgeYrs

maximumAgeYrs=double

Units: Number Min: 0 Max: 100

Maximum age of simulated humans

name

name=string

Units: string

Name of intervention

popSize

popSize=int

Units: Count Min: 1 Max: 100000

Population size

wuID

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

assimMode

assimMode=("0" or "1")

Units: Code

Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)

mode

mode=("2" or "3" or "4")

Units: Code

Transmission simulation mode

ModelOptions

→ scenario → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).

The list of recognised options can be found in the code at: include/util/ModelOptions.hpp and should also be in the wiki.

option

→ scenario → ModelOptions → option

<option
    name=string
    value=boolean
  />

Attributes

name

name=string

Option name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.

value

value=boolean

Option value (true/false). Each option has a default value (may be true or false) which is used if the option is not listed.

demography

→ scenario → demography

<demography
    name=string
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Documentation (type)

Units: List of elements

Description of demography

Attributes

name

name=string

Units: string

Name of demography data

growthRate

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population.

ageGroup

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

poppercent

poppercent=double

upperbound

upperbound=double

monitoring

→ scenario → monitoring

<monitoring
    name=string
  >
IN THIS ORDER:
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Documentation (type)

Units: List of elements

Description of surveys

Attributes

name

name=string

Units: string

Name of monitoring data

SurveyOptions

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

surveys

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
  >
IN THIS ORDER:
|   <surveyTime ... /> 
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

detectionLimit

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

surveyTime

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time; 0 means just before start of main sim and is a valid survey-point. Reported data is either from a point-time survey (immediate data) or is collected over the previous year (data from previous timesteps-per-year period). Simulation will end immediately after last survey is taken.

ageGroup

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upperbound

upperbound=double

interventions

<interventions
    name=string
  >
IN THIS ORDER:
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| ( <anopheles ... /> )*
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

List of interventions

Documentation (type)

Units: List of elements

List of interventions

Attributes

name

name=string

Units: string

Name of age specific intervention

vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

vaccineType

vaccineType=int

Units: Code

Type of vaccine

halfLifeYrs

→ scenario → interventions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

value

value=double

TODO

efficacyB

→ scenario → interventions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

value

value=double

TODO

initialEfficacy

→ scenario → interventions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

value

value=double

TODO

iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

name

name=string

Units: string

Name of age specific intervention

freq

freq=double

ACR

ACR=double

proph

proph=int

tolPeriod

tolPeriod=int

atten

atten=double

anopheles

→ scenario → interventions → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <VADescription ... /> ]
</anopheles>

Attributes

mosquito

mosquito=string

ITNDescription

→ scenario → interventions → anopheles → ITNDescription

<ITNDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</ITNDescription>

Attributes

name

name=string

Units: string

Name of Insecticide Treated Net intervention

deterrency

→ scenario → interventions → anopheles → ITNDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability (before decay).

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

preprandialKillingEffect

→ scenario → interventions → anopheles → ITNDescription → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

postprandialKillingEffect

→ scenario → interventions → anopheles → ITNDescription → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

IRSDescription

→ scenario → interventions → anopheles → IRSDescription

<IRSDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <killingEffect ... /> 
</IRSDescription>

Attributes

name

name=string

Units: string

Name of Indoor Residual Spraying intervention

deterrency

→ scenario → interventions → anopheles → IRSDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

killingEffect

→ scenario → interventions → anopheles → IRSDescription → killingEffect

<killingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

VADescription

→ scenario → interventions → anopheles → VADescription

<VADescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</VADescription>

deterrency

Attributes

name

name=string

Units: string

Name of mosquito deterrency intervention

deterrency

→ scenario → interventions → anopheles → VADescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

continuous

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
</continuous>

vaccine

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

timed

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <VectorAvailability ... /> ]
| [ <ipti ... /> ]
| [ <larviciding ... /> ]
</intervention>

Attributes

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

drugRegimen

→ scenario → healthSystem → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

firstLine

firstLine=string

Units: Drug code

Code for first line drug

secondLine

secondLine=string

Units: Drug code

Code for second line drug

inpatient

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

initialACR

→ scenario → healthSystem → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

CQ

→ scenario → healthSystem → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

value

value=double

TODO

SP

→ scenario → healthSystem → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

value

value=double

TODO

AQ

→ scenario → healthSystem → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

value

value=double

TODO

SPAQ

→ scenario → healthSystem → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

value

value=double

TODO

ACT

→ scenario → healthSystem → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

value

value=double

TODO

QN

→ scenario → healthSystem → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

value

value=double

TODO

selfTreatment

→ scenario → healthSystem → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

value

value=double

TODO

compliance

→ scenario → healthSystem → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

pSeekOfficialCareUncomplicated1

→ scenario → healthSystem → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSelfTreatUncomplicated

→ scenario → healthSystem → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

value

value=double

TODO

pSeekOfficialCareUncomplicated2

→ scenario → healthSystem → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSeekOfficialCareSevere

→ scenario → healthSystem → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease seeks official care

Attributes

value

value=double

TODO

pSequelaeInpatient

<pSequelaeInpatient>
IN THIS ORDER:
| ( <item ... /> )+
</pSequelaeInpatient>

item

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients

item

→ scenario → healthSystem → pSequelaeInpatient → item

<item
    value=double
    maxAgeYrs=double
  />

Attributes

value

value=double

TODO

maxAgeYrs

maxAgeYrs=double

Units: Years Min: 0 Max: 100

Upper bound of age group

CFR

→ scenario → healthSystem → CFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

group

→ scenario → healthSystem → CFR → group

<group
    cfr=double
    lowerbound=double
  />

Attributes

cfr

cfr=double

Units: Proportion Min: 0 Max: 1

Case fatality rate

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

changeEIR

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

EIRDaily

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Innoculations per person per day

Value of daily EIR; when multiple values are given for a single timestep they are averaged.

Attributes

origin

origin=string

MDA

→ scenario → interventions → timed → intervention → MDA

<MDA
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

vaccinate

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → timed → intervention → ITN

<ITN
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IRS

→ scenario → interventions → timed → intervention → IRS

<IRS
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of IRS deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

VectorAvailability

→ scenario → interventions → timed → intervention → VectorAvailability

<VectorAvailability
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of a mosquito detterent deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → timed → intervention → ipti

<ipti
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

larviciding

→ scenario → interventions → timed → intervention → larviciding

<larviciding>
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

anopheles

Documentation (element)

Simple larviciding intervention description.

anopheles

→ scenario → interventions → timed → intervention → larviciding → anopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

mosquito

mosquito=string

effectiveness

effectiveness=double

Units: none Min: 0 Max: 1

Proportion to reduce emergence rates by.

duration

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

EventScheduler

<EventScheduler
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <CaseManagementTree ... /> 
|   <ClinicalOutcomes ... /> 
</EventScheduler>

Documentation (element)

Units: List of elements

Description of case management and clinical events.

Attributes

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

CaseManagementTree

<CaseManagementTree
    mask=int
  >
IN THIS ORDER:
| ( <CM_pBranchSet ... /> )*
| ( <CM_leaf ... /> )+
</CaseManagementTree>

Documentation (element)

Units: List of elements

Attributes

mask

mask=int

Units: None Min: 0 Max: 0xFFFFFFFF

Value used to mask decision ids before selecting a branch/leaf.

CM_pBranchSet

→ scenario → EventScheduler → CaseManagementTree → CM_pBranchSet

<CM_pBranchSet
    ID=int
  >
IN THIS ORDER:
| ( <CM_pBranch ... /> )+
</CM_pBranchSet>

CM_pBranch

Documentation (element)

A probability branch node: contains a list of outcome nodes along with probabilities, which link to another probability/test branch or leaf node.

Attributes

ID

ID=int

Units: ID

Decision identifier.

CM_pBranch

→ scenario → EventScheduler → CaseManagementTree → CM_pBranchSet → CM_pBranch

<CM_pBranch
    outcome=int
    p=double
  />

Attributes

outcome

outcome=int

ID of next probability/test branch or leaf node.

p

p=double

Units: Proportion Min: 0 Max: 1

Probability of this outcome

CM_leaf

→ scenario → EventScheduler → CaseManagementTree → CM_leaf

<CM_leaf
    ID=int
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</CM_leaf>

medicate

Documentation (element)

End points of the case management tree, listing treatments.

Attributes

ID

ID=int

Units: ID

Decision identifier.

medicate

→ scenario → EventScheduler → CaseManagementTree → CM_leaf → medicate

<medicate
    name=string
    qty=double
    time=double
  />

Attributes

name

name=string

Units: string

Abbreviated name of drug compound

qty

qty=double

Units: mg

Quantity of drug compound

time

time=double

Units: hours Min: 0

Number of hours past start of timestep the drug is medicated at (usually 0).

ClinicalOutcomes

→ scenario → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes
    severeMask=int
  >
IN THIS ORDER:
| ( <outcomes ... /> )+
</ClinicalOutcomes>

outcomes

Documentation (element)

Tables describing the probability of death and the expected length of hospital stay.

The ID looked up in each table is the final outcome ID of the case-management tree binary or-ed with the mask given here.

Attributes

severeMask

severeMask=int

Units: None Min: 0 Max: 0xFFFFFFFF

Value used to mask the final ID from the case-management tree before looking up values here.

outcomes

→ scenario → EventScheduler → ClinicalOutcomes → outcomes

<outcomes
    ID=int
    pDeath=double
    hospitalizationDaysDeath=int
    hospitalizationDaysRecover=int
  />

Documentation (element)

Parameters for a path through the case-management tree (i.e. table row).

Attributes

ID

ID=int

pDeath

pDeath=double

Units: None Min: 0 Max: 1

The probability of death. This probability is applied once-only for each case, irrespective of the branch (thus entries with p=0 for UC cases are probably needed).

hospitalizationDaysDeath

hospitalizationDaysDeath=int

Units: Days Min: 0

hospitalizationDaysRecover

hospitalizationDaysRecover=int

Units: Days Min: 0

healthSystem

→ scenario → healthSystem

<healthSystem
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</healthSystem>

Documentation (element)

Units: List of elements

Description of (old) health system model.

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

entoData

→ scenario → entoData

<entoData
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Documentation (type)

Units: List of elements

Data for entomodel

Attributes

name

name=string

Units: string

Name of entomology data

nonVector

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

vector

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
</vector>

anopheles

Documentation (element)

Parameters for the vector transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <eir ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Attributes

mosquito

mosquito=string

propInfected

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

propInfectious

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

eir

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    b1=double
    a2=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Innoculations per person per day

Attributes

a0

a0=double

a1

a1=double

b1

b1=double

a2

a2=double

b2

b2=double

EIRRotateAngle

EIRRotateAngle=double

mosq

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqSeekingDeathRate=double
    mosqSeekingDuration=double
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

mosqRestDuration

mosqRestDuration=int

extrinsicIncubationPeriod

extrinsicIncubationPeriod=int

mosqSeekingDeathRate

mosqSeekingDeathRate=double

mosqSeekingDuration

mosqSeekingDuration=double

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

mosqProbOvipositing

mosqProbOvipositing=double

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

name

name=string

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

drugDescription

<drugDescription>
IN THIS ORDER:
| ( <drug ... /> )+
</drugDescription>

drug

Documentation (element)

Units: List of elements

Drug model parameters

drug

→ scenario → drugDescription → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (element)

Sequence of drug descriptions forming a library of drug parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → drugDescription → drug → PD

<PD>
IN THIS ORDER:
| ( <allele ... /> )+
</PD>

allele

allele

→ scenario → drugDescription → drug → PD → allele

<allele
    name=string
  >
IN THIS ORDER:
|   <initial_frequency ... /> 
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</allele>

Documentation (element)

PD parameters per allele, plus initial frequency of each allele.

Note: we assume a one-to-one correspondance of drugs to loci, hence each drug has an independent set of alleles here.

Attributes

name

name=string

initial_frequency

→ scenario → drugDescription → drug → PD → allele → initial_frequency

<initial_frequency>
    double
</initial_frequency>

Documentation (element)

Units: relative frequency Min: 0

Frequency, relative to the total frequency of all alleles for this drug/locus.

max_killing_rate

→ scenario → drugDescription → drug → PD → allele → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → drugDescription → drug → PD → allele → IC50

<IC50>
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

slope

→ scenario → drugDescription → drug → PD → allele → slope

<slope>
    double
</slope>

Documentation (element)

Units: no units

n — Slope of the concentration effect curve

PK

→ scenario → drugDescription → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
|   <half_life ... /> 
|   <vol_dist ... /> 
</PK>

negligible_concentration

→ scenario → drugDescription → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

half_life

→ scenario → drugDescription → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimintation rate (which is: ln(2) / half_life).

vol_dist

→ scenario → drugDescription → drug → PK → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

parameters

→ scenario → parameters

<parameters
    interval=int
    iseed=int
    delta=double
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Units: List of elements

Parameters for mathematical model

Documentation (type)

Units: List of elements

Parameter vector

Attributes

interval

interval=int

Units: Days

Simulation step

iseed

iseed=int

Units: Number

Seed for RNG

delta

delta=double

Units: ? Redundant

this no longer seems to be used

latentp

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

name

name=string

Units: string

Name of parameter

number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

value

value=double

Units: Number Min: 0

Parameter value

include

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 13 documentation

Generated from: scenario_13.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    maximumAgeYrs=double
    name=string
    popSize=int
    wuID=int
    assimMode=("0" or "1")
    mode=("2" or "3" or "4")
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_13.xsd"
  >
IN THIS ORDER:
|   <ModelOptions ... /> 
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <healthSystem ... /> 
|   <entoData ... /> 
| [ <drugDescription ... /> ]
|   <parameters ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

schemaVersion

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

analysisNo

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

maximumAgeYrs

maximumAgeYrs=double

Units: Number Min: 0 Max: 100

Maximum age of simulated humans

name

name=string

Units: string

Name of intervention

popSize

popSize=int

Units: Count Min: 1 Max: 100000

Population size

wuID

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

assimMode

assimMode=("0" or "1")

Units: Code

Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)

mode

mode=("2" or "3" or "4")

Units: Code

Transmission simulation mode

ModelOptions

→ scenario → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

option

Documentation (element)

All model options (bug fixes, choices between models, etc.).

The list of recognised options can be found in the code at: include/util/ModelOptions.hpp and should also be in the wiki.

option

→ scenario → ModelOptions → option

<option
    name=string
    value=boolean
  />

Attributes

name

name=string

Option name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.

value

value=boolean

Option value (true/false). Each option has a default value (may be true or false) which is used if the option is not listed.

demography

→ scenario → demography

<demography
    name=string
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Documentation (type)

Units: List of elements

Description of demography

Attributes

name

name=string

Units: string

Name of demography data

growthRate

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population.

ageGroup

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

poppercent

poppercent=double

upperbound

upperbound=double

monitoring

→ scenario → monitoring

<monitoring
    name=string
  >
IN THIS ORDER:
|   <SurveyOptions ... /> 
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Documentation (type)

Units: List of elements

Description of surveys

Attributes

name

name=string

Units: string

Name of monitoring data

SurveyOptions

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

option

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

surveys

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
  >
IN THIS ORDER:
|   <surveyTime ... /> 
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

detectionLimit

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

surveyTime

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time; 0 means just before start of main sim and is a valid survey-point. Reported data is either from a point-time survey (immediate data) or is collected over the previous year (data from previous timesteps-per-year period). Simulation will end immediately after last survey is taken.

ageGroup

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upperbound

upperbound=double

interventions

<interventions
    name=string
  >
IN THIS ORDER:
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| ( <anopheles ... /> )*
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

List of interventions

Documentation (type)

Units: List of elements

List of interventions

Attributes

name

name=string

Units: string

Name of age specific intervention

vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

vaccineType

vaccineType=int

Units: Code

Type of vaccine

halfLifeYrs

→ scenario → interventions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

value

value=double

TODO

efficacyB

→ scenario → interventions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

value

value=double

TODO

initialEfficacy

→ scenario → interventions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

value

value=double

TODO

iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

name

name=string

Units: string

Name of age specific intervention

freq

freq=double

ACR

ACR=double

proph

proph=int

tolPeriod

tolPeriod=int

atten

atten=double

anopheles

→ scenario → interventions → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <VADescription ... /> ]
</anopheles>

Attributes

mosquito

mosquito=string

ITNDescription

→ scenario → interventions → anopheles → ITNDescription

<ITNDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</ITNDescription>

Attributes

name

name=string

Units: string

Name of Insecticide Treated Net intervention

deterrency

→ scenario → interventions → anopheles → ITNDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability (before decay).

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

preprandialKillingEffect

→ scenario → interventions → anopheles → ITNDescription → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

postprandialKillingEffect

→ scenario → interventions → anopheles → ITNDescription → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

IRSDescription

→ scenario → interventions → anopheles → IRSDescription

<IRSDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <killingEffect ... /> 
</IRSDescription>

Attributes

name

name=string

Units: string

Name of Indoor Residual Spraying intervention

deterrency

→ scenario → interventions → anopheles → IRSDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

killingEffect

→ scenario → interventions → anopheles → IRSDescription → killingEffect

<killingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

VADescription

→ scenario → interventions → anopheles → VADescription

<VADescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</VADescription>

deterrency

Attributes

name

name=string

Units: string

Name of mosquito deterrency intervention

deterrency

→ scenario → interventions → anopheles → VADescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

continuous

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
</continuous>

vaccine

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

timed

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <VectorAvailability ... /> ]
| [ <ipti ... /> ]
| [ <larviciding ... /> ]
</intervention>

Attributes

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

drugRegimen

→ scenario → healthSystem → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

firstLine

firstLine=string

Units: Drug code

Code for first line drug

secondLine

secondLine=string

Units: Drug code

Code for second line drug

inpatient

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

initialACR

→ scenario → healthSystem → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

CQ

→ scenario → healthSystem → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

value

value=double

TODO

SP

→ scenario → healthSystem → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

value

value=double

TODO

AQ

→ scenario → healthSystem → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

value

value=double

TODO

SPAQ

→ scenario → healthSystem → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

value

value=double

TODO

ACT

→ scenario → healthSystem → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

value

value=double

TODO

QN

→ scenario → healthSystem → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

value

value=double

TODO

selfTreatment

→ scenario → healthSystem → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

value

value=double

TODO

compliance

→ scenario → healthSystem → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

pSeekOfficialCareUncomplicated1

→ scenario → healthSystem → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSelfTreatUncomplicated

→ scenario → healthSystem → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

value

value=double

TODO

pSeekOfficialCareUncomplicated2

→ scenario → healthSystem → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSeekOfficialCareSevere

→ scenario → healthSystem → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease seeks official care

Attributes

value

value=double

TODO

pSequelaeInpatient

<pSequelaeInpatient>
IN THIS ORDER:
| ( <item ... /> )+
</pSequelaeInpatient>

item

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients

item

→ scenario → healthSystem → pSequelaeInpatient → item

<item
    value=double
    maxAgeYrs=double
  />

Attributes

value

value=double

TODO

maxAgeYrs

maxAgeYrs=double

Units: Years Min: 0 Max: 100

Upper bound of age group

CFR

→ scenario → healthSystem → CFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

group

→ scenario → healthSystem → CFR → group

<group
    cfr=double
    lowerbound=double
  />

Attributes

cfr

cfr=double

Units: Proportion Min: 0 Max: 1

Case fatality rate

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

changeEIR

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

EIRDaily

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Innoculations per person per day

Value of daily EIR; when multiple values are given for a single timestep they are averaged.

Attributes

origin

origin=string

MDA

→ scenario → interventions → timed → intervention → MDA

<MDA
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

vaccinate

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → timed → intervention → ITN

<ITN
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IRS

→ scenario → interventions → timed → intervention → IRS

<IRS
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of IRS deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

VectorAvailability

→ scenario → interventions → timed → intervention → VectorAvailability

<VectorAvailability
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of a mosquito detterent deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → timed → intervention → ipti

<ipti
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

larviciding

→ scenario → interventions → timed → intervention → larviciding

<larviciding>
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

anopheles

Documentation (element)

Simple larviciding intervention description.

anopheles

→ scenario → interventions → timed → intervention → larviciding → anopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

mosquito

mosquito=string

effectiveness

effectiveness=double

Units: none Min: 0 Max: 1

Proportion to reduce emergence rates by.

duration

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

EventScheduler

<EventScheduler
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <CaseManagementTree ... /> 
|   <ClinicalOutcomes ... /> 
</EventScheduler>

Documentation (element)

Units: List of elements

Description of case management and clinical events.

Attributes

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

CaseManagementTree

<CaseManagementTree
    mask=int
  >
IN THIS ORDER:
| ( <CM_pBranchSet ... /> )*
| ( <CM_leaf ... /> )+
</CaseManagementTree>

Documentation (element)

Units: List of elements

Attributes

mask

mask=int

Units: None Min: 0 Max: 0xFFFFFFFF

Value used to mask decision ids before selecting a branch/leaf.

CM_pBranchSet

→ scenario → EventScheduler → CaseManagementTree → CM_pBranchSet

<CM_pBranchSet
    ID=int
  >
IN THIS ORDER:
| ( <CM_pBranch ... /> )+
</CM_pBranchSet>

CM_pBranch

Documentation (element)

A probability branch node: contains a list of outcome nodes along with probabilities, which link to another probability/test branch or leaf node.

Attributes

ID

ID=int

Units: ID

Decision identifier.

CM_pBranch

→ scenario → EventScheduler → CaseManagementTree → CM_pBranchSet → CM_pBranch

<CM_pBranch
    outcome=int
    p=double
  />

Attributes

outcome

outcome=int

ID of next probability/test branch or leaf node.

p

p=double

Units: Proportion Min: 0 Max: 1

Probability of this outcome

CM_leaf

→ scenario → EventScheduler → CaseManagementTree → CM_leaf

<CM_leaf
    ID=int
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</CM_leaf>

medicate

Documentation (element)

End points of the case management tree, listing treatments.

Attributes

ID

ID=int

Units: ID

Decision identifier.

medicate

→ scenario → EventScheduler → CaseManagementTree → CM_leaf → medicate

<medicate
    name=string
    qty=double
    time=int
  />

Attributes

name

name=string

Units: string

Abbreviated name of drug compound

qty

qty=double

Units: mg

Quantity of drug compound

time

time=int

Units: Minutes Min: 0

Number of minutes past start of timestep the drug is medicated at (usually 0).

ClinicalOutcomes

→ scenario → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes
    severeMask=int
  >
IN THIS ORDER:
| ( <outcomes ... /> )+
</ClinicalOutcomes>

outcomes

Documentation (element)

Tables describing the probability of death and the expected length of hospital stay.

The ID looked up in each table is the final outcome ID of the case-management tree binary or-ed with the mask given here.

Attributes

severeMask

severeMask=int

Units: None Min: 0 Max: 0xFFFFFFFF

Value used to mask the final ID from the case-management tree before looking up values here.

outcomes

→ scenario → EventScheduler → ClinicalOutcomes → outcomes

<outcomes
    ID=int
    pDeath=double
    hospitalizationDaysDeath=int
    hospitalizationDaysRecover=int
  />

Documentation (element)

Parameters for a path through the case-management tree (i.e. table row).

Attributes

ID

ID=int

pDeath

pDeath=double

Units: None Min: 0 Max: 1

The probability of death. This probability is applied once-only for each case, irrespective of the branch (thus entries with p=0 for UC cases are probably needed).

hospitalizationDaysDeath

hospitalizationDaysDeath=int

Units: Days Min: 0

hospitalizationDaysRecover

hospitalizationDaysRecover=int

Units: Days Min: 0

healthSystem

→ scenario → healthSystem

<healthSystem
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</healthSystem>

Documentation (element)

Units: List of elements

Description of (old) health system model.

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

entoData

→ scenario → entoData

<entoData
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Documentation (type)

Units: List of elements

Data for entomodel

Attributes

name

name=string

Units: string

Name of entomology data

nonVector

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

vector

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
</vector>

anopheles

Documentation (element)

Parameters for the vector transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <eir ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Attributes

mosquito

mosquito=string

propInfected

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

propInfectious

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

eir

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    b1=double
    a2=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Innoculations per person per day

Attributes

a0

a0=double

a1

a1=double

b1

b1=double

a2

a2=double

b2

b2=double

EIRRotateAngle

EIRRotateAngle=double

mosq

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqSeekingDeathRate=double
    mosqSeekingDuration=double
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

mosqRestDuration

mosqRestDuration=int

extrinsicIncubationPeriod

extrinsicIncubationPeriod=int

mosqSeekingDeathRate

mosqSeekingDeathRate=double

mosqSeekingDuration

mosqSeekingDuration=double

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

mosqProbOvipositing

mosqProbOvipositing=double

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

name

name=string

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

drugDescription

<drugDescription>
IN THIS ORDER:
|   <genome ... /> 
|   <drugs ... /> 
</drugDescription>

genome
drugs

Documentation (element)

Units: List of elements

Drug model parameters

genome

→ scenario → drugDescription → genome

<genome>
IN THIS ORDER:
|   <content ... /> 
|   <distribution ... /> 
</genome>

content

→ scenario → drugDescription → genome → content

<content>
IN THIS ORDER:
| ( <gene ... /> )+
</content>

gene

gene

→ scenario → drugDescription → genome → content → gene

<gene
    name=string
  >
IN THIS ORDER:
| ( <mutation ... /> )+
</gene>

mutation

Attributes

name

name=string

mutation

→ scenario → drugDescription → genome → content → gene → mutation

<mutation
    cost=double
    position=integer
  />

Attributes

cost

cost=double

position

position=integer

distribution

→ scenario → drugDescription → genome → distribution

<distribution>
IN THIS ORDER:
| ( <genomeInstance ... /> )+
</distribution>

genomeInstance

genomeInstance

→ scenario → drugDescription → genome → distribution → genomeInstance

<genomeInstance
    proportion=integer
  >
IN THIS ORDER:
| ( <allele ... /> )+
</genomeInstance>

allele

Attributes

proportion

proportion=integer

allele

→ scenario → drugDescription → genome → distribution → genomeInstance → allele

<allele
    mutations=integer
    name=string
  />

Attributes

mutations

mutations=integer

name

name=string

drugs

→ scenario → drugDescription → drugs

<drugs
  [ synergy=string ]
  >
IN THIS ORDER:
|   <compound ... /> 
</drugs>

compound

Attributes

synergy

synergy=string

compound

→ scenario → drugDescription → drugs → compound

<compound
    acronym=string
    name=string
  >
IN THIS ORDER:
|   <pk ... /> 
|   <pd ... /> 
</compound>

Attributes

acronym

acronym=string

name

name=string

pk

→ scenario → drugDescription → drugs → compound → pk

<pk>
</pk>

ageGroup

ageGroup

→ scenario → drugDescription → drugs → compound → pk → ageGroup

<ageGroup
    F=integer
    Vd=double
    t12=integer
  [ minAge=double ]
  />

Attributes

F

F=integer

Bioavailability (unsure of the units we will be using)

Vd

Vd=double

Volume of Distribution (l/kg)

t12

t12=integer

Units: Number

Half-life (days)

minAge

minAge=double

pd

→ scenario → drugDescription → drugs → compound → pd

<pd>
IN THIS ORDER:
| ( <genomeRule ... /> )+
</pd>

genomeRule

genomeRule

→ scenario → drugDescription → drugs → compound → pd → genomeRule

<genomeRule>
</genomeRule>

matchMutation

→ scenario → drugDescription → drugs → compound → pd → genomeRule → matchMutation

<matchMutation
    present=boolean
    gene=string
    pos=integer
  />

Attributes

present

present=boolean

gene

gene=string

pos

pos=integer

ageGroup

→ scenario → drugDescription → drugs → compound → pd → genomeRule → ageGroup

<ageGroup
    c50=integer
    k1=double
    n=integer
  [ minAge=double ]
  />

Attributes

c50

c50=integer

Half maximal effect concentration (mg/l)

k1

k1=double

Units: Proportion Min: 0 Max: 1

Maximal parasite killing rate (per day)

n

n=integer

Slope of the concentration effect curve (no units)

minAge

minAge=double

parameters

→ scenario → parameters

<parameters
    interval=int
    iseed=int
    delta=double
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Units: List of elements

Parameters for mathematical model

Documentation (type)

Units: List of elements

Parameter vector

Attributes

interval

interval=int

Units: Days

Simulation step

iseed

iseed=int

Units: Number

Seed for RNG

delta

delta=double

Units: ? Redundant

this no longer seems to be used

latentp

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

name

name=string

Units: string

Name of parameter

number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

value

value=double

Units: Number Min: 0

Parameter value

include

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 12 documentation

Generated from: scenario_12.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    maximumAgeYrs=double
    name=string
    popSize=int
    modelVersion=int
    wuID=int
    assimMode=("0" or "1")
    mode=("2" or "3" or "4")
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_12.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <healthSystem ... /> 
|   <entoData ... /> 
| [ <drugDescription ... /> ]
|   <parameters ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

schemaVersion

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

analysisNo

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

maximumAgeYrs

maximumAgeYrs=double

Units: Number Min: 0 Max: 100

Maximum age of simulated humans

name

name=string

Units: string

Name of intervention

popSize

popSize=int

Units: Count Min: 1 Max: 100000

Population size

modelVersion

modelVersion=int

Units: Code Min: 0 Max: 100000000

Model Version

wuID

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

assimMode

assimMode=("0" or "1")

Units: Code

Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)

mode

mode=("2" or "3" or "4")

Units: Code

Transmission simulation mode

demography

→ scenario → demography

<demography
    name=string
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Documentation (type)

Units: List of elements

Description of demography

Attributes

name

name=string

Units: string

Name of demography data

growthRate

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population.

ageGroup

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

poppercent

poppercent=double

upperbound

upperbound=double

monitoring

→ scenario → monitoring

<monitoring
    name=string
  >
IN THIS ORDER:
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Documentation (type)

Units: List of elements

Description of surveys

Attributes

name

name=string

Units: string

Name of monitoring data

surveys

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
    summaryOption=int
  >
IN THIS ORDER:
|   <surveyTime ... /> 
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

detectionLimit

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

summaryOption

summaryOption=int

Units: Code

Requested output variables

surveyTime

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time; 0 means just before start of main sim and is a valid survey-point. Reported data is either from a point-time survey (immediate data) or is collected over the previous year (data from previous timesteps-per-year period). Simulation will end immediately after last survey is taken.

ageGroup

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upperbound

upperbound=double

interventions

<interventions
    name=string
  >
IN THIS ORDER:
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| ( <anopheles ... /> )*
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

List of interventions

Documentation (type)

Units: List of elements

List of interventions

Attributes

name

name=string

Units: string

Name of age specific intervention

vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

vaccineType

vaccineType=int

Units: Code

Type of vaccine

halfLifeYrs

→ scenario → interventions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

value

value=double

TODO

efficacyB

→ scenario → interventions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

value

value=double

TODO

initialEfficacy

→ scenario → interventions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

value

value=double

TODO

iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

name

name=string

Units: string

Name of age specific intervention

freq

freq=double

ACR

ACR=double

proph

proph=int

tolPeriod

tolPeriod=int

atten

atten=double

anopheles

→ scenario → interventions → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <VADescription ... /> ]
</anopheles>

Attributes

mosquito

mosquito=string

ITNDescription

→ scenario → interventions → anopheles → ITNDescription

<ITNDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</ITNDescription>

Attributes

name

name=string

Units: string

Name of Insecticide Treated Net intervention

deterrency

→ scenario → interventions → anopheles → ITNDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability (before decay).

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

preprandialKillingEffect

→ scenario → interventions → anopheles → ITNDescription → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

postprandialKillingEffect

→ scenario → interventions → anopheles → ITNDescription → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

IRSDescription

→ scenario → interventions → anopheles → IRSDescription

<IRSDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <killingEffect ... /> 
</IRSDescription>

Attributes

name

name=string

Units: string

Name of Indoor Residual Spraying intervention

deterrency

→ scenario → interventions → anopheles → IRSDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

killingEffect

→ scenario → interventions → anopheles → IRSDescription → killingEffect

<killingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

VADescription

→ scenario → interventions → anopheles → VADescription

<VADescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</VADescription>

deterrency

Attributes

name

name=string

Units: string

Name of mosquito deterrency intervention

deterrency

→ scenario → interventions → anopheles → VADescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

continuous

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
</continuous>

vaccine

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

timed

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <VectorAvailability ... /> ]
| [ <ipti ... /> ]
| [ <larviciding ... /> ]
</intervention>

Attributes

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

drugRegimen

→ scenario → healthSystem → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

firstLine

firstLine=string

Units: Drug code

Code for first line drug

secondLine

secondLine=string

Units: Drug code

Code for second line drug

inpatient

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

initialACR

→ scenario → healthSystem → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

CQ

→ scenario → healthSystem → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

value

value=double

TODO

SP

→ scenario → healthSystem → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

value

value=double

TODO

AQ

→ scenario → healthSystem → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

value

value=double

TODO

SPAQ

→ scenario → healthSystem → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

value

value=double

TODO

ACT

→ scenario → healthSystem → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

value

value=double

TODO

QN

→ scenario → healthSystem → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

value

value=double

TODO

selfTreatment

→ scenario → healthSystem → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

value

value=double

TODO

compliance

→ scenario → healthSystem → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

pSeekOfficialCareUncomplicated1

→ scenario → healthSystem → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSelfTreatUncomplicated

→ scenario → healthSystem → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

value

value=double

TODO

pSeekOfficialCareUncomplicated2

→ scenario → healthSystem → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSeekOfficialCareSevere

→ scenario → healthSystem → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease seeks official care

Attributes

value

value=double

TODO

pSequelaeInpatient

<pSequelaeInpatient>
IN THIS ORDER:
| ( <item ... /> )+
</pSequelaeInpatient>

item

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients

item

→ scenario → healthSystem → pSequelaeInpatient → item

<item
    value=double
    maxAgeYrs=double
  />

Attributes

value

value=double

TODO

maxAgeYrs

maxAgeYrs=double

Units: Years Min: 0 Max: 100

Upper bound of age group

CFR

→ scenario → healthSystem → CFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

group

→ scenario → healthSystem → CFR → group

<group
    cfr=double
    lowerbound=double
  />

Attributes

cfr

cfr=double

Units: Proportion Min: 0 Max: 1

Case fatality rate

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

changeEIR

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

EIRDaily

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Innoculations per person per day

Value of daily EIR; when multiple values are given for a single timestep they are averaged.

Attributes

origin

origin=string

MDA

→ scenario → interventions → timed → intervention → MDA

<MDA
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

vaccinate

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → timed → intervention → ITN

<ITN
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IRS

→ scenario → interventions → timed → intervention → IRS

<IRS
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of IRS deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

VectorAvailability

→ scenario → interventions → timed → intervention → VectorAvailability

<VectorAvailability
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of a mosquito detterent deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → timed → intervention → ipti

<ipti
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

larviciding

→ scenario → interventions → timed → intervention → larviciding

<larviciding>
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

anopheles

Documentation (element)

Simple larviciding intervention description.

anopheles

→ scenario → interventions → timed → intervention → larviciding → anopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

mosquito

mosquito=string

effectiveness

effectiveness=double

Units: none Min: 0 Max: 1

Proportion to reduce emergence rates by.

duration

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

EventScheduler

<EventScheduler
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <CaseManagementTree ... /> 
|   <ClinicalOutcome ... /> 
</EventScheduler>

Documentation (element)

Units: List of elements

Description of case management and clinical events.

Attributes

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

CaseManagementTree

<CaseManagementTree
    mask=int
  >
IN THIS ORDER:
| ( <CM_pBranchSet ... /> )*
| ( <CM_leaf ... /> )+
</CaseManagementTree>

Documentation (element)

Units: List of elements

Attributes

mask

mask=int

Units: None Min: 0 Max: 0xFFFFFFFF

Value used to mask decision ids before selecting a branch/leaf.

CM_pBranchSet

→ scenario → EventScheduler → CaseManagementTree → CM_pBranchSet

<CM_pBranchSet
    ID=int
  >
IN THIS ORDER:
| ( <CM_pBranch ... /> )+
</CM_pBranchSet>

CM_pBranch

Documentation (element)

A probability branch node: contains a list of outcome nodes along with probabilities, which link to another probability/test branch or leaf node.

Attributes

ID

ID=int

Units: ID

Decision identifier.

CM_pBranch

→ scenario → EventScheduler → CaseManagementTree → CM_pBranchSet → CM_pBranch

<CM_pBranch
    outcome=int
    p=double
  />

Attributes

outcome

outcome=int

ID of next probability/test branch or leaf node.

p

p=double

Units: Proportion Min: 0 Max: 1

Probability of this outcome

CM_leaf

→ scenario → EventScheduler → CaseManagementTree → CM_leaf

<CM_leaf
    ID=int
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</CM_leaf>

medicate

Documentation (element)

End points of the case management tree, listing treatments.

Attributes

ID

ID=int

Units: ID

Decision identifier.

medicate

→ scenario → EventScheduler → CaseManagementTree → CM_leaf → medicate

<medicate
    name=string
    qty=double
    time=int
  />

Attributes

name

name=string

Units: string

Abbreviated name of drug compound

qty

qty=double

Units: mg

Quantity of drug compound

time

time=int

Units: Minutes Min: 0

Number of minutes past start of timestep the drug is medicated at (usually 0).

ClinicalOutcome

→ scenario → EventScheduler → ClinicalOutcome

<ClinicalOutcome
    mask=int
  >
IN THIS ORDER:
| ( <path ... /> )+
</ClinicalOutcome>

path

Documentation (element)

Tables describing the probability of death and the expected length of hospital stay.

The ID looked up in each table is the final outcome ID of the case-management tree binary or-ed with the mask given here.

Attributes

mask

mask=int

Units: None Min: 0 Max: 0xFFFFFFFF

Value used to mask the final ID from the case-management tree before looking up values here.

path

→ scenario → EventScheduler → ClinicalOutcome → path

<path
    ID=int
    pDeath=double
    hospitalizationDuration=int
  />

Documentation (element)

Parameters for a path through the case-management tree (i.e. table row).

Attributes

ID

ID=int

pDeath

pDeath=double

The probability of death. This probability is applied once-only for each case, irrespective of the branch (thus entries with p=0 for UC cases are probably needed).

hospitalizationDuration

hospitalizationDuration=int

The median length of stay in hospital. (Use median rather than a distribution because data should be more reliable and the effect of heterogeneity should be small.)

healthSystem

→ scenario → healthSystem

<healthSystem
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</healthSystem>

Documentation (element)

Units: List of elements

Description of (old) health system model.

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

entoData

→ scenario → entoData

<entoData
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Documentation (type)

Units: List of elements

Data for entomodel

Attributes

name

name=string

Units: string

Name of entomology data

nonVector

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

vector

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
</vector>

anopheles

Documentation (element)

Parameters for the vector transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <eir ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Attributes

mosquito

mosquito=string

propInfected

propInfected=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.

propInfectious

propInfectious=double

Units: Proportion Min: 0 Max: 1

Initial guess of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.

eir

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    b1=double
    a2=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Innoculations per person per day

Attributes

a0

a0=double

a1

a1=double

b1

b1=double

a2

a2=double

b2

b2=double

EIRRotateAngle

EIRRotateAngle=double

mosq

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqSeekingDeathRate=double
    mosqSeekingDuration=double
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

mosqRestDuration

mosqRestDuration=int

extrinsicIncubationPeriod

extrinsicIncubationPeriod=int

mosqSeekingDeathRate

mosqSeekingDeathRate=double

mosqSeekingDuration

mosqSeekingDuration=double

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

mosqProbOvipositing

mosqProbOvipositing=double

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

name

name=string

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

drugDescription

<drugDescription>
IN THIS ORDER:
|   <genome ... /> 
|   <drugs ... /> 
</drugDescription>

genome
drugs

Documentation (element)

Units: List of elements

Drug model parameters

genome

→ scenario → drugDescription → genome

<genome>
IN THIS ORDER:
|   <content ... /> 
|   <distribution ... /> 
</genome>

content

→ scenario → drugDescription → genome → content

<content>
IN THIS ORDER:
| ( <gene ... /> )+
</content>

gene

gene

→ scenario → drugDescription → genome → content → gene

<gene
    name=string
  >
IN THIS ORDER:
| ( <mutation ... /> )+
</gene>

mutation

Attributes

name

name=string

mutation

→ scenario → drugDescription → genome → content → gene → mutation

<mutation
    cost=double
    position=integer
  />

Attributes

cost

cost=double

position

position=integer

distribution

→ scenario → drugDescription → genome → distribution

<distribution>
IN THIS ORDER:
| ( <genomeInstance ... /> )+
</distribution>

genomeInstance

genomeInstance

→ scenario → drugDescription → genome → distribution → genomeInstance

<genomeInstance
    proportion=integer
  >
IN THIS ORDER:
| ( <allele ... /> )+
</genomeInstance>

allele

Attributes

proportion

proportion=integer

allele

→ scenario → drugDescription → genome → distribution → genomeInstance → allele

<allele
    mutations=integer
    name=string
  />

Attributes

mutations

mutations=integer

name

name=string

drugs

→ scenario → drugDescription → drugs

<drugs
  [ synergy=string ]
  >
IN THIS ORDER:
|   <compound ... /> 
</drugs>

compound

Attributes

synergy

synergy=string

compound

→ scenario → drugDescription → drugs → compound

<compound
    acronym=string
    name=string
  >
IN THIS ORDER:
|   <pk ... /> 
|   <pd ... /> 
</compound>

Attributes

acronym

acronym=string

name

name=string

pk

→ scenario → drugDescription → drugs → compound → pk

<pk>
</pk>

ageGroup

ageGroup

→ scenario → drugDescription → drugs → compound → pk → ageGroup

<ageGroup
    F=integer
    Vd=double
    t12=integer
  [ minAge=double ]
  />

Attributes

F

F=integer

Bioavailability (unsure of the units we will be using)

Vd

Vd=double

Volume of Distribution (l/kg)

t12

t12=integer

Units: Number

Half-life (days)

minAge

minAge=double

pd

→ scenario → drugDescription → drugs → compound → pd

<pd>
IN THIS ORDER:
| ( <genomeRule ... /> )+
</pd>

genomeRule

genomeRule

→ scenario → drugDescription → drugs → compound → pd → genomeRule

<genomeRule>
</genomeRule>

matchMutation

→ scenario → drugDescription → drugs → compound → pd → genomeRule → matchMutation

<matchMutation
    present=boolean
    gene=string
    pos=integer
  />

Attributes

present

present=boolean

gene

gene=string

pos

pos=integer

ageGroup

→ scenario → drugDescription → drugs → compound → pd → genomeRule → ageGroup

<ageGroup
    c50=integer
    k1=double
    n=integer
  [ minAge=double ]
  />

Attributes

c50

c50=integer

Half maximal effect concentration (mg/l)

k1

k1=double

Units: Proportion Min: 0 Max: 1

Maximal parasite killing rate (per day)

n

n=integer

Slope of the concentration effect curve (no units)

minAge

minAge=double

parameters

→ scenario → parameters

<parameters
    interval=int
    iseed=int
    delta=double
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Units: List of elements

Parameters for mathematical model

Documentation (type)

Units: List of elements

Parameter vector

Attributes

interval

interval=int

Units: Days

Simulation step

iseed

iseed=int

Units: Number

Seed for RNG

delta

delta=double

Units: ? Redundant

this no longer seems to be used

latentp

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

name

name=string

Units: string

Name of parameter

number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

value

value=double

Units: Number Min: 0

Parameter value

include

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 11 documentation

Generated from: scenario_11.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    maximumAgeYrs=double
    name=string
    popSize=int
    simulationDuration=int
    modelVersion=int
    wuID=int
    assimMode=("0" or "1")
    mode=("2" or "3" or "4")
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_11.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
| [ <caseManagements ... /> ]
| [ <healthSystem ... /> ]
|   <entoData ... /> 
| [ <drugDescription ... /> ]
|   <parameters ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

schemaVersion

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

analysisNo

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

maximumAgeYrs

maximumAgeYrs=double

Units: Number Min: 0 Max: 100

Maximum age of simulated humans

name

name=string

Units: string

Name of intervention

popSize

popSize=int

Units: Count Min: 1 Max: 100000

Population size

simulationDuration

simulationDuration=int

Units: Time steps Min: 1 Max: 36500

Duration of main simulation

modelVersion

modelVersion=int

Units: Code Min: 0 Max: 100000000

Model Version

wuID

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

assimMode

assimMode=("0" or "1")

Units: Code

Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)

mode

mode=("2" or "3" or "4")

Units: Code

Transmission simulation mode

demography

→ scenario → demography

<demography
    name=string
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Documentation (type)

Units: List of elements

Description of demography

Attributes

name

name=string

Units: string

Name of demography data

growthRate

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population.

ageGroup

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

poppercent

poppercent=double

upperbound

upperbound=double

monitoring

→ scenario → monitoring

<monitoring
    name=string
  >
IN THIS ORDER:
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Documentation (type)

Units: List of elements

Description of surveys

Attributes

name

name=string

Units: string

Name of monitoring data

surveys

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
    summaryOption=int
  >
IN THIS ORDER:
|   <surveyTime ... /> 
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

detectionLimit

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

summaryOption

summaryOption=int

Units: Code

Requested output variables

surveyTime

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time

ageGroup

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upperbound

upperbound=double

interventions

<interventions
    name=string
  >
IN THIS ORDER:
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| ( <anopheles ... /> )*
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

List of interventions

Documentation (type)

Units: List of elements

List of interventions

Attributes

name

name=string

Units: string

Name of age specific intervention

vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

vaccineType

vaccineType=int

Units: Code

Type of vaccine

halfLifeYrs

→ scenario → interventions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

value

value=double

TODO

efficacyB

→ scenario → interventions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

value

value=double

TODO

initialEfficacy

→ scenario → interventions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

value

value=double

TODO

iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

name

name=string

Units: string

Name of age specific intervention

freq

freq=double

ACR

ACR=double

proph

proph=int

tolPeriod

tolPeriod=int

atten

atten=double

anopheles

→ scenario → interventions → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <VADescription ... /> ]
</anopheles>

Attributes

mosquito

mosquito=string

ITNDescription

→ scenario → interventions → anopheles → ITNDescription

<ITNDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</ITNDescription>

Attributes

name

name=string

Units: string

Name of Insecticide Treated Net intervention

deterrency

→ scenario → interventions → anopheles → ITNDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability (before decay).

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

preprandialKillingEffect

→ scenario → interventions → anopheles → ITNDescription → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

postprandialKillingEffect

→ scenario → interventions → anopheles → ITNDescription → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

IRSDescription

→ scenario → interventions → anopheles → IRSDescription

<IRSDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <killingEffect ... /> 
</IRSDescription>

Attributes

name

name=string

Units: string

Name of Indoor Residual Spraying intervention

deterrency

→ scenario → interventions → anopheles → IRSDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

killingEffect

→ scenario → interventions → anopheles → IRSDescription → killingEffect

<killingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

VADescription

→ scenario → interventions → anopheles → VADescription

<VADescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</VADescription>

deterrency

Attributes

name

name=string

Units: string

Name of mosquito deterrency intervention

deterrency

→ scenario → interventions → anopheles → VADescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

continuous

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
</continuous>

vaccine

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

timed

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <VectorAvailability ... /> ]
| [ <ipti ... /> ]
| [ <larviciding ... /> ]
</intervention>

Attributes

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

drugRegimen

→ scenario → healthSystem → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

firstLine

firstLine=string

Units: Drug code

Code for first line drug

secondLine

secondLine=string

Units: Drug code

Code for second line drug

inpatient

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

initialACR

→ scenario → healthSystem → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

CQ

→ scenario → healthSystem → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

value

value=double

TODO

SP

→ scenario → healthSystem → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

value

value=double

TODO

AQ

→ scenario → healthSystem → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

value

value=double

TODO

SPAQ

→ scenario → healthSystem → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

value

value=double

TODO

ACT

→ scenario → healthSystem → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

value

value=double

TODO

QN

→ scenario → healthSystem → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

value

value=double

TODO

selfTreatment

→ scenario → healthSystem → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

value

value=double

TODO

compliance

→ scenario → healthSystem → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

pSeekOfficialCareUncomplicated1

→ scenario → healthSystem → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSelfTreatUncomplicated

→ scenario → healthSystem → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

value

value=double

TODO

pSeekOfficialCareUncomplicated2

→ scenario → healthSystem → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSeekOfficialCareSevere

→ scenario → healthSystem → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease seeks official care

Attributes

value

value=double

TODO

pSequelaeInpatient

<pSequelaeInpatient>
IN THIS ORDER:
| ( <item ... /> )+
</pSequelaeInpatient>

item

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients

item

→ scenario → healthSystem → pSequelaeInpatient → item

<item
    value=double
    maxAgeYrs=double
  />

Attributes

value

value=double

TODO

maxAgeYrs

maxAgeYrs=double

Units: Years Min: 0 Max: 100

Upper bound of age group

CFR

→ scenario → healthSystem → CFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

group

→ scenario → healthSystem → CFR → group

<group
    cfr=double
    lowerbound=double
  />

Attributes

cfr

cfr=double

Units: Proportion Min: 0 Max: 1

Case fatality rate

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

changeEIR

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

EIRDaily

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Innoculations per person per day

Value of daily EIR; when multiple values are given for a single timestep they are averaged.

Attributes

origin

origin=string

MDA

→ scenario → interventions → timed → intervention → MDA

<MDA
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

vaccinate

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → timed → intervention → ITN

<ITN
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IRS

→ scenario → interventions → timed → intervention → IRS

<IRS
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of IRS deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

VectorAvailability

→ scenario → interventions → timed → intervention → VectorAvailability

<VectorAvailability
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of a mosquito detterent deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → timed → intervention → ipti

<ipti
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

larviciding

→ scenario → interventions → timed → intervention → larviciding

<larviciding>
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

anopheles

Documentation (element)

Simple larviciding intervention description.

anopheles

→ scenario → interventions → timed → intervention → larviciding → anopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

mosquito

mosquito=string

effectiveness

effectiveness=double

Units: none Min: 0 Max: 1

Proportion to reduce emergence rates by.

duration

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

caseManagements

<caseManagements
    name=string
    reportingPeriodMemory=int
  >
IN THIS ORDER:
| ( <caseManagement ... /> )+
</caseManagements>

caseManagement

Documentation (element)

Units: List of elements

List of case managment interventions

Documentation (type)

Units: List of elements

List of age-specific case managment descriptions

Attributes

name

name=string

Units: string

Name of age specific intervention

reportingPeriodMemory

reportingPeriodMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

caseManagement

<caseManagement
    maxAgeYrs=decimal
  >
IN THIS ORDER:
|   <uc1 ... /> 
|   <uc2 ... /> 
|   <sev ... /> 
|   <nmfP ... /> 
|   <nmfNP ... /> 
|   <decisions ... /> 
</caseManagement>

Documentation (element)

Units: List of elements

Age-specific case management description, describes entry-points and decisions, with entry-point-specific decision probabilities

Attributes

maxAgeYrs

maxAgeYrs=decimal

Units: Years Min: 0 Max: 100

Upper bound of age group

uc1

→ scenario → caseManagements → caseManagement → uc1

<uc1>
IN THIS ORDER:
| ( <endPoint ... /> )+
</uc1>

endPoint

endPoint

→ scenario → caseManagements → caseManagement → uc1 → endPoint

<endPoint
    decision=int
    p=double
  />

Attributes

decision

decision=int

Foreign key reference to outcome node

p

p=double

Units: Proportion Min: 0 Max: 1

Probability of outcome

uc2

→ scenario → caseManagements → caseManagement → uc2

<uc2>
IN THIS ORDER:
| ( <endPoint ... /> )+
</uc2>

endPoint

sev

→ scenario → caseManagements → caseManagement → sev

<sev>
IN THIS ORDER:
| ( <endPoint ... /> )+
</sev>

endPoint

nmfP

→ scenario → caseManagements → caseManagement → nmfP

<nmfP>
IN THIS ORDER:
| ( <endPoint ... /> )+
</nmfP>

endPoint

nmfNP

→ scenario → caseManagements → caseManagement → nmfNP

<nmfNP>
IN THIS ORDER:
| ( <endPoint ... /> )+
</nmfNP>

endPoint

decisions

→ scenario → caseManagements → caseManagement → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )+
</decisions>

decision

decision

→ scenario → caseManagements → caseManagement → decisions → decision

<decision
    id=int
  >
IN THIS ORDER:
| ( <medicate ... /> )+
</decision>

medicate

Documentation (element)

Units: List of elements

describes treatment decisions, a list of medicate descisions.

Attributes

id

id=int

Units: Number

Key of decision

medicate

→ scenario → caseManagements → caseManagement → decisions → decision → medicate

<medicate
    name=string
    qty=double
    time=int
  />

Attributes

name

name=string

Units: string

Name of drug compound

qty

qty=double

Units: Number

Quantity of drug compound

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

healthSystem

→ scenario → healthSystem

<healthSystem
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</healthSystem>

Documentation (element)

Units: List of elements

Description of health system

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

entoData

→ scenario → entoData

<entoData
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Documentation (type)

Units: List of elements

Data for entomodel

Attributes

name

name=string

Units: string

Name of entomology data

nonVector

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

vector

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
</vector>

anopheles

Documentation (element)

Parameters for the vector transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <eir ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Attributes

mosquito

mosquito=string

propInfected

propInfected=double

Units: Proportion Min: 0 Max: 1

Proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t).

propInfectious

propInfectious=double

Units: Proportion Min: 0 Max: 1

Proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t).

eir

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    b1=double
    a2=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Innoculations per person per day

Attributes

a0

a0=double

a1

a1=double

b1

b1=double

a2

a2=double

b2

b2=double

EIRRotateAngle

EIRRotateAngle=double

mosq

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqSeekingDeathRate=double
    mosqSeekingDuration=double
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

mosqRestDuration

mosqRestDuration=int

extrinsicIncubationPeriod

extrinsicIncubationPeriod=int

mosqSeekingDeathRate

mosqSeekingDeathRate=double

mosqSeekingDuration

mosqSeekingDuration=double

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

mosqProbOvipositing

mosqProbOvipositing=double

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

name

name=string

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

drugDescription

<drugDescription>
IN THIS ORDER:
|   <genome ... /> 
|   <drugs ... /> 
</drugDescription>

genome
drugs

Documentation (element)

Units: List of elements

Drug model parameters

genome

→ scenario → drugDescription → genome

<genome>
IN THIS ORDER:
|   <content ... /> 
|   <distribution ... /> 
</genome>

content

→ scenario → drugDescription → genome → content

<content>
IN THIS ORDER:
| ( <gene ... /> )+
</content>

gene

gene

→ scenario → drugDescription → genome → content → gene

<gene
    name=string
  >
IN THIS ORDER:
| ( <mutation ... /> )+
</gene>

mutation

Attributes

name

name=string

mutation

→ scenario → drugDescription → genome → content → gene → mutation

<mutation
    cost=double
    position=integer
  />

Attributes

cost

cost=double

position

position=integer

distribution

→ scenario → drugDescription → genome → distribution

<distribution>
IN THIS ORDER:
| ( <genomeInstance ... /> )+
</distribution>

genomeInstance

genomeInstance

→ scenario → drugDescription → genome → distribution → genomeInstance

<genomeInstance
    proportion=integer
  >
IN THIS ORDER:
| ( <allele ... /> )+
</genomeInstance>

allele

Attributes

proportion

proportion=integer

allele

→ scenario → drugDescription → genome → distribution → genomeInstance → allele

<allele
    mutations=integer
    name=string
  />

Attributes

mutations

mutations=integer

name

name=string

drugs

→ scenario → drugDescription → drugs

<drugs
  [ synergy=string ]
  >
IN THIS ORDER:
|   <compound ... /> 
</drugs>

compound

Attributes

synergy

synergy=string

compound

→ scenario → drugDescription → drugs → compound

<compound
    acronym=string
    name=string
  >
IN THIS ORDER:
|   <pk ... /> 
|   <pd ... /> 
</compound>

Attributes

acronym

acronym=string

name

name=string

pk

→ scenario → drugDescription → drugs → compound → pk

<pk>
</pk>

ageGroup

ageGroup

→ scenario → drugDescription → drugs → compound → pk → ageGroup

<ageGroup
    F=integer
    Vd=double
    t12=integer
  [ minAge=double ]
  />

Attributes

F

F=integer

Bioavailability (unsure of the units we will be using)

Vd

Vd=double

Volume of Distribution (l/kg)

t12

t12=integer

Units: Number

Half-life (days)

minAge

minAge=double

pd

→ scenario → drugDescription → drugs → compound → pd

<pd>
IN THIS ORDER:
| ( <genomeRule ... /> )+
</pd>

genomeRule

genomeRule

→ scenario → drugDescription → drugs → compound → pd → genomeRule

<genomeRule>
</genomeRule>

matchMutation

→ scenario → drugDescription → drugs → compound → pd → genomeRule → matchMutation

<matchMutation
    present=boolean
    gene=string
    pos=integer
  />

Attributes

present

present=boolean

gene

gene=string

pos

pos=integer

ageGroup

→ scenario → drugDescription → drugs → compound → pd → genomeRule → ageGroup

<ageGroup
    c50=integer
    k1=double
    n=integer
  [ minAge=double ]
  />

Attributes

c50

c50=integer

Half maximal effect concentration (mg/l)

k1

k1=double

Units: Proportion Min: 0 Max: 1

Maximal parasite killing rate (per day)

n

n=integer

Slope of the concentration effect curve (no units)

minAge

minAge=double

parameters

→ scenario → parameters

<parameters
    interval=int
    iseed=int
    delta=double
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Units: List of elements

Parameters for mathematical model

Documentation (type)

Units: List of elements

Parameter vector

Attributes

interval

interval=int

Units: Days

Simulation step

iseed

iseed=int

Units: Number

Seed for RNG

delta

delta=double

Units: ? Redundant

this no longer seems to be used

latentp

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

name

name=string

Units: string

Name of parameter

number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

value

value=double

Units: Number Min: 0

Parameter value

include

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 10 documentation

Generated from: scenario_10.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    maximumAgeYrs=double
    name=string
    popSize=int
    simulationDuration=int
    modelVersion=int
    wuID=int
    assimMode=("0" or "1")
    mode=("2" or "3" or "4")
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_10.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
| [ <caseManagements ... /> ]
| [ <healthSystem ... /> ]
|   <entoData ... /> 
| [ <drugDescription ... /> ]
|   <parameters ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

schemaVersion

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

analysisNo

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

maximumAgeYrs

maximumAgeYrs=double

Units: Number Min: 0 Max: 100

Maximum age of simulated humans

name

name=string

Units: string

Name of intervention

popSize

popSize=int

Units: Count Min: 1 Max: 100000

Population size

simulationDuration

simulationDuration=int

Units: Time steps Min: 1 Max: 36500

Duration of main simulation

modelVersion

modelVersion=int

Units: Code Min: 0 Max: 100000000

Model Version

wuID

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

assimMode

assimMode=("0" or "1")

Units: Code

Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)

mode

mode=("2" or "3" or "4")

Units: Code

Transmission simulation mode

demography

→ scenario → demography

<demography
    name=string
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Documentation (type)

Units: List of elements

Description of demography

Attributes

name

name=string

Units: string

Name of demography data

growthRate

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population.

ageGroup

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

poppercent

poppercent=double

upperbound

upperbound=double

monitoring

→ scenario → monitoring

<monitoring
    name=string
  >
IN THIS ORDER:
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Documentation (type)

Units: List of elements

Description of surveys

Attributes

name

name=string

Units: string

Name of monitoring data

surveys

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
    summaryOption=int
  >
IN THIS ORDER:
|   <surveyTime ... /> 
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

detectionLimit

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

summaryOption

summaryOption=int

Units: Code

Requested output variables

surveyTime

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time

ageGroup

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upperbound

upperbound=double

interventions

<interventions
    name=string
  >
IN THIS ORDER:
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| ( <anopheles ... /> )*
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

List of interventions

Documentation (type)

Units: List of elements

List of interventions

Attributes

name

name=string

Units: string

Name of age specific intervention

vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

vaccineType

vaccineType=int

Units: Code

Type of vaccine

halfLifeYrs

→ scenario → interventions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

value

value=double

TODO

efficacyB

→ scenario → interventions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

value

value=double

TODO

initialEfficacy

→ scenario → interventions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

value

value=double

TODO

iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

name

name=string

Units: string

Name of age specific intervention

freq

freq=double

ACR

ACR=double

proph

proph=int

tolPeriod

tolPeriod=int

atten

atten=double

anopheles

→ scenario → interventions → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <VADescription ... /> ]
</anopheles>

Attributes

mosquito

mosquito=string

ITNDescription

→ scenario → interventions → anopheles → ITNDescription

<ITNDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</ITNDescription>

Attributes

name

name=string

Units: string

Name of Insecticide Treated Net intervention

deterrency

→ scenario → interventions → anopheles → ITNDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability (before decay).

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

preprandialKillingEffect

→ scenario → interventions → anopheles → ITNDescription → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

postprandialKillingEffect

→ scenario → interventions → anopheles → ITNDescription → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

IRSDescription

→ scenario → interventions → anopheles → IRSDescription

<IRSDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <killingEffect ... /> 
</IRSDescription>

Attributes

name

name=string

Units: string

Name of Indoor Residual Spraying intervention

deterrency

→ scenario → interventions → anopheles → IRSDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

killingEffect

→ scenario → interventions → anopheles → IRSDescription → killingEffect

<killingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

VADescription

→ scenario → interventions → anopheles → VADescription

<VADescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</VADescription>

deterrency

Attributes

name

name=string

Units: string

Name of mosquito deterrency intervention

deterrency

→ scenario → interventions → anopheles → VADescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

continuous

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
</continuous>

vaccine

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

timed

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <VectorAvailability ... /> ]
| [ <ipti ... /> ]
| [ <larviciding ... /> ]
</intervention>

Attributes

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

drugRegimen

→ scenario → healthSystem → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

firstLine

firstLine=string

Units: Drug code

Code for first line drug

secondLine

secondLine=string

Units: Drug code

Code for second line drug

inpatient

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

initialACR

→ scenario → healthSystem → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

CQ

→ scenario → healthSystem → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

value

value=double

TODO

SP

→ scenario → healthSystem → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

value

value=double

TODO

AQ

→ scenario → healthSystem → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

value

value=double

TODO

SPAQ

→ scenario → healthSystem → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

value

value=double

TODO

ACT

→ scenario → healthSystem → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

value

value=double

TODO

QN

→ scenario → healthSystem → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

value

value=double

TODO

selfTreatment

→ scenario → healthSystem → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

value

value=double

TODO

compliance

→ scenario → healthSystem → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

pSeekOfficialCareUncomplicated1

→ scenario → healthSystem → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSelfTreatUncomplicated

→ scenario → healthSystem → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

value

value=double

TODO

pSeekOfficialCareUncomplicated2

→ scenario → healthSystem → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSeekOfficialCareSevere

→ scenario → healthSystem → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease seeks official care

Attributes

value

value=double

TODO

pSequelaeInpatient

<pSequelaeInpatient>
IN THIS ORDER:
| ( <item ... /> )+
</pSequelaeInpatient>

item

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients

item

→ scenario → healthSystem → pSequelaeInpatient → item

<item
    value=double
    maxAgeYrs=double
  />

Attributes

value

value=double

TODO

maxAgeYrs

maxAgeYrs=double

Units: Years Min: 0 Max: 100

Upper bound of age group

CFR

→ scenario → healthSystem → CFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

group

→ scenario → healthSystem → CFR → group

<group
    cfr=double
    lowerbound=double
  />

Attributes

cfr

cfr=double

Units: Proportion Min: 0 Max: 1

Case fatality rate

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

changeEIR

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

EIRDaily

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Number Min: 1

Value of daily EIR

Attributes

origin

origin=string

MDA

→ scenario → interventions → timed → intervention → MDA

<MDA
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

vaccinate

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → timed → intervention → ITN

<ITN
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IRS

→ scenario → interventions → timed → intervention → IRS

<IRS
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of IRS deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

VectorAvailability

→ scenario → interventions → timed → intervention → VectorAvailability

<VectorAvailability
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of a mosquito detterent deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → timed → intervention → ipti

<ipti
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

larviciding

→ scenario → interventions → timed → intervention → larviciding

<larviciding>
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

anopheles

Documentation (element)

Simple larviciding intervention description.

anopheles

→ scenario → interventions → timed → intervention → larviciding → anopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

mosquito

mosquito=string

effectiveness

effectiveness=double

Units: none Min: 0 Max: 1

Proportion to reduce emergence rates by.

duration

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

caseManagements

<caseManagements
    name=string
    reportingPeriodMemory=int
  >
IN THIS ORDER:
| ( <caseManagement ... /> )+
</caseManagements>

caseManagement

Documentation (element)

Units: List of elements

List of case managment interventions

Documentation (type)

Units: List of elements

List of age-specific case managment descriptions

Attributes

name

name=string

Units: string

Name of age specific intervention

reportingPeriodMemory

reportingPeriodMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

caseManagement

<caseManagement
    maxAgeYrs=decimal
  >
IN THIS ORDER:
|   <uc1 ... /> 
|   <uc2 ... /> 
|   <sev ... /> 
|   <nmfP ... /> 
|   <nmfNP ... /> 
|   <decisions ... /> 
</caseManagement>

Documentation (element)

Units: List of elements

Age-specific case management description, describes entry-points and decisions, with entry-point-specific decision probabilities

Attributes

maxAgeYrs

maxAgeYrs=decimal

Units: Years Min: 0 Max: 100

Upper bound of age group

uc1

→ scenario → caseManagements → caseManagement → uc1

<uc1>
IN THIS ORDER:
| ( <endPoint ... /> )+
</uc1>

endPoint

endPoint

→ scenario → caseManagements → caseManagement → uc1 → endPoint

<endPoint
    decision=int
    p=double
  />

Attributes

decision

decision=int

Foreign key reference to outcome node

p

p=double

Units: Proportion Min: 0 Max: 1

Probability of outcome

uc2

→ scenario → caseManagements → caseManagement → uc2

<uc2>
IN THIS ORDER:
| ( <endPoint ... /> )+
</uc2>

endPoint

sev

→ scenario → caseManagements → caseManagement → sev

<sev>
IN THIS ORDER:
| ( <endPoint ... /> )+
</sev>

endPoint

nmfP

→ scenario → caseManagements → caseManagement → nmfP

<nmfP>
IN THIS ORDER:
| ( <endPoint ... /> )+
</nmfP>

endPoint

nmfNP

→ scenario → caseManagements → caseManagement → nmfNP

<nmfNP>
IN THIS ORDER:
| ( <endPoint ... /> )+
</nmfNP>

endPoint

decisions

→ scenario → caseManagements → caseManagement → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )+
</decisions>

decision

decision

→ scenario → caseManagements → caseManagement → decisions → decision

<decision
    id=int
  >
IN THIS ORDER:
| ( <medicate ... /> )+
</decision>

medicate

Documentation (element)

Units: List of elements

describes treatment decisions, a list of medicate descisions.

Attributes

id

id=int

Units: Number

Key of decision

medicate

→ scenario → caseManagements → caseManagement → decisions → decision → medicate

<medicate
    name=string
    qty=double
    time=int
  />

Attributes

name

name=string

Units: string

Name of drug compound

qty

qty=double

Units: Number

Quantity of drug compound

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

healthSystem

→ scenario → healthSystem

<healthSystem
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</healthSystem>

Documentation (element)

Units: List of elements

Description of health system

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

entoData

→ scenario → entoData

<entoData
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Documentation (type)

Units: List of elements

Data for entomodel

Attributes

name

name=string

Units: string

Name of entomology data

nonVector

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

vector

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
</vector>

anopheles

Documentation (element)

Parameters for the vector transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <eir ... /> ]
| [ <emergence ... /> ]
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Attributes

mosquito

mosquito=string

eir

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    a2=double
    b1=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Description of entomological inoculation rate. Usually one of the eir and emergence elements are provided. If both are given, the emergence rate is validated against the eir. Providing an eir allows emergence rate calculations when emergence-rate data is not provided or not valid.

Attributes

a0

a0=double

a1

a1=double

a2

a2=double

b1

b1=double

b2

b2=double

EIRRotateAngle

EIRRotateAngle=double

emergence

→ scenario → entoData → vector → anopheles → emergence

<emergence>
IN THIS ORDER:
|   <emergenceRate ... /> 
|   <kappa ... /> 
|   <N_v ... /> 
|   <O_v ... /> 
|   <S_v ... /> 
</emergence>

Documentation (element)

Data to drive simulation from a pre-calculated emergence rate. Usually one of the eir and emergence elements are provided. If just emergence data is given the simulation is run from this; if both are given, the emergence rate is validated against the eir.

emergenceRate

→ scenario → entoData → vector → anopheles → emergence → emergenceRate

<emergenceRate>
IN THIS ORDER:
| ( <item ... /> )+
</emergenceRate>

item

Documentation (element)

Units: Mosquitoes per human Min: 0 Max: inf

Mosquitoes emerging per day of the year, per human.

item

→ scenario → entoData → vector → anopheles → emergence → emergenceRate → item

<item>
    double
</item>

kappa

→ scenario → entoData → vector → anopheles → emergence → kappa

<kappa>
IN THIS ORDER:
| ( <item ... /> )+
</kappa>

item

Documentation (element)

Units: Min: 0 Max: 1

Human infectivity (probability of infection of a mosquito biting a human) over last mosqRestDuration+extrinsicIncubationPeriod days.

N_v

→ scenario → entoData → vector → anopheles → emergence → N_v

<N_v>
IN THIS ORDER:
| ( <item ... /> )+
</N_v>

item

Documentation (element)

Units: individuals Min: 0 Max: inf

Total population of mosquitoes over the last mosqRestDuration+extrinsicIncubationPeriod days, per human.

O_v

→ scenario → entoData → vector → anopheles → emergence → O_v

<O_v>
IN THIS ORDER:
| ( <item ... /> )+
</O_v>

item

Documentation (element)

Units: individuals Min: 0 Max: inf

Population of infected mosquitoes over the last mosqRestDuration+extrinsicIncubationPeriod days, per human.

S_v

→ scenario → entoData → vector → anopheles → emergence → S_v

<S_v>
IN THIS ORDER:
| ( <item ... /> )+
</S_v>

item

Documentation (element)

Units: individuals Min: 0 Max: inf

Population of infectious mosquitoes over the last mosqRestDuration+extrinsicIncubationPeriod days, per human.

mosq

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqSeekingDeathRate=double
    mosqSeekingDuration=double
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

mosqRestDuration

mosqRestDuration=int

extrinsicIncubationPeriod

extrinsicIncubationPeriod=int

mosqSeekingDeathRate

mosqSeekingDeathRate=double

mosqSeekingDuration

mosqSeekingDuration=double

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

mosqProbOvipositing

mosqProbOvipositing=double

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

name

name=string

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

drugDescription

<drugDescription>
IN THIS ORDER:
|   <genome ... /> 
|   <drugs ... /> 
</drugDescription>

genome
drugs

Documentation (element)

Units: List of elements

Drug model parameters

genome

→ scenario → drugDescription → genome

<genome>
IN THIS ORDER:
|   <content ... /> 
|   <distribution ... /> 
</genome>

content

→ scenario → drugDescription → genome → content

<content>
IN THIS ORDER:
| ( <gene ... /> )+
</content>

gene

gene

→ scenario → drugDescription → genome → content → gene

<gene
    name=string
  >
IN THIS ORDER:
| ( <mutation ... /> )+
</gene>

mutation

Attributes

name

name=string

mutation

→ scenario → drugDescription → genome → content → gene → mutation

<mutation
    cost=double
    position=integer
  />

Attributes

cost

cost=double

position

position=integer

distribution

→ scenario → drugDescription → genome → distribution

<distribution>
IN THIS ORDER:
| ( <genomeInstance ... /> )+
</distribution>

genomeInstance

genomeInstance

→ scenario → drugDescription → genome → distribution → genomeInstance

<genomeInstance
    proportion=integer
  >
IN THIS ORDER:
| ( <allele ... /> )+
</genomeInstance>

allele

Attributes

proportion

proportion=integer

allele

→ scenario → drugDescription → genome → distribution → genomeInstance → allele

<allele
    mutations=integer
    name=string
  />

Attributes

mutations

mutations=integer

name

name=string

drugs

→ scenario → drugDescription → drugs

<drugs
  [ synergy=string ]
  >
IN THIS ORDER:
|   <compound ... /> 
</drugs>

compound

Attributes

synergy

synergy=string

compound

→ scenario → drugDescription → drugs → compound

<compound
    acronym=string
    name=string
  >
IN THIS ORDER:
|   <pk ... /> 
|   <pd ... /> 
</compound>

Attributes

acronym

acronym=string

name

name=string

pk

→ scenario → drugDescription → drugs → compound → pk

<pk>
</pk>

ageGroup

ageGroup

→ scenario → drugDescription → drugs → compound → pk → ageGroup

<ageGroup
    F=integer
    Vd=double
    t12=integer
  [ minAge=double ]
  />

Attributes

F

F=integer

Bioavailability (unsure of the units we will be using)

Vd

Vd=double

Volume of Distribution (l/kg)

t12

t12=integer

Units: Number

Half-life (days)

minAge

minAge=double

pd

→ scenario → drugDescription → drugs → compound → pd

<pd>
IN THIS ORDER:
| ( <genomeRule ... /> )+
</pd>

genomeRule

genomeRule

→ scenario → drugDescription → drugs → compound → pd → genomeRule

<genomeRule>
</genomeRule>

matchMutation

→ scenario → drugDescription → drugs → compound → pd → genomeRule → matchMutation

<matchMutation
    present=boolean
    gene=string
    pos=integer
  />

Attributes

present

present=boolean

gene

gene=string

pos

pos=integer

ageGroup

→ scenario → drugDescription → drugs → compound → pd → genomeRule → ageGroup

<ageGroup
    c50=integer
    k1=double
    n=integer
  [ minAge=double ]
  />

Attributes

c50

c50=integer

Half maximal effect concentration (mg/l)

k1

k1=double

Units: Proportion Min: 0 Max: 1

Maximal parasite killing rate (per day)

n

n=integer

Slope of the concentration effect curve (no units)

minAge

minAge=double

parameters

→ scenario → parameters

<parameters
    interval=int
    iseed=int
    delta=double
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters for mathematical model

Documentation (type)

Units: List of elements

Parameter vector

Attributes

interval

interval=int

Units: Days

Simulation step

iseed

iseed=int

Units: Number

Seed for RNG

delta

delta=double

Units: ? Redundant

this no longer seems to be used

latentp

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

name

name=string

Units: string

Name of parameter

number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

value

value=double

Units: Number Min: 0

Parameter value

include

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 9 documentation

Generated from: scenario_9.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    maximumAgeYrs=double
    name=string
    popSize=int
    simulationDuration=int
    modelVersion=int
    wuID=int
    assimMode=("0" or "1")
    mode=("2" or "3" or "4")
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_9.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
| [ <caseManagements ... /> ]
| [ <healthSystem ... /> ]
|   <entoData ... /> 
|   <parameters ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

schemaVersion

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

analysisNo

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

maximumAgeYrs

maximumAgeYrs=double

Units: Number Min: 0 Max: 100

Maximum age of simulated humans

name

name=string

Units: string

Name of intervention

popSize

popSize=int

Units: Count Min: 1 Max: 100000

Population size

simulationDuration

simulationDuration=int

Units: Time steps Min: 1 Max: 36500

Duration of main simulation

modelVersion

modelVersion=int

Units: Code Min: 0 Max: 100000000

Model Version

wuID

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

assimMode

assimMode=("0" or "1")

Units: Code

Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)

mode

mode=("2" or "3" or "4")

Units: Code

Transmission simulation mode

demography

→ scenario → demography

<demography
    name=string
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Documentation (type)

Units: List of elements

Description of demography

Attributes

name

name=string

Units: string

Name of demography data

growthRate

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population.

ageGroup

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

poppercent

poppercent=double

upperbound

upperbound=double

monitoring

→ scenario → monitoring

<monitoring
    name=string
  >
IN THIS ORDER:
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Documentation (type)

Units: List of elements

Description of surveys

Attributes

name

name=string

Units: string

Name of monitoring data

surveys

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
    summaryOption=int
  >
IN THIS ORDER:
|   <surveyTime ... /> 
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

detectionLimit

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

summaryOption

summaryOption=int

Units: Code

Requested output variables

surveyTime

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time

ageGroup

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upperbound

upperbound=double

interventions

<interventions
    name=string
  >
IN THIS ORDER:
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| ( <anopheles ... /> )*
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

List of interventions

Documentation (type)

Units: List of elements

List of interventions

Attributes

name

name=string

Units: string

Name of age specific intervention

vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

vaccineType

vaccineType=int

Units: Code

Type of vaccine

halfLifeYrs

→ scenario → interventions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

value

value=double

TODO

efficacyB

→ scenario → interventions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

value

value=double

TODO

initialEfficacy

→ scenario → interventions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

value

value=double

TODO

iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=double
  />

Attributes

name

name=string

Units: string

Name of age specific intervention

freq

freq=double

ACR

ACR=double

proph

proph=int

tolPeriod

tolPeriod=int

atten

atten=double

anopheles

→ scenario → interventions → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <VADescription ... /> ]
</anopheles>

Attributes

mosquito

mosquito=string

ITNDescription

→ scenario → interventions → anopheles → ITNDescription

<ITNDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</ITNDescription>

Attributes

name

name=string

Units: string

Name of Insecticide Treated Net intervention

deterrency

→ scenario → interventions → anopheles → ITNDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability (before decay).

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

preprandialKillingEffect

→ scenario → interventions → anopheles → ITNDescription → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

postprandialKillingEffect

→ scenario → interventions → anopheles → ITNDescription → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

IRSDescription

→ scenario → interventions → anopheles → IRSDescription

<IRSDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <killingEffect ... /> 
</IRSDescription>

Attributes

name

name=string

Units: string

Name of Indoor Residual Spraying intervention

deterrency

→ scenario → interventions → anopheles → IRSDescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

killingEffect

→ scenario → interventions → anopheles → IRSDescription → killingEffect

<killingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

VADescription

→ scenario → interventions → anopheles → VADescription

<VADescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</VADescription>

deterrency

Attributes

name

name=string

Units: string

Name of mosquito deterrency intervention

deterrency

→ scenario → interventions → anopheles → VADescription → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

continuous

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
</continuous>

vaccine

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

timed

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <VectorAvailability ... /> ]
| [ <ipti ... /> ]
| [ <larviciding ... /> ]
</intervention>

Attributes

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

drugRegimen

→ scenario → healthSystem → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

firstLine

firstLine=string

Units: Drug code

Code for first line drug

secondLine

secondLine=string

Units: Drug code

Code for second line drug

inpatient

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

initialACR

→ scenario → healthSystem → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

CQ

→ scenario → healthSystem → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

value

value=double

TODO

SP

→ scenario → healthSystem → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

value

value=double

TODO

AQ

→ scenario → healthSystem → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

value

value=double

TODO

SPAQ

→ scenario → healthSystem → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

value

value=double

TODO

ACT

→ scenario → healthSystem → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

value

value=double

TODO

QN

→ scenario → healthSystem → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

value

value=double

TODO

selfTreatment

→ scenario → healthSystem → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

value

value=double

TODO

compliance

→ scenario → healthSystem → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

pSeekOfficialCareUncomplicated1

→ scenario → healthSystem → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSelfTreatUncomplicated

→ scenario → healthSystem → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

value

value=double

TODO

pSeekOfficialCareUncomplicated2

→ scenario → healthSystem → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSeekOfficialCareSevere

→ scenario → healthSystem → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease seeks official care

Attributes

value

value=double

TODO

pSequelaeInpatient

<pSequelaeInpatient>
IN THIS ORDER:
| ( <item ... /> )+
</pSequelaeInpatient>

item

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients

item

→ scenario → healthSystem → pSequelaeInpatient → item

<item
    value=double
    maxAgeYrs=double
  />

Attributes

value

value=double

TODO

maxAgeYrs

maxAgeYrs=double

Units: Years Min: 0 Max: 100

Upper bound of age group

CFR

→ scenario → healthSystem → CFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

group

→ scenario → healthSystem → CFR → group

<group
    cfr=double
    lowerbound=double
  />

Attributes

cfr

cfr=double

Units: Proportion Min: 0 Max: 1

Case fatality rate

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

changeEIR

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

EIRDaily

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Number Min: 1

Value of daily EIR

Attributes

origin

origin=string

MDA

→ scenario → interventions → timed → intervention → MDA

<MDA
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

vaccinate

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → timed → intervention → ITN

<ITN
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IRS

→ scenario → interventions → timed → intervention → IRS

<IRS
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of IRS deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

VectorAvailability

→ scenario → interventions → timed → intervention → VectorAvailability

<VectorAvailability
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of a mosquito detterent deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → timed → intervention → ipti

<ipti
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

larviciding

→ scenario → interventions → timed → intervention → larviciding

<larviciding>
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

anopheles

Documentation (element)

Simple larviciding intervention description.

anopheles

→ scenario → interventions → timed → intervention → larviciding → anopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

mosquito

mosquito=string

effectiveness

effectiveness=double

Units: none Min: 0 Max: 1

Proportion to reduce emergence rates by.

duration

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

caseManagements

<caseManagements
    name=string
    reportingPeriodMemory=int
  >
IN THIS ORDER:
| ( <caseManagement ... /> )+
</caseManagements>

caseManagement

Documentation (element)

Units: List of elements

List of case managment interventions

Documentation (type)

Units: List of elements

List of age-specific case managment descriptions

Attributes

name

name=string

Units: string

Name of age specific intervention

reportingPeriodMemory

reportingPeriodMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

caseManagement

<caseManagement
    maxAgeYrs=decimal
  >
IN THIS ORDER:
|   <uc1 ... /> 
|   <uc2 ... /> 
|   <sev ... /> 
|   <nmfP ... /> 
|   <nmfNP ... /> 
|   <decisions ... /> 
</caseManagement>

Documentation (element)

Units: List of elements

Age-specific case management description, describes entry-points and decisions, with entry-point-specific decision probabilities

Attributes

maxAgeYrs

maxAgeYrs=decimal

Units: Years Min: 0 Max: 100

Upper bound of age group

uc1

→ scenario → caseManagements → caseManagement → uc1

<uc1>
IN THIS ORDER:
| ( <endPoint ... /> )+
</uc1>

endPoint

endPoint

→ scenario → caseManagements → caseManagement → uc1 → endPoint

<endPoint
    decision=int
    p=double
  />

Attributes

decision

decision=int

Foreign key reference to outcome node

p

p=double

Units: Proportion Min: 0 Max: 1

Probability of outcome

uc2

→ scenario → caseManagements → caseManagement → uc2

<uc2>
IN THIS ORDER:
| ( <endPoint ... /> )+
</uc2>

endPoint

sev

→ scenario → caseManagements → caseManagement → sev

<sev>
IN THIS ORDER:
| ( <endPoint ... /> )+
</sev>

endPoint

nmfP

→ scenario → caseManagements → caseManagement → nmfP

<nmfP>
IN THIS ORDER:
| ( <endPoint ... /> )+
</nmfP>

endPoint

nmfNP

→ scenario → caseManagements → caseManagement → nmfNP

<nmfNP>
IN THIS ORDER:
| ( <endPoint ... /> )+
</nmfNP>

endPoint

decisions

→ scenario → caseManagements → caseManagement → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )+
</decisions>

decision

decision

→ scenario → caseManagements → caseManagement → decisions → decision

<decision
    id=int
  >
IN THIS ORDER:
| ( <medicate ... /> )+
</decision>

medicate

Documentation (element)

Units: List of elements

describes treatment decisions, a list of medicate descisions.

Attributes

id

id=int

Units: Number

Key of decision

medicate

→ scenario → caseManagements → caseManagement → decisions → decision → medicate

<medicate
    name=string
    qty=double
    time=int
  />

Attributes

name

name=string

Units: string

Name of drug compound

qty

qty=double

Units: Number

Quantity of drug compound

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

healthSystem

→ scenario → healthSystem

<healthSystem
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</healthSystem>

Documentation (element)

Units: List of elements

Description of health system

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

entoData

→ scenario → entoData

<entoData
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Documentation (type)

Units: List of elements

Data for entomodel

Attributes

name

name=string

Units: string

Name of entomology data

nonVector

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

vector

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
</vector>

anopheles

Documentation (element)

Parameters for the vector transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <eir ... /> ]
| [ <emergence ... /> ]
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Attributes

mosquito

mosquito=string

eir

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    a2=double
    b1=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Attributes

a0

a0=double

a1

a1=double

a2

a2=double

b1

b1=double

b2

b2=double

EIRRotateAngle

EIRRotateAngle=double

emergence

→ scenario → entoData → vector → anopheles → emergence

<emergence>
IN THIS ORDER:
|   <emergenceRate ... /> 
|   <kappa ... /> 
|   <N_v ... /> 
|   <O_v ... /> 
|   <S_v ... /> 
</emergence>

Documentation (element)

emergenceRate

→ scenario → entoData → vector → anopheles → emergence → emergenceRate

<emergenceRate>
IN THIS ORDER:
| ( <item ... /> )+
</emergenceRate>

item

Documentation (element)

Units: Mosquitoes per human Min: 0 Max: inf

Mosquitoes emerging per day of the year, per human.

item

→ scenario → entoData → vector → anopheles → emergence → emergenceRate → item

<item>
    double
</item>

kappa

→ scenario → entoData → vector → anopheles → emergence → kappa

<kappa>
IN THIS ORDER:
| ( <item ... /> )+
</kappa>

item

Documentation (element)

Units: Min: 0 Max: 1

Human infectivity (probability of infection of a mosquito biting a human) over last mosqRestDuration+extrinsicIncubationPeriod days.

N_v

→ scenario → entoData → vector → anopheles → emergence → N_v

<N_v>
IN THIS ORDER:
| ( <item ... /> )+
</N_v>

item

Documentation (element)

Units: individuals Min: 0 Max: inf

Total population of mosquitoes over the last mosqRestDuration+extrinsicIncubationPeriod days, per human.

O_v

→ scenario → entoData → vector → anopheles → emergence → O_v

<O_v>
IN THIS ORDER:
| ( <item ... /> )+
</O_v>

item

Documentation (element)

Units: individuals Min: 0 Max: inf

Population of infected mosquitoes over the last mosqRestDuration+extrinsicIncubationPeriod days, per human.

S_v

→ scenario → entoData → vector → anopheles → emergence → S_v

<S_v>
IN THIS ORDER:
| ( <item ... /> )+
</S_v>

item

Documentation (element)

Units: individuals Min: 0 Max: inf

Population of infectious mosquitoes over the last mosqRestDuration+extrinsicIncubationPeriod days, per human.

mosq

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqSeekingDeathRate=double
    mosqSeekingDuration=double
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

mosqRestDuration

mosqRestDuration=int

extrinsicIncubationPeriod

extrinsicIncubationPeriod=int

mosqSeekingDeathRate

mosqSeekingDeathRate=double

mosqSeekingDuration

mosqSeekingDuration=double

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

mosqProbOvipositing

mosqProbOvipositing=double

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    name=string
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

name

name=string

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

parameters

→ scenario → parameters

<parameters
    interval=int
    iseed=int
    delta=double
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters for mathematical model

Documentation (type)

Units: List of elements

Parameter vector

Attributes

interval

interval=int

Units: Days

Simulation step

iseed

iseed=int

Units: Number

Seed for RNG

delta

delta=double

Units: ? Redundant

this no longer seems to be used

latentp

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

name

name=string

Units: string

Name of parameter

number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

value

value=double

Units: Number Min: 0

Parameter value

include

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 8 documentation

Generated from: scenario_8.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    maximumAgeYrs=double
    name=string
    popSize=int
    simulationDuration=int
    modelVersion=int
    wuID=int
    assimMode=("0" or "1")
    mode=("2" or "3" or "4")
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_8.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
| [ <caseManagements ... /> ]
| [ <healthSystem ... /> ]
|   <entoData ... /> 
|   <parameters ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

schemaVersion

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

analysisNo

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

maximumAgeYrs

maximumAgeYrs=double

Units: Number Min: 0 Max: 100

Maximum age of simulated humans

name

name=string

Units: string

Name of intervention

popSize

popSize=int

Units: Count Min: 1 Max: 100000

Population size

simulationDuration

simulationDuration=int

Units: Time steps Min: 1 Max: 36500

Duration of main simulation

modelVersion

modelVersion=int

Units: Code Min: 0 Max: 100000000

Model Version

wuID

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

assimMode

assimMode=("0" or "1")

Units: Code

Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)

mode

mode=("2" or "3" or "4")

Units: Code

Transmission simulation mode

demography

→ scenario → demography

<demography
    name=string
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Documentation (type)

Units: List of elements

Description of demography

Attributes

name

name=string

Units: string

Name of demography data

growthRate

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population.

ageGroup

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

poppercent

poppercent=double

upperbound

upperbound=double

monitoring

→ scenario → monitoring

<monitoring
    name=string
  >
IN THIS ORDER:
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Documentation (type)

Units: List of elements

Description of surveys

Attributes

name

name=string

Units: string

Name of monitoring data

surveys

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
    summaryOption=int
  >
IN THIS ORDER:
|   <surveyTime ... /> 
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

detectionLimit

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

summaryOption

summaryOption=int

Units: Code

Requested output variables

surveyTime

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time

ageGroup

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upperbound

upperbound=double

interventions

<interventions
    name=string
  >
IN THIS ORDER:
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

List of interventions

Documentation (type)

Units: List of elements

List of interventions

Attributes

name

name=string

Units: string

Name of age specific intervention

vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

vaccineType

vaccineType=int

Units: Code

Type of vaccine

halfLifeYrs

→ scenario → interventions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

value

value=double

TODO

efficacyB

→ scenario → interventions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

value

value=double

TODO

initialEfficacy

→ scenario → interventions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

value

value=double

TODO

iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=int
  />

Attributes

name

name=string

Units: string

Name of age specific intervention

freq

freq=double

ACR

ACR=double

proph

proph=int

tolPeriod

tolPeriod=int

atten

atten=int

ITNDescription

→ scenario → interventions → ITNDescription

<ITNDescription
    name=string
  >
IN THIS ORDER:
| ( <anopheles ... /> )+
</ITNDescription>

anopheles

Attributes

name

name=string

Units: string

Name of Insecticide Treated Net intervention

anopheles

→ scenario → interventions → ITNDescription → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anopheles>

Attributes

mosquito

mosquito=string

deterrency

→ scenario → interventions → ITNDescription → anopheles → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability (before decay).

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

preprandialKillingEffect

→ scenario → interventions → ITNDescription → anopheles → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

postprandialKillingEffect

→ scenario → interventions → ITNDescription → anopheles → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

IRSDescription

→ scenario → interventions → IRSDescription

<IRSDescription
    name=string
  >
IN THIS ORDER:
| ( <anopheles ... /> )+
</IRSDescription>

anopheles

Attributes

name

name=string

Units: string

Name of Indoor Residual Spraying intervention

anopheles

→ scenario → interventions → IRSDescription → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <killingEffect ... /> 
</anopheles>

Attributes

mosquito

mosquito=string

deterrency

→ scenario → interventions → IRSDescription → anopheles → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

killingEffect

→ scenario → interventions → IRSDescription → anopheles → killingEffect

<killingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

continuous

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
</continuous>

vaccine

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

timed

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <ipti ... /> ]
| [ <larviciding ... /> ]
</intervention>

Attributes

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

drugRegimen

→ scenario → healthSystem → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

firstLine

firstLine=string

Units: Drug code

Code for first line drug

secondLine

secondLine=string

Units: Drug code

Code for second line drug

inpatient

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

initialACR

→ scenario → healthSystem → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

CQ

→ scenario → healthSystem → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

value

value=double

TODO

SP

→ scenario → healthSystem → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

value

value=double

TODO

AQ

→ scenario → healthSystem → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

value

value=double

TODO

SPAQ

→ scenario → healthSystem → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

value

value=double

TODO

ACT

→ scenario → healthSystem → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

value

value=double

TODO

QN

→ scenario → healthSystem → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

value

value=double

TODO

selfTreatment

→ scenario → healthSystem → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

value

value=double

TODO

compliance

→ scenario → healthSystem → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

pSeekOfficialCareUncomplicated1

→ scenario → healthSystem → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSelfTreatUncomplicated

→ scenario → healthSystem → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

value

value=double

TODO

pSeekOfficialCareUncomplicated2

→ scenario → healthSystem → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSeekOfficialCareSevere

→ scenario → healthSystem → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease seeks official care

Attributes

value

value=double

TODO

pSequelaeInpatient

<pSequelaeInpatient>
IN THIS ORDER:
| ( <item ... /> )+
</pSequelaeInpatient>

item

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients

item

→ scenario → healthSystem → pSequelaeInpatient → item

<item
    value=double
    maxAgeYrs=double
  />

Attributes

value

value=double

TODO

maxAgeYrs

maxAgeYrs=double

Units: Years Min: 0 Max: 100

Upper bound of age group

CFR

→ scenario → healthSystem → CFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

group

→ scenario → healthSystem → CFR → group

<group
    cfr=double
    lowerbound=double
  />

Attributes

cfr

cfr=double

Units: Proportion Min: 0 Max: 1

Case fatality rate

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

changeEIR

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

EIRDaily

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Number Min: 1

Value of daily EIR

Attributes

origin

origin=string

MDA

→ scenario → interventions → timed → intervention → MDA

<MDA
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

vaccinate

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → timed → intervention → ITN

<ITN
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IRS

→ scenario → interventions → timed → intervention → IRS

<IRS
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of IRS deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → timed → intervention → ipti

<ipti
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

larviciding

→ scenario → interventions → timed → intervention → larviciding

<larviciding>
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

anopheles

Documentation (element)

Simple larviciding intervention description.

anopheles

→ scenario → interventions → timed → intervention → larviciding → anopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

mosquito

mosquito=string

effectiveness

effectiveness=double

Units: none Min: 0 Max: 1

Proportion to reduce emergence rates by.

duration

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

caseManagements

<caseManagements
    name=string
    reportingPeriodMemory=int
  >
IN THIS ORDER:
| ( <caseManagement ... /> )+
</caseManagements>

caseManagement

Documentation (element)

Units: List of elements

List of case managment interventions

Documentation (type)

Units: List of elements

List of age-specific case managment descriptions

Attributes

name

name=string

Units: string

Name of age specific intervention

reportingPeriodMemory

reportingPeriodMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

caseManagement

<caseManagement
    maxAgeYrs=decimal
  >
IN THIS ORDER:
|   <uc1 ... /> 
|   <uc2 ... /> 
|   <sev ... /> 
|   <nmfP ... /> 
|   <nmfNP ... /> 
|   <decisions ... /> 
</caseManagement>

Documentation (element)

Units: List of elements

Age-specific case management description, describes entry-points and decisions, with entry-point-specific decision probabilities

Attributes

maxAgeYrs

maxAgeYrs=decimal

Units: Years Min: 0 Max: 100

Upper bound of age group

uc1

→ scenario → caseManagements → caseManagement → uc1

<uc1>
IN THIS ORDER:
| ( <endPoint ... /> )+
</uc1>

endPoint

endPoint

→ scenario → caseManagements → caseManagement → uc1 → endPoint

<endPoint
    decision=int
    p=double
  />

Attributes

decision

decision=int

Foreign key reference to outcome node

p

p=double

Units: Proportion Min: 0 Max: 1

Probability of outcome

uc2

→ scenario → caseManagements → caseManagement → uc2

<uc2>
IN THIS ORDER:
| ( <endPoint ... /> )+
</uc2>

endPoint

sev

→ scenario → caseManagements → caseManagement → sev

<sev>
IN THIS ORDER:
| ( <endPoint ... /> )+
</sev>

endPoint

nmfP

→ scenario → caseManagements → caseManagement → nmfP

<nmfP>
IN THIS ORDER:
| ( <endPoint ... /> )+
</nmfP>

endPoint

nmfNP

→ scenario → caseManagements → caseManagement → nmfNP

<nmfNP>
IN THIS ORDER:
| ( <endPoint ... /> )+
</nmfNP>

endPoint

decisions

→ scenario → caseManagements → caseManagement → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )+
</decisions>

decision

decision

→ scenario → caseManagements → caseManagement → decisions → decision

<decision
    id=int
  >
IN THIS ORDER:
| ( <medicate ... /> )+
</decision>

medicate

Documentation (element)

Units: List of elements

describes treatment decisions, a list of medicate descisions.

Attributes

id

id=int

Units: Number

Key of decision

medicate

→ scenario → caseManagements → caseManagement → decisions → decision → medicate

<medicate
    name=string
    qty=int
    time=int
  />

Attributes

name

name=string

Units: string

Name of drug compound

qty

qty=int

Units: Number

Quantity of drug compound

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

healthSystem

→ scenario → healthSystem

<healthSystem
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</healthSystem>

Documentation (element)

Units: List of elements

Description of health system

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

entoData

→ scenario → entoData

<entoData
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Documentation (type)

Units: List of elements

Data for entomodel

Attributes

name

name=string

Units: string

Name of entomology data

nonVector

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

vector

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters for the vector transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <eir ... /> ]
| [ <emergence ... /> ]
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Attributes

mosquito

mosquito=string

eir

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    a2=double
    b1=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Attributes

a0

a0=double

a1

a1=double

a2

a2=double

b1

b1=double

b2

b2=double

EIRRotateAngle

EIRRotateAngle=double

emergence

→ scenario → entoData → vector → anopheles → emergence

<emergence>
IN THIS ORDER:
|   <emergenceRate ... /> 
|   <kappa ... /> 
|   <N_v ... /> 
|   <O_v ... /> 
|   <S_v ... /> 
</emergence>

Documentation (element)

emergenceRate

→ scenario → entoData → vector → anopheles → emergence → emergenceRate

<emergenceRate>
IN THIS ORDER:
| ( <item ... /> )+
</emergenceRate>

item

Documentation (element)

Units: Mosquitoes per human Min: 0 Max: inf

Mosquitoes emerging per day of the year, per human.

item

→ scenario → entoData → vector → anopheles → emergence → emergenceRate → item

<item>
    double
</item>

kappa

→ scenario → entoData → vector → anopheles → emergence → kappa

<kappa>
IN THIS ORDER:
| ( <item ... /> )+
</kappa>

item

Documentation (element)

Units: Min: 0 Max: 1

Human infectivity (probability of infection of a mosquito biting a human) over last mosqRestDuration+extrinsicIncubationPeriod days.

N_v

→ scenario → entoData → vector → anopheles → emergence → N_v

<N_v>
IN THIS ORDER:
| ( <item ... /> )+
</N_v>

item

Documentation (element)

Units: individuals Min: 0 Max: inf

Total population of mosquitoes over the last mosqRestDuration+extrinsicIncubationPeriod days, per human.

O_v

→ scenario → entoData → vector → anopheles → emergence → O_v

<O_v>
IN THIS ORDER:
| ( <item ... /> )+
</O_v>

item

Documentation (element)

Units: individuals Min: 0 Max: inf

Population of infected mosquitoes over the last mosqRestDuration+extrinsicIncubationPeriod days, per human.

S_v

→ scenario → entoData → vector → anopheles → emergence → S_v

<S_v>
IN THIS ORDER:
| ( <item ... /> )+
</S_v>

item

Documentation (element)

Units: individuals Min: 0 Max: inf

Population of infectious mosquitoes over the last mosqRestDuration+extrinsicIncubationPeriod days, per human.

mosq

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqSeekingDeathRate=double
    mosqSeekingDuration=double
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

mosqRestDuration

mosqRestDuration=int

extrinsicIncubationPeriod

extrinsicIncubationPeriod=int

mosqSeekingDeathRate

mosqSeekingDeathRate=double

mosqSeekingDuration

mosqSeekingDuration=double

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

mosqProbOvipositing

mosqProbOvipositing=double

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

nonHumanHosts

→ scenario → entoData → vector → nonHumanHosts

<nonHumanHosts
  [ name=string ]
    populationSize=int
  />

Documentation (element)

Populations of non-human hosts (must also have species-specific parameters).

Attributes

name

name=string

populationSize

populationSize=int

parameters

→ scenario → parameters

<parameters
    interval=int
    iseed=int
    delta=double
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters for mathematical model

Documentation (type)

Units: List of elements

Parameter vector

Attributes

interval

interval=int

Units: Days

Simulation step

iseed

iseed=int

Units: Number

Seed for RNG

delta

delta=double

Units: ? Redundant

this no longer seems to be used

latentp

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

name

name=string

Units: string

Name of parameter

number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

value

value=double

Units: Number Min: 0

Parameter value

include

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 7 documentation

Generated from: scenario_7.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    maximumAgeYrs=double
    name=string
    popSize=int
    simulationDuration=int
    modelVersion=int
    wuID=int
    assimMode=("0" or "1")
    mode=("1" or "2" or "3" or "4")
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_7.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
| [ <caseManagements ... /> ]
| [ <healthSystem ... /> ]
|   <entoData ... /> 
|   <parameters ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

schemaVersion

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

analysisNo

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

maximumAgeYrs

maximumAgeYrs=double

Units: Number Min: 0 Max: 100

Maximum age of simulated humans

name

name=string

Units: string

Name of intervention

popSize

popSize=int

Units: Count Min: 1 Max: 100000

Population size

simulationDuration

simulationDuration=int

Units: Time steps Min: 1 Max: 36500

Duration of main simulation

modelVersion

modelVersion=int

Units: Code Min: 0 Max: 100000000

Model Version

wuID

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

assimMode

assimMode=("0" or "1")

Units: Code

Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)

mode

mode=("1" or "2" or "3" or "4")

Units: Code

Simulation mode

demography

→ scenario → demography

<demography
    name=string
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Documentation (type)

Units: List of elements

Description of demography

Attributes

name

name=string

Units: string

Name of demography data

growthRate

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population.

ageGroup

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

poppercent

poppercent=double

upperbound

upperbound=double

monitoring

→ scenario → monitoring

<monitoring
    name=string
  >
IN THIS ORDER:
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Documentation (type)

Units: List of elements

Description of surveys

Attributes

name

name=string

Units: string

Name of monitoring data

surveys

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
    summaryOption=int
  >
IN THIS ORDER:
|   <surveyTime ... /> 
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

detectionLimit

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

summaryOption

summaryOption=int

Units: Code

Requested output variables

surveyTime

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time

ageGroup

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upperbound

upperbound=double

interventions

<interventions
    name=string
  >
IN THIS ORDER:
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

List of interventions

Documentation (type)

Units: List of elements

List of interventions

Attributes

name

name=string

Units: string

Name of age specific intervention

vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

vaccineType

vaccineType=int

Units: Code

Type of vaccine

halfLifeYrs

→ scenario → interventions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

value

value=double

TODO

efficacyB

→ scenario → interventions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

value

value=double

TODO

initialEfficacy

→ scenario → interventions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

value

value=double

TODO

iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=int
  />

Attributes

name

name=string

Units: string

Name of age specific intervention

freq

freq=double

ACR

ACR=double

proph

proph=int

tolPeriod

tolPeriod=int

atten

atten=int

ITNDescription

→ scenario → interventions → ITNDescription

<ITNDescription
    name=string
  >
IN THIS ORDER:
| ( <anopheles ... /> )+
</ITNDescription>

anopheles

Attributes

name

name=string

Units: string

Name of Insecticide Treated Net intervention

anopheles

→ scenario → interventions → ITNDescription → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anopheles>

Attributes

mosquito

mosquito=string

deterrency

→ scenario → interventions → ITNDescription → anopheles → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability (before decay).

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

preprandialKillingEffect

→ scenario → interventions → ITNDescription → anopheles → preprandialKillingEffect

<preprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

postprandialKillingEffect

→ scenario → interventions → ITNDescription → anopheles → postprandialKillingEffect

<postprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

IRSDescription

→ scenario → interventions → IRSDescription

<IRSDescription
    name=string
  >
IN THIS ORDER:
| ( <anopheles ... /> )+
</IRSDescription>

anopheles

Attributes

name

name=string

Units: string

Name of Indoor Residual Spraying intervention

anopheles

→ scenario → interventions → IRSDescription → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <killingEffect ... /> 
</anopheles>

Attributes

mosquito

mosquito=string

deterrency

→ scenario → interventions → IRSDescription → anopheles → deterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

killingEffect

→ scenario → interventions → IRSDescription → anopheles → killingEffect

<killingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

Units: None Min: 0 Max: 1

One minus this multiplies the survival rate of resting mosquitoes.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

continuous

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
</continuous>

vaccine

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

timed

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <ipti ... /> ]
</intervention>

Attributes

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

drugRegimen

→ scenario → healthSystem → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

firstLine

firstLine=string

Units: Drug code

Code for first line drug

secondLine

secondLine=string

Units: Drug code

Code for second line drug

inpatient

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

initialACR

→ scenario → healthSystem → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

CQ

→ scenario → healthSystem → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

value

value=double

TODO

SP

→ scenario → healthSystem → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

value

value=double

TODO

AQ

→ scenario → healthSystem → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

value

value=double

TODO

SPAQ

→ scenario → healthSystem → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

value

value=double

TODO

ACT

→ scenario → healthSystem → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

value

value=double

TODO

QN

→ scenario → healthSystem → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

value

value=double

TODO

selfTreatment

→ scenario → healthSystem → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

value

value=double

TODO

compliance

→ scenario → healthSystem → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

pSeekOfficialCareUncomplicated1

→ scenario → healthSystem → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSelfTreatUncomplicated

→ scenario → healthSystem → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

value

value=double

TODO

pSeekOfficialCareUncomplicated2

→ scenario → healthSystem → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSeekOfficialCareSevere

→ scenario → healthSystem → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease seeks official care

Attributes

value

value=double

TODO

pSequelaeInpatient

<pSequelaeInpatient>
IN THIS ORDER:
| ( <item ... /> )+
</pSequelaeInpatient>

item

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients

item

→ scenario → healthSystem → pSequelaeInpatient → item

<item
    value=double
    maxAgeYrs=double
  />

Attributes

value

value=double

TODO

maxAgeYrs

maxAgeYrs=double

Units: Years Min: 0 Max: 100

Upper bound of age group

CFR

→ scenario → healthSystem → CFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

group

→ scenario → healthSystem → CFR → group

<group
    cfr=double
    lowerbound=double
  />

Attributes

cfr

cfr=double

Units: Proportion Min: 0 Max: 1

Case fatality rate

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

changeEIR

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

EIRDaily

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Number Min: 1

Value of daily EIR

Attributes

origin

origin=string

MDA

→ scenario → interventions → timed → intervention → MDA

<MDA
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

vaccinate

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → timed → intervention → ITN

<ITN
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IRS

→ scenario → interventions → timed → intervention → IRS

<IRS
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of IRS deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → timed → intervention → ipti

<ipti
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

caseManagements

<caseManagements
    name=string
    reportingPeriodMemory=int
  >
IN THIS ORDER:
| ( <caseManagement ... /> )+
</caseManagements>

caseManagement

Documentation (element)

Units: List of elements

List of case managment interventions

Documentation (type)

Units: List of elements

List of age-specific case managment descriptions

Attributes

name

name=string

Units: string

Name of age specific intervention

reportingPeriodMemory

reportingPeriodMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

caseManagement

<caseManagement
    maxAgeYrs=decimal
  >
IN THIS ORDER:
|   <uc1 ... /> 
|   <uc2 ... /> 
|   <sev ... /> 
|   <nmfP ... /> 
|   <nmfNP ... /> 
|   <decisions ... /> 
</caseManagement>

Documentation (element)

Units: List of elements

Age-specific case management description, describes entry-points and decisions, with entry-point-specific decision probabilities

Attributes

maxAgeYrs

maxAgeYrs=decimal

Units: Years Min: 0 Max: 100

Upper bound of age group

uc1

→ scenario → caseManagements → caseManagement → uc1

<uc1>
IN THIS ORDER:
| ( <endPoint ... /> )+
</uc1>

endPoint

endPoint

→ scenario → caseManagements → caseManagement → uc1 → endPoint

<endPoint
    decision=int
    p=double
  />

Attributes

decision

decision=int

Foreign key reference to outcome node

p

p=double

Units: Proportion Min: 0 Max: 1

Probability of outcome

uc2

→ scenario → caseManagements → caseManagement → uc2

<uc2>
IN THIS ORDER:
| ( <endPoint ... /> )+
</uc2>

endPoint

sev

→ scenario → caseManagements → caseManagement → sev

<sev>
IN THIS ORDER:
| ( <endPoint ... /> )+
</sev>

endPoint

nmfP

→ scenario → caseManagements → caseManagement → nmfP

<nmfP>
IN THIS ORDER:
| ( <endPoint ... /> )+
</nmfP>

endPoint

nmfNP

→ scenario → caseManagements → caseManagement → nmfNP

<nmfNP>
IN THIS ORDER:
| ( <endPoint ... /> )+
</nmfNP>

endPoint

decisions

→ scenario → caseManagements → caseManagement → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )+
</decisions>

decision

decision

→ scenario → caseManagements → caseManagement → decisions → decision

<decision
    id=int
  >
IN THIS ORDER:
| ( <medicate ... /> )+
</decision>

medicate

Documentation (element)

Units: List of elements

describes treatment decisions, a list of medicate descisions.

Attributes

id

id=int

Units: Number

Key of decision

medicate

→ scenario → caseManagements → caseManagement → decisions → decision → medicate

<medicate
    name=string
    qty=int
    time=int
  />

Attributes

name

name=string

Units: string

Name of drug compound

qty

qty=int

Units: Number

Quantity of drug compound

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

healthSystem

→ scenario → healthSystem

<healthSystem
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</healthSystem>

Documentation (element)

Units: List of elements

Description of health system

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

entoData

→ scenario → entoData

<entoData
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Documentation (type)

Units: List of elements

Data for entomodel

Attributes

name

name=string

Units: string

Name of entomology data

nonVector

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

vector

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters for the vector transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
|   <eir ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Attributes

mosquito

mosquito=string

eir

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    a2=double
    b1=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Element

Description of entomological inoculation rate

Attributes

a0

a0=double

a1

a1=double

a2

a2=double

b1

b1=double

b2

b2=double

EIRRotateAngle

EIRRotateAngle=double

mosq

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqSeekingDeathRate=double
    mosqSeekingDuration=double
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
    emergenceRateFilename=string
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

mosqRestDuration

mosqRestDuration=int

extrinsicIncubationPeriod

extrinsicIncubationPeriod=int

mosqSeekingDeathRate

mosqSeekingDeathRate=double

mosqSeekingDuration

mosqSeekingDuration=double

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

mosqProbOvipositing

mosqProbOvipositing=double

emergenceRateFilename

emergenceRateFilename=string

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

nonHumanHosts

→ scenario → entoData → vector → nonHumanHosts

<nonHumanHosts
  [ name=string ]
    populationSize=int
  />

Documentation (element)

Populations of non-human hosts (must also have species-specific parameters).

Attributes

name

name=string

populationSize

populationSize=int

parameters

→ scenario → parameters

<parameters
    interval=int
    iseed=int
    delta=double
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters for mathematical model

Documentation (type)

Units: List of elements

Parameter vector

Attributes

interval

interval=int

Units: Days

Simulation step

iseed

iseed=int

Units: Number

Seed for RNG

delta

delta=double

Units: ? Redundant

this no longer seems to be used

latentp

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

name

name=string

Units: string

Name of parameter

number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

value

value=double

Units: Number Min: 0

Parameter value

include

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 6 documentation

Generated from: scenario_6.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    maximumAgeYrs=double
    name=string
    popSize=int
    simulationDuration=int
    modelVersion=int
    wuID=int
    assimMode=("0" or "1")
    mode=("1" or "2" or "3" or "4")
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_6.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
| [ <caseManagements ... /> ]
| [ <healthSystem ... /> ]
|   <entoData ... /> 
|   <parameters ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

schemaVersion

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

analysisNo

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

maximumAgeYrs

maximumAgeYrs=double

Units: Number Min: 0 Max: 100

Maximum age of simulated humans

name

name=string

Units: string

Name of intervention

popSize

popSize=int

Units: Count Min: 1 Max: 100000

Population size

simulationDuration

simulationDuration=int

Units: Time steps Min: 1 Max: 36500

Duration of main simulation

modelVersion

modelVersion=int

Units: Code Min: 0 Max: 100000000

Model Version

wuID

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

assimMode

assimMode=("0" or "1")

Units: Code

Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)

mode

mode=("1" or "2" or "3" or "4")

Units: Code

Simulation mode

demography

→ scenario → demography

<demography
    name=string
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Documentation (type)

Units: List of elements

Description of demography

Attributes

name

name=string

Units: string

Name of demography data

growthRate

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population.

ageGroup

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

poppercent

poppercent=double

upperbound

upperbound=double

monitoring

→ scenario → monitoring

<monitoring
    name=string
  >
IN THIS ORDER:
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Documentation (type)

Units: List of elements

Description of surveys

Attributes

name

name=string

Units: string

Name of monitoring data

surveys

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
    summaryOption=int
  >
IN THIS ORDER:
|   <surveyTime ... /> 
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

detectionLimit

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

summaryOption

summaryOption=int

Units: Code

Requested output variables

surveyTime

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time

ageGroup

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upperbound

upperbound=double

interventions

<interventions
    name=string
  >
IN THIS ORDER:
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

List of interventions

Documentation (type)

Units: List of elements

List of interventions

Attributes

name

name=string

Units: string

Name of age specific intervention

vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

vaccineType

vaccineType=int

Units: Code

Type of vaccine

halfLifeYrs

→ scenario → interventions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

value

value=double

TODO

efficacyB

→ scenario → interventions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

value

value=double

TODO

initialEfficacy

→ scenario → interventions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

value

value=double

TODO

iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=int
  />

Attributes

name

name=string

Units: string

Name of age specific intervention

freq

freq=double

ACR

ACR=double

proph

proph=int

tolPeriod

tolPeriod=int

atten

atten=int

continuous

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
</continuous>

vaccine

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

timed

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <IRS ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <ipti ... /> ]
</intervention>

Attributes

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

drugRegimen

→ scenario → healthSystem → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

firstLine

firstLine=string

Units: Drug code

Code for first line drug

secondLine

secondLine=string

Units: Drug code

Code for second line drug

inpatient

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

initialACR

→ scenario → healthSystem → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

CQ

→ scenario → healthSystem → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

value

value=double

TODO

SP

→ scenario → healthSystem → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

value

value=double

TODO

AQ

→ scenario → healthSystem → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

value

value=double

TODO

SPAQ

→ scenario → healthSystem → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

value

value=double

TODO

ACT

→ scenario → healthSystem → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

value

value=double

TODO

QN

→ scenario → healthSystem → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

value

value=double

TODO

selfTreatment

→ scenario → healthSystem → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

value

value=double

TODO

compliance

→ scenario → healthSystem → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

pSeekOfficialCareUncomplicated1

→ scenario → healthSystem → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSelfTreatUncomplicated

→ scenario → healthSystem → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

value

value=double

TODO

pSeekOfficialCareUncomplicated2

→ scenario → healthSystem → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSeekOfficialCareSevere

→ scenario → healthSystem → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease seeks official care

Attributes

value

value=double

TODO

pSequelaeInpatient

<pSequelaeInpatient>
IN THIS ORDER:
| ( <item ... /> )+
</pSequelaeInpatient>

item

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients

item

→ scenario → healthSystem → pSequelaeInpatient → item

<item
    value=double
    maxAgeYrs=double
  />

Attributes

value

value=double

TODO

maxAgeYrs

maxAgeYrs=double

Units: Years Min: 0 Max: 100

Upper bound of age group

CFR

→ scenario → healthSystem → CFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

group

→ scenario → healthSystem → CFR → group

<group
    cfr=double
    lowerbound=double
  />

Attributes

cfr

cfr=double

Units: Proportion Min: 0 Max: 1

Case fatality rate

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

changeEIR

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

EIRDaily

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Number Min: 1

Value of daily EIR

Attributes

origin

origin=string

MDA

→ scenario → interventions → timed → intervention → MDA

<MDA
    maxAge=double
    minAge=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IRS

→ scenario → interventions → timed → intervention → IRS

<IRS/>

vaccinate

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
    maxAge=double
    minAge=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → timed → intervention → ITN

<ITN
    maxAge=double
    minAge=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → timed → intervention → ipti

<ipti
    maxAge=double
    minAge=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

caseManagements

<caseManagements
    name=string
    reportingPeriodMemory=int
  >
IN THIS ORDER:
| ( <caseManagement ... /> )+
</caseManagements>

caseManagement

Documentation (element)

Units: List of elements

List of case managment interventions

Documentation (type)

Units: List of elements

List of age-specific case managment descriptions

Attributes

name

name=string

Units: string

Name of age specific intervention

reportingPeriodMemory

reportingPeriodMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

caseManagement

<caseManagement
    maxAgeYrs=decimal
  >
IN THIS ORDER:
|   <uc1 ... /> 
|   <uc2 ... /> 
|   <sev ... /> 
|   <nmfP ... /> 
|   <nmfNP ... /> 
|   <decisions ... /> 
</caseManagement>

Documentation (element)

Units: List of elements

Age-specific case management description, describes entry-points and decisions, with entry-point-specific decision probabilities

Attributes

maxAgeYrs

maxAgeYrs=decimal

Units: Years Min: 0 Max: 100

Upper bound of age group

uc1

→ scenario → caseManagements → caseManagement → uc1

<uc1>
IN THIS ORDER:
| ( <endPoint ... /> )+
</uc1>

endPoint

endPoint

→ scenario → caseManagements → caseManagement → uc1 → endPoint

<endPoint
    decision=int
    p=double
  />

Attributes

decision

decision=int

Foreign key reference to outcome node

p

p=double

Units: Proportion Min: 0 Max: 1

Probability of outcome

uc2

→ scenario → caseManagements → caseManagement → uc2

<uc2>
IN THIS ORDER:
| ( <endPoint ... /> )+
</uc2>

endPoint

sev

→ scenario → caseManagements → caseManagement → sev

<sev>
IN THIS ORDER:
| ( <endPoint ... /> )+
</sev>

endPoint

nmfP

→ scenario → caseManagements → caseManagement → nmfP

<nmfP>
IN THIS ORDER:
| ( <endPoint ... /> )+
</nmfP>

endPoint

nmfNP

→ scenario → caseManagements → caseManagement → nmfNP

<nmfNP>
IN THIS ORDER:
| ( <endPoint ... /> )+
</nmfNP>

endPoint

decisions

→ scenario → caseManagements → caseManagement → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )+
</decisions>

decision

decision

→ scenario → caseManagements → caseManagement → decisions → decision

<decision
    id=int
  >
IN THIS ORDER:
| ( <medicate ... /> )+
</decision>

medicate

Documentation (element)

Units: List of elements

describes treatment decisions, a list of medicate descisions.

Attributes

id

id=int

Units: Number

Key of decision

medicate

→ scenario → caseManagements → caseManagement → decisions → decision → medicate

<medicate
    name=string
    qty=int
    time=int
  />

Attributes

name

name=string

Units: string

Name of drug compound

qty

qty=int

Units: Number

Quantity of drug compound

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

healthSystem

→ scenario → healthSystem

<healthSystem
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</healthSystem>

Documentation (element)

Units: List of elements

Description of health system

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

entoData

→ scenario → entoData

<entoData
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Documentation (type)

Units: List of elements

Data for entomodel

Attributes

name

name=string

Units: string

Name of entomology data

nonVector

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

vector

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters for the vector transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
|   <eir ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Attributes

mosquito

mosquito=string

eir

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    a2=double
    b1=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Element

Description of entomological inoculation rate

Attributes

a0

a0=double

a1

a1=double

a2

a2=double

b1

b1=double

b2

b2=double

EIRRotateAngle

EIRRotateAngle=double

mosq

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqSeekingDeathRate=double
    mosqSeekingDuration=double
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
    emergenceRateFilename=string
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

mosqRestDuration

mosqRestDuration=int

extrinsicIncubationPeriod

extrinsicIncubationPeriod=int

mosqSeekingDeathRate

mosqSeekingDeathRate=double

mosqSeekingDuration

mosqSeekingDuration=double

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

mosqProbOvipositing

mosqProbOvipositing=double

emergenceRateFilename

emergenceRateFilename=string

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

nonHumanHosts

→ scenario → entoData → vector → nonHumanHosts

<nonHumanHosts
  [ name=string ]
    populationSize=int
  />

Documentation (element)

Populations of non-human hosts (must also have species-specific parameters).

Attributes

name

name=string

populationSize

populationSize=int

parameters

→ scenario → parameters

<parameters
    interval=int
    iseed=int
    delta=double
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters for mathematical model

Documentation (type)

Units: List of elements

Parameter vector

Attributes

interval

interval=int

Units: Days

Simulation step

iseed

iseed=int

Units: Number

Seed for RNG

delta

delta=double

Units: ? Redundant

this no longer seems to be used

latentp

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

name

name=string

Units: string

Name of parameter

number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

value

value=double

Units: Number Min: 0

Parameter value

include

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 5 documentation

Generated from: scenario_5.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    maximumAgeYrs=double
    name=string
    popSize=int
    simulationDuration=int
    modelVersion=int
    wuID=int
    assimMode=("0" or "1")
    mode=("1" or "2" or "3" or "4")
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_5.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
| [ <caseManagements ... /> ]
|   <healthSystem ... /> 
|   <entoData ... /> 
|   <parameters ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

schemaVersion

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

analysisNo

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

maximumAgeYrs

maximumAgeYrs=double

Units: Number Min: 0 Max: 100

Maximum age of simulated humans

name

name=string

Units: string

Name of intervention

popSize

popSize=int

Units: Count Min: 1 Max: 100000

Population size

simulationDuration

simulationDuration=int

Units: Time steps Min: 1 Max: 36500

Duration of main simulation

modelVersion

modelVersion=int

Units: Code Min: 0 Max: 100000000

Model Version

wuID

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

assimMode

assimMode=("0" or "1")

Units: Code

Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)

mode

mode=("1" or "2" or "3" or "4")

Units: Code

Simulation mode

demography

→ scenario → demography

<demography
    name=string
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Documentation (type)

Units: List of elements

Description of demography

Attributes

name

name=string

Units: string

Name of demography data

growthRate

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population.

ageGroup

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

poppercent

poppercent=double

upperbound

upperbound=double

monitoring

→ scenario → monitoring

<monitoring
    name=string
  >
IN THIS ORDER:
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Documentation (type)

Units: List of elements

Description of surveys

Attributes

name

name=string

Units: string

Name of monitoring data

surveys

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
    summaryOption=int
  >
IN THIS ORDER:
|   <surveyTime ... /> 
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

detectionLimit

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

summaryOption

summaryOption=int

Units: Code

Requested output variables

surveyTime

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time

ageGroup

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upperbound

upperbound=double

interventions

<interventions
    name=string
  >
IN THIS ORDER:
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

List of interventions

Documentation (type)

Units: List of elements

List of interventions

Attributes

name

name=string

Units: string

Name of age specific intervention

vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

vaccineType

vaccineType=int

Units: Code

Type of vaccine

halfLifeYrs

→ scenario → interventions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

value

value=double

TODO

efficacyB

→ scenario → interventions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

value

value=double

TODO

initialEfficacy

→ scenario → interventions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

value

value=double

TODO

iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=int
  />

Attributes

name

name=string

Units: string

Name of age specific intervention

freq

freq=double

ACR

ACR=double

proph

proph=int

tolPeriod

tolPeriod=int

atten

atten=int

continuous

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
</continuous>

vaccine

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

timed

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <IRS ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <ipti ... /> ]
</intervention>

Attributes

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

drugRegimen

→ scenario → healthSystem → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

firstLine

firstLine=string

Units: Drug code

Code for first line drug

secondLine

secondLine=string

Units: Drug code

Code for second line drug

inpatient

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

initialACR

→ scenario → healthSystem → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

CQ

→ scenario → healthSystem → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

value

value=double

TODO

SP

→ scenario → healthSystem → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

value

value=double

TODO

AQ

→ scenario → healthSystem → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

value

value=double

TODO

SPAQ

→ scenario → healthSystem → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

value

value=double

TODO

ACT

→ scenario → healthSystem → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

value

value=double

TODO

QN

→ scenario → healthSystem → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

value

value=double

TODO

selfTreatment

→ scenario → healthSystem → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

value

value=double

TODO

compliance

→ scenario → healthSystem → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

pSeekOfficialCareUncomplicated1

→ scenario → healthSystem → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSelfTreatUncomplicated

→ scenario → healthSystem → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

value

value=double

TODO

pSeekOfficialCareUncomplicated2

→ scenario → healthSystem → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSeekOfficialCareSevere

→ scenario → healthSystem → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease seeks official care

Attributes

value

value=double

TODO

pSequelaeInpatient

<pSequelaeInpatient>
IN THIS ORDER:
| ( <item ... /> )+
</pSequelaeInpatient>

item

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients

item

→ scenario → healthSystem → pSequelaeInpatient → item

<item
    value=double
    maxAgeYrs=double
  />

Attributes

value

value=double

TODO

maxAgeYrs

maxAgeYrs=double

Units: Years Min: 0 Max: 100

Upper bound of age group

CFR

→ scenario → healthSystem → CFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

group

→ scenario → healthSystem → CFR → group

<group
    cfr=double
    lowerbound=double
  />

Attributes

cfr

cfr=double

Units: Proportion Min: 0 Max: 1

Case fatality rate

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

changeEIR

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

EIRDaily

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Number Min: 1

Value of daily EIR

Attributes

origin

origin=string

MDA

→ scenario → interventions → timed → intervention → MDA

<MDA
    maxAge=double
    minAge=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IRS

→ scenario → interventions → timed → intervention → IRS

<IRS/>

vaccinate

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
    maxAge=double
    minAge=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → timed → intervention → ITN

<ITN
    maxAge=double
    minAge=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → timed → intervention → ipti

<ipti
    maxAge=double
    minAge=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

caseManagements

<caseManagements
    name=string
  >
IN THIS ORDER:
| ( <caseManagement ... /> )+
</caseManagements>

caseManagement

Documentation (element)

Units: List of elements

List of case managment interventions

Documentation (type)

Units: List of elements

List of age-specific case managment descriptions

Attributes

name

name=string

Units: string

Name of age specific intervention

caseManagement

<caseManagement
  [ minAgeYrs=decimal ]
    maxAgeYrs=decimal
  >
IN THIS ORDER:
|   <uc1 ... /> 
|   <uc2 ... /> 
|   <sev ... /> 
|   <nmf ... /> 
|   <decisions ... /> 
</caseManagement>

Documentation (element)

Units: List of elements

Age-specific case management description, describes entry-points and decisions, with entry-point-specific decision probabilities

Attributes

minAgeYrs

minAgeYrs=decimal

maxAgeYrs

maxAgeYrs=decimal

Units: Years Min: 0 Max: 100

Upper bound of age group

uc1

→ scenario → caseManagements → caseManagement → uc1

<uc1>
IN THIS ORDER:
| ( <endPoint ... /> )+
</uc1>

endPoint

endPoint

→ scenario → caseManagements → caseManagement → uc1 → endPoint

<endPoint
    decision=int
    p=double
  />

Attributes

decision

decision=int

Foreign key reference to outcome node

p

p=double

Units: Proportion Min: 0 Max: 1

Probability of outcome

uc2

→ scenario → caseManagements → caseManagement → uc2

<uc2>
IN THIS ORDER:
| ( <endPoint ... /> )+
</uc2>

endPoint

sev

→ scenario → caseManagements → caseManagement → sev

<sev>
IN THIS ORDER:
| ( <endPoint ... /> )+
</sev>

endPoint

nmf

→ scenario → caseManagements → caseManagement → nmf

<nmf>
IN THIS ORDER:
| ( <endPoint ... /> )+
</nmf>

endPoint

decisions

→ scenario → caseManagements → caseManagement → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )+
</decisions>

decision

decision

→ scenario → caseManagements → caseManagement → decisions → decision

<decision
    id=int
  >
IN THIS ORDER:
| ( <medicate ... /> )+
</decision>

medicate

Documentation (element)

Units: List of elements

describes treatment decisions, a list of medicate descisions.

Attributes

id

id=int

Units: Number

Key of decision

medicate

→ scenario → caseManagements → caseManagement → decisions → decision → medicate

<medicate
    name=string
    qty=int
    time=int
  />

Attributes

name

name=string

Units: string

Name of drug compound

qty

qty=int

Units: Number

Quantity of drug compound

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

healthSystem

→ scenario → healthSystem

<healthSystem
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</healthSystem>

Documentation (element)

Units: List of elements

Description of health system

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

entoData

→ scenario → entoData

<entoData
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Documentation (type)

Units: List of elements

Data for entomodel

Attributes

name

name=string

Units: string

Name of entomology data

nonVector

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

vector

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters for the vector transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
|   <eir ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Attributes

mosquito

mosquito=string

eir

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    a2=double
    b1=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Element

Description of entomological inoculation rate

Attributes

a0

a0=double

a1

a1=double

a2

a2=double

b1

b1=double

b2

b2=double

EIRRotateAngle

EIRRotateAngle=double

mosq

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqSeekingDeathRate=double
    mosqSeekingDuration=double
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
    emergenceRateFilename=string
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

mosqRestDuration

mosqRestDuration=int

extrinsicIncubationPeriod

extrinsicIncubationPeriod=int

mosqSeekingDeathRate

mosqSeekingDeathRate=double

mosqSeekingDuration

mosqSeekingDuration=double

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

mosqProbOvipositing

mosqProbOvipositing=double

emergenceRateFilename

emergenceRateFilename=string

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

nonHumanHosts

→ scenario → entoData → vector → nonHumanHosts

<nonHumanHosts
  [ name=string ]
    populationSize=int
  />

Documentation (element)

Populations of non-human hosts (must also have species-specific parameters).

Attributes

name

name=string

populationSize

populationSize=int

parameters

→ scenario → parameters

<parameters
    interval=int
    iseed=int
    delta=double
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters for mathematical model

Documentation (type)

Units: List of elements

Parameter vector

Attributes

interval

interval=int

Units: Days

Simulation step

iseed

iseed=int

Units: Number

Seed for RNG

delta

delta=double

Units: ? Redundant

this no longer seems to be used

latentp

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

name

name=string

Units: string

Name of parameter

number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

value

value=double

Units: Number Min: 0

Parameter value

include

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 4 documentation

Generated from: scenario_4.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    maximumAgeYrs=double
    name=string
    popSize=int
    simulationDuration=int
    modelVersion=int
    wuID=int
    assimMode=("0" or "1")
    mode=("1" or "2" or "3" or "4")
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_4.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
| [ <caseManagements ... /> ]
|   <healthSystem ... /> 
|   <entoData ... /> 
|   <parameters ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

schemaVersion

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

analysisNo

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

maximumAgeYrs

maximumAgeYrs=double

Units: Number Min: 0 Max: 100

Maximum age of simulated humans

name

name=string

Units: string

Name of intervention

popSize

popSize=int

Units: Count Min: 1 Max: 100000

Population size

simulationDuration

simulationDuration=int

Units: Time steps Min: 1 Max: 36500

Duration of main simulation

modelVersion

modelVersion=int

Units: Code Min: 0 Max: 100000000

Model Version

wuID

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

assimMode

assimMode=("0" or "1")

Units: Code

Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)

mode

mode=("1" or "2" or "3" or "4")

Units: Code

Simulation mode

demography

→ scenario → demography

<demography
    name=string
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Documentation (type)

Units: List of elements

Description of demography

Attributes

name

name=string

Units: string

Name of demography data

growthRate

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population.

ageGroup

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

poppercent

poppercent=double

upperbound

upperbound=double

monitoring

→ scenario → monitoring

<monitoring
    name=string
  >
IN THIS ORDER:
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Documentation (type)

Units: List of elements

Description of surveys

Attributes

name

name=string

Units: string

Name of monitoring data

surveys

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
    summaryOption=int
  >
IN THIS ORDER:
|   <surveyTime ... /> 
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

detectionLimit

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

summaryOption

summaryOption=int

Units: Code

Requested output variables

surveyTime

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time

ageGroup

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upperbound

upperbound=double

interventions

<interventions
    name=string
  >
IN THIS ORDER:
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

List of interventions

Documentation (type)

Units: List of elements

List of interventions

Attributes

name

name=string

Units: string

Name of age specific intervention

vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

vaccineType

vaccineType=int

Units: Code

Type of vaccine

halfLifeYrs

→ scenario → interventions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

value

value=double

TODO

efficacyB

→ scenario → interventions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

value

value=double

TODO

initialEfficacy

→ scenario → interventions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

value

value=double

TODO

iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=int
  />

Attributes

name

name=string

Units: string

Name of age specific intervention

freq

freq=double

ACR

ACR=double

proph

proph=int

tolPeriod

tolPeriod=int

atten

atten=int

continuous

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
</continuous>

vaccine

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

timed

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <IRS ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <ipti ... /> ]
</intervention>

Attributes

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

drugRegimen

→ scenario → healthSystem → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

firstLine

firstLine=string

Units: Drug code

Code for first line drug

secondLine

secondLine=string

Units: Drug code

Code for second line drug

inpatient

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

initialACR

→ scenario → healthSystem → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

CQ

→ scenario → healthSystem → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

value

value=double

TODO

SP

→ scenario → healthSystem → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

value

value=double

TODO

AQ

→ scenario → healthSystem → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

value

value=double

TODO

SPAQ

→ scenario → healthSystem → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

value

value=double

TODO

ACT

→ scenario → healthSystem → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

value

value=double

TODO

QN

→ scenario → healthSystem → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

value

value=double

TODO

selfTreatment

→ scenario → healthSystem → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

value

value=double

TODO

compliance

→ scenario → healthSystem → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

pSeekOfficialCareUncomplicated1

→ scenario → healthSystem → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSelfTreatUncomplicated

→ scenario → healthSystem → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

value

value=double

TODO

pSeekOfficialCareUncomplicated2

→ scenario → healthSystem → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSeekOfficialCareSevere

→ scenario → healthSystem → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease seeks official care

Attributes

value

value=double

TODO

pSequelaeInpatient

<pSequelaeInpatient>
IN THIS ORDER:
| ( <item ... /> )+
</pSequelaeInpatient>

item

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients

item

→ scenario → healthSystem → pSequelaeInpatient → item

<item
    value=double
    maxAgeYrs=double
  />

Attributes

value

value=double

TODO

maxAgeYrs

maxAgeYrs=double

Units: Years Min: 0 Max: 100

Upper bound of age group

CFR

→ scenario → healthSystem → CFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

group

→ scenario → healthSystem → CFR → group

<group
    cfr=double
    lowerbound=double
  />

Attributes

cfr

cfr=double

Units: Proportion Min: 0 Max: 1

Case fatality rate

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

changeEIR

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

EIRDaily

→ scenario → entoData → nonVector → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Number Min: 1

Value of daily EIR

Attributes

origin

origin=string

MDA

→ scenario → interventions → timed → intervention → MDA

<MDA
    maxAge=double
    minAge=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IRS

→ scenario → interventions → timed → intervention → IRS

<IRS/>

vaccinate

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
    maxAge=double
    minAge=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → timed → intervention → ITN

<ITN
    maxAge=double
    minAge=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → timed → intervention → ipti

<ipti
    maxAge=double
    minAge=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

caseManagements

<caseManagements
    name=string
  >
IN THIS ORDER:
| ( <caseManagement ... /> )+
</caseManagements>

caseManagement

Documentation (element)

Units: List of elements

List of case managment interventions

Documentation (type)

Units: List of elements

List of age-specific case managment descriptions

Attributes

name

name=string

Units: string

Name of age specific intervention

caseManagement

<caseManagement
  [ minAgeYrs=decimal ]
    maxAgeYrs=decimal
  >
IN THIS ORDER:
|   <uc1 ... /> 
|   <uc2 ... /> 
|   <sev ... /> 
|   <nmf ... /> 
|   <decisions ... /> 
</caseManagement>

Documentation (element)

Units: List of elements

Age-specific case management description, describes entry-points and decisions, with entry-point-specific decision probabilities

Attributes

minAgeYrs

minAgeYrs=decimal

maxAgeYrs

maxAgeYrs=decimal

Units: Years Min: 0 Max: 100

Upper bound of age group

uc1

→ scenario → caseManagements → caseManagement → uc1

<uc1>
IN THIS ORDER:
| ( <endPoint ... /> )+
</uc1>

endPoint

endPoint

→ scenario → caseManagements → caseManagement → uc1 → endPoint

<endPoint
    decision=int
    p=double
  />

Attributes

decision

decision=int

Foreign key reference to outcome node

p

p=double

Units: Proportion Min: 0 Max: 1

Probability of outcome

uc2

→ scenario → caseManagements → caseManagement → uc2

<uc2>
IN THIS ORDER:
| ( <endPoint ... /> )+
</uc2>

endPoint

sev

→ scenario → caseManagements → caseManagement → sev

<sev>
IN THIS ORDER:
| ( <endPoint ... /> )+
</sev>

endPoint

nmf

→ scenario → caseManagements → caseManagement → nmf

<nmf>
IN THIS ORDER:
| ( <endPoint ... /> )+
</nmf>

endPoint

decisions

→ scenario → caseManagements → caseManagement → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )+
</decisions>

decision

decision

→ scenario → caseManagements → caseManagement → decisions → decision

<decision
    id=int
  >
IN THIS ORDER:
| ( <medicate ... /> )+
</decision>

medicate

Documentation (element)

Units: List of elements

describes treatment decisions, a list of medicate descisions.

Attributes

id

id=int

Units: Number

Key of decision

medicate

→ scenario → caseManagements → caseManagement → decisions → decision → medicate

<medicate
    name=string
    qty=int
    time=int
  />

Attributes

name

name=string

Units: string

Name of drug compound

qty

qty=int

Units: Number

Quantity of drug compound

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

healthSystem

→ scenario → healthSystem

<healthSystem
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</healthSystem>

Documentation (element)

Units: List of elements

Description of health system

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

entoData

→ scenario → entoData

<entoData
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Documentation (type)

Units: List of elements

Data for entomodel

Attributes

name

name=string

Units: string

Name of entomology data

nonVector

→ scenario → entoData → nonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

EIRDaily

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

vector

→ scenario → entoData → vector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters for the vector transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
|   <eir ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Attributes

mosquito

mosquito=string

eir

→ scenario → entoData → vector → anopheles → eir

<eir
    a0=double
    a1=double
    a2=double
    b1=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Element

Description of entomological inoculation rate

Attributes

a0

a0=double

a1

a1=double

a2

a2=double

b1

b1=double

b2

b2=double

EIRRotateAngle

EIRRotateAngle=double

mosq

→ scenario → entoData → vector → anopheles → mosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqSeekingDeathRate=double
    mosqSeekingDuration=double
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
    emergenceRateFilename=string
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

mosqRestDuration

mosqRestDuration=int

extrinsicIncubationPeriod

extrinsicIncubationPeriod=int

mosqSeekingDeathRate

mosqSeekingDeathRate=double

mosqSeekingDuration

mosqSeekingDuration=double

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

mosqProbOvipositing

mosqProbOvipositing=double

emergenceRateFilename

emergenceRateFilename=string

nonHumanHosts

→ scenario → entoData → vector → anopheles → nonHumanHosts

<nonHumanHosts
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Units: List of elements

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

nonHumanHosts

→ scenario → entoData → vector → nonHumanHosts

<nonHumanHosts
  [ name=string ]
    populationSize=int
  />

Documentation (element)

Populations of non-human hosts (must also have species-specific parameters).

Attributes

name

name=string

populationSize

populationSize=int

parameters

→ scenario → parameters

<parameters
    interval=int
    iseed=int
    delta=double
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters for mathematical model

Documentation (type)

Units: List of elements

Parameter vector

Attributes

interval

interval=int

Units: Days

Simulation step

iseed

iseed=int

Units: Number

Seed for RNG

delta

delta=double

Units: ? Redundant

this no longer seems to be used

latentp

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

name

name=string

Units: string

Name of parameter

number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

value

value=double

Units: Number Min: 0

Parameter value

include

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 3 documentation

Generated from: scenario_3.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    maximumAgeYrs=double
    name=string
    popSize=int
    simulationDuration=int
    modelVersion=int
    wuID=int
    assimMode=("0" or "1")
    mode=("1" or "2" or "3" or "4")
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_3.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
| [ <caseManagements ... /> ]
|   <healthSystem ... /> 
|   <entoData ... /> 
|   <parameters ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

schemaVersion

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

analysisNo

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

maximumAgeYrs

maximumAgeYrs=double

Units: Number Min: 0 Max: 100

Maximum age of simulated humans

name

name=string

Units: string

Name of intervention

popSize

popSize=int

Units: Count Min: 1 Max: 100000

Population size

simulationDuration

simulationDuration=int

Units: Time steps Min: 1 Max: 36500

Duration of main simulation

modelVersion

modelVersion=int

Units: Code Min: 0 Max: 100000000

Model Version

wuID

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

assimMode

assimMode=("0" or "1")

Units: Code

Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)

mode

mode=("1" or "2" or "3" or "4")

Units: Code

Simulation mode

demography

→ scenario → demography

<demography
    name=string
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

Documentation (element)

Units: List of elements

Description of demography

Documentation (type)

Units: List of elements

Description of demography

Attributes

name

name=string

Units: string

Name of demography data

growthRate

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population.

ageGroup

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

List of age groups included in demography or surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

poppercent

poppercent=double

upperbound

upperbound=double

monitoring

→ scenario → monitoring

<monitoring
    name=string
  >
IN THIS ORDER:
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Units: List of elements

Description of surveys

Documentation (type)

Units: List of elements

Description of surveys

Attributes

name

name=string

Units: string

Name of monitoring data

surveys

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
    summaryOption=int
  >
IN THIS ORDER:
|   <surveyTime ... /> 
</surveys>

surveyTime

Documentation (element)

Units: List of elements

List of survey times

Attributes

detectionLimit

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

summaryOption

summaryOption=int

Units: Code

Requested output variables

surveyTime

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time

ageGroup

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upperbound

upperbound=double

interventions

<interventions
    name=string
  >
IN THIS ORDER:
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

Units: List of elements

List of interventions

Documentation (type)

Units: List of elements

List of interventions

Attributes

name

name=string

Units: string

Name of age specific intervention

vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

vaccineType

vaccineType=int

Units: Code

Type of vaccine

halfLifeYrs

→ scenario → interventions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

value

value=double

TODO

efficacyB

→ scenario → interventions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

value

value=double

TODO

initialEfficacy

→ scenario → interventions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

value

value=double

TODO

iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=int
  />

Attributes

name

name=string

Units: string

Name of age specific intervention

freq

freq=double

ACR

ACR=double

proph

proph=int

tolPeriod

tolPeriod=int

atten

atten=int

continuous

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
</continuous>

vaccine

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for vaccination

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

timed

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <IRS ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <ipti ... /> ]
</intervention>

Attributes

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</changeHS>

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

drugRegimen

→ scenario → healthSystem → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Units: List of elements

Description of drug regimen

Attributes

firstLine

firstLine=string

Units: Drug code

Code for first line drug

secondLine

secondLine=string

Units: Drug code

Code for second line drug

inpatient

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

initialACR

→ scenario → healthSystem → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

CQ

→ scenario → healthSystem → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

value

value=double

TODO

SP

→ scenario → healthSystem → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

value

value=double

TODO

AQ

→ scenario → healthSystem → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

value

value=double

TODO

SPAQ

→ scenario → healthSystem → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

value

value=double

TODO

ACT

→ scenario → healthSystem → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

value

value=double

TODO

QN

→ scenario → healthSystem → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

value

value=double

TODO

selfTreatment

→ scenario → healthSystem → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

value

value=double

TODO

compliance

→ scenario → healthSystem → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

pSeekOfficialCareUncomplicated1

→ scenario → healthSystem → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSelfTreatUncomplicated

→ scenario → healthSystem → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

value

value=double

TODO

pSeekOfficialCareUncomplicated2

→ scenario → healthSystem → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSeekOfficialCareSevere

→ scenario → healthSystem → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease seeks official care

Attributes

value

value=double

TODO

pSequelaeInpatient

<pSequelaeInpatient>
IN THIS ORDER:
| ( <item ... /> )+
</pSequelaeInpatient>

item

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients

item

→ scenario → healthSystem → pSequelaeInpatient → item

<item
    value=double
    maxAgeYrs=double
  />

Attributes

value

value=double

TODO

maxAgeYrs

maxAgeYrs=double

Units: Years Min: 0 Max: 100

Upper bound of age group

CFR

→ scenario → healthSystem → CFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

group

→ scenario → healthSystem → CFR → group

<group
    cfr=double
    lowerbound=double
  />

Attributes

cfr

cfr=double

Units: Proportion Min: 0 Max: 1

Case fatality rate

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

changeEIR

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    name=string
    inputType=("EIR" or "Fourier")
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | ( <EIRDaily ... /> )+
| | ( <anopheles ... /> )+
</changeEIR>

Documentation (type)

Units: List of elements

Data for entomodel: TODO: choice element

Attributes

name

name=string

Units: string

Name of entomology data

inputType

inputType=("EIR" or "Fourier")

EIRDaily

→ scenario → entoData → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Units: Number Min: 0

Value of daily EIR

Attributes

origin

origin=string

anopheles

→ scenario → entoData → anopheles

<anopheles
    mosquito=string
    useNv0Guess=boolean
  >
IN THIS ORDER:
|   <eir ... /> 
|   <mosq ... /> 
</anopheles>

eir
mosq

Attributes

mosquito

mosquito=string

useNv0Guess

useNv0Guess=boolean

eir

→ scenario → entoData → anopheles → eir

<eir
    a0=double
    a1=double
    a2=double
    b1=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

Units: Element

Description of entomological inoculation rate

Attributes

a0

a0=double

a1

a1=double

a2

a2=double

b1

b1=double

b2

b2=double

EIRRotateAngle

EIRRotateAngle=double

mosq

→ scenario → entoData → anopheles → mosq

<mosq
    mosqRestDuration=int
    mosqSeekingDeathRate=double
    mosqSeekingDuration=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
  />

Documentation (element)

Units: List of elements

Vector species

Attributes

mosqRestDuration

mosqRestDuration=int

mosqSeekingDeathRate

mosqSeekingDeathRate=double

mosqSeekingDuration

mosqSeekingDuration=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

mosqProbOvipositing

mosqProbOvipositing=double

MDA

→ scenario → interventions → timed → intervention → MDA

<MDA
    maxAge=double
    minAge=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of mass drug deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IRS

→ scenario → interventions → timed → intervention → IRS

<IRS/>

vaccinate

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
    maxAge=double
    minAge=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of vaccine deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → timed → intervention → ITN

<ITN
    maxAge=double
    minAge=double
    coverage=double
  />

Documentation (element)

Units: List of elements

Description of ITN deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → timed → intervention → ipti

<ipti
    maxAge=double
    minAge=double
    coverage=double
  />

Documentation (element)

Units: List of elements

List of age groups for IPTi distribution

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

caseManagements

<caseManagements
    name=string
  >
IN THIS ORDER:
| ( <caseManagement ... /> )+
</caseManagements>

caseManagement

Documentation (element)

Units: List of elements

List of case managment interventions

Documentation (type)

Units: List of elements

List of age-specific case managment descriptions

Attributes

name

name=string

Units: string

Name of age specific intervention

caseManagement

<caseManagement
  [ minAgeYrs=decimal ]
    maxAgeYrs=decimal
  >
IN THIS ORDER:
|   <uc1 ... /> 
|   <uc2 ... /> 
|   <sev ... /> 
|   <nmf ... /> 
|   <decisions ... /> 
</caseManagement>

Documentation (element)

Units: List of elements

Age-specific case management description, describes entry-points and decisions, with entry-point-specific decision probabilities

Attributes

minAgeYrs

minAgeYrs=decimal

maxAgeYrs

maxAgeYrs=decimal

Units: Years Min: 0 Max: 100

Upper bound of age group

uc1

→ scenario → caseManagements → caseManagement → uc1

<uc1>
IN THIS ORDER:
| ( <endPoint ... /> )+
</uc1>

endPoint

endPoint

→ scenario → caseManagements → caseManagement → uc1 → endPoint

<endPoint
    decision=int
    p=double
  />

Attributes

decision

decision=int

Foreign key reference to outcome node

p

p=double

Units: Proportion Min: 0 Max: 1

Probability of outcome

uc2

→ scenario → caseManagements → caseManagement → uc2

<uc2>
IN THIS ORDER:
| ( <endPoint ... /> )+
</uc2>

endPoint

sev

→ scenario → caseManagements → caseManagement → sev

<sev>
IN THIS ORDER:
| ( <endPoint ... /> )+
</sev>

endPoint

nmf

→ scenario → caseManagements → caseManagement → nmf

<nmf>
IN THIS ORDER:
| ( <endPoint ... /> )+
</nmf>

endPoint

decisions

→ scenario → caseManagements → caseManagement → decisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )+
</decisions>

decision

decision

→ scenario → caseManagements → caseManagement → decisions → decision

<decision
    id=int
  >
IN THIS ORDER:
| ( <medicate ... /> )+
</decision>

medicate

Documentation (element)

Units: List of elements

describes treatment decisions, a list of medicate descisions.

Attributes

id

id=int

Units: Number

Key of decision

medicate

→ scenario → caseManagements → caseManagement → decisions → decision → medicate

<medicate
    name=string
    qty=int
    time=int
  />

Attributes

name

name=string

Units: string

Name of drug compound

qty

qty=int

Units: Number

Quantity of drug compound

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

healthSystem

→ scenario → healthSystem

<healthSystem
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</healthSystem>

Documentation (element)

Units: List of elements

Description of health system

Documentation (type)

Units: List of elements

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

entoData

→ scenario → entoData

<entoData
    name=string
    inputType=("EIR" or "Fourier")
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | ( <EIRDaily ... /> )+
| | ( <anopheles ... /> )+
</entoData>

Documentation (element)

Units: List of elements

Description of entomological data

Documentation (type)

Units: List of elements

Data for entomodel: TODO: choice element

Attributes

name

name=string

Units: string

Name of entomology data

inputType

inputType=("EIR" or "Fourier")

parameters

→ scenario → parameters

<parameters
    interval=int
    iseed=int
    delta=double
    eipDuration=int
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

parameter

Documentation (element)

Parameters for mathematical model

Documentation (type)

Units: List of elements

Parameter vector

Attributes

interval

interval=int

Units: Days

Simulation step

iseed

iseed=int

Units: Number

Seed for RNG

delta

delta=double

Units: ? Redundant

this no longer seems to be used

eipDuration

eipDuration=int

Units: Count Min: 0 Max: 50

The duration of sporogony in days

latentp

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

→ scenario → parameters → parameter

<parameter
    name=string
    number=int
    value=double
  [ include=boolean ]
  />

Attributes

name

name=string

Units: string

Name of parameter

number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

value

value=double

Units: Number Min: 0

Parameter value

include

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

Schema 2 documentation

Generated from: scenario_2.xsd.

Key:

  abc           required (one)
[ def ]         optional (zero or one)
( ghi )*        any number (zero or more)
( jkl )+        at least one
( mno ){2,inf}  two or more occurrences

scenario

→ scenario

<scenario
    schemaVersion=int
    analysisNo=int
    maximumAgeYrs=double
    name=string
    popSize=int
    simulationDuration=int
    modelVersion=int
    wuID=int
    assimMode=("0" or "1")
    mode=("1" or "2" or "3" or "4")
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="scenario_2.xsd"
  >
IN THIS ORDER:
|   <demography ... /> 
|   <monitoring ... /> 
|   <interventions ... /> 
| [ <caseManagements ... /> ]
|   <healthSystem ... /> 
|   <entoData ... /> 
|   <parameters ... /> 
</scenario>

Documentation (element)

Units: List of elements

Description of scenario

Attributes

schemaVersion

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

analysisNo

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

maximumAgeYrs

maximumAgeYrs=double

Units: Number Min: 0 Max: 100

Maximum age of simulated humans

name

name=string

Units: string

Name of intervention

popSize

popSize=int

Units: Count Min: 1 Max: 100000

Population size

simulationDuration

simulationDuration=int

Units: Time steps Min: 1 Max: 36500

Duration of main simulation

modelVersion

modelVersion=int

Units: Code Min: 0 Max: 100000000

Model Version

wuID

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

assimMode

assimMode=("0" or "1")

Units: Code

Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)

mode

mode=("1" or "2" or "3" or "4")

Units: Code

Simulation mode

demography

→ scenario → demography

<demography
    name=string
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

ageGroup

name=string

Units: string

Name of demography data

growthRate

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population.

ageGroup

→ scenario → demography → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

poppercent

poppercent=double

upperbound

upperbound=double

monitoring

→ scenario → monitoring

<monitoring
    name=string
  >
IN THIS ORDER:
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

name=string

Units: string

Name of monitoring data

surveys

→ scenario → monitoring → surveys

<surveys
    detectionLimit=double
    summaryOption=int
  >
IN THIS ORDER:
|   <surveyTime ... /> 
</surveys>

surveyTime

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

summaryOption

summaryOption=int

Units: Code

Requested output variables

surveyTime

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

Survey time

ageGroup

→ scenario → monitoring → ageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

group

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upperbound

upperbound=double

interventions

<interventions
    name=string
  >
IN THIS ORDER:
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| [ <ITNDescription ... /> ]
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

name=string

Units: string

Name of age specific intervention

vaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

vaccineType

vaccineType=int

Units: Code

Type of vaccine

halfLifeYrs

→ scenario → interventions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

value=double

TODO

efficacyB

→ scenario → interventions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

value=double

TODO

initialEfficacy

→ scenario → interventions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

value

value=double

TODO

iptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

infGenotype

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → iptiDescription → infGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=int
  />

Attributes

name

name=string

Units: string

Name of age specific intervention

freq

freq=double

ACR

ACR=double

proph

proph=int

tolPeriod

tolPeriod=int

atten

atten=int

ITNDescription

→ scenario → interventions → ITNDescription

<ITNDescription>
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <pu0 ... /> 
|   <pu1 ... /> 
|   <sporogonyGonotrophy ... /> 
</ITNDescription>

halfLifeYrs

→ scenario → interventions → ITNDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

value=double

TODO

pu0

→ scenario → interventions → ITNDescription → pu0

<pu0
    value=double
  />

value=double

TODO

pu1

→ scenario → interventions → ITNDescription → pu1

<pu1
    value=double
  />

value=double

TODO

sporogonyGonotrophy

→ scenario → interventions → ITNDescription → sporogonyGonotrophy

<sporogonyGonotrophy
    value=double
  />

value=double

TODO

continuous

→ scenario → interventions → continuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
</continuous>

vaccine

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  />

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  />

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  />

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

timed

→ scenario → interventions → timed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

intervention

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <IRS ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <ipti ... /> ]
</intervention>

Attributes

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</changeHS>

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

drugRegimen

→ scenario → healthSystem → drugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

firstLine=string

Units: Drug code

Code for first line drug

secondLine

secondLine=string

Units: Drug code

Code for second line drug

inpatient

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

initialACR

→ scenario → healthSystem → initialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

CQ

→ scenario → healthSystem → initialACR → CQ

<CQ
    value=double
  />

value=double

TODO

SP

→ scenario → healthSystem → initialACR → SP

<SP
    value=double
  />

value=double

TODO

AQ

→ scenario → healthSystem → initialACR → AQ

<AQ
    value=double
  />

value=double

TODO

SPAQ

→ scenario → healthSystem → initialACR → SPAQ

<SPAQ
    value=double
  />

value=double

TODO

ACT

→ scenario → healthSystem → initialACR → ACT

<ACT
    value=double
  />

value=double

TODO

QN

→ scenario → healthSystem → initialACR → QN

<QN
    value=double
  />

value=double

TODO

selfTreatment

→ scenario → healthSystem → initialACR → selfTreatment

<selfTreatment
    value=double
  />

value=double

TODO

compliance

→ scenario → healthSystem → compliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

nonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

pSeekOfficialCareUncomplicated1

→ scenario → healthSystem → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

value=double

TODO

pSelfTreatUncomplicated

→ scenario → healthSystem → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

value=double

TODO

pSeekOfficialCareUncomplicated2

→ scenario → healthSystem → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

value=double

TODO

pSeekOfficialCareSevere

→ scenario → healthSystem → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

value=double

TODO

pSequelaeInpatient

<pSequelaeInpatient>
IN THIS ORDER:
| ( <item ... /> )+
</pSequelaeInpatient>

item

Documentation (element)

Units: List of elements

List of age specific probabilities of sequelae in inpatients

item

→ scenario → healthSystem → pSequelaeInpatient → item

<item
    value=double
    maxAgeYrs=double
  />

Attributes

value

value=double

TODO

maxAgeYrs

maxAgeYrs=double

Units: Years Min: 0 Max: 100

Upper bound of age group

CFR

→ scenario → healthSystem → CFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

group

→ scenario → healthSystem → CFR → group

<group
    cfr=double
    lowerbound=double
  />

Attributes

cfr

cfr=double

Units: Proportion Min: 0 Max: 1

Case fatality rate

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

changeEIR

→ scenario → interventions → timed → intervention → changeEIR

<changeEIR
    name=string
    inputType=("EIR" or "Fourier")
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| | ( <EIRDaily ... /> )+
| | ( <anopheles ... /> )+
</changeEIR>

name=string

Units: string

Name of entomology data

inputType

inputType=("EIR" or "Fourier")

EIRDaily

→ scenario → entoData → EIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

origin=string

anopheles

→ scenario → entoData → anopheles

<anopheles
    mosquito=string
    useNv0Guess=boolean
  >
IN THIS ORDER:
|   <eir ... /> 
|   <mosq ... /> 
</anopheles>

eir
mosq

Attributes

mosquito

mosquito=string

useNv0Guess

useNv0Guess=boolean

eir

→ scenario → entoData → anopheles → eir

<eir
    a0=double
    a1=double
    a2=double
    b1=double
    b2=double
    EIRRotateAngle=double
  />

a0=double

a1

a1=double

a2

a2=double

b1

b1=double

b2

b2=double

EIRRotateAngle

EIRRotateAngle=double

mosq

→ scenario → entoData → anopheles → mosq

<mosq
    mosqRestDuration=int
    mosqSeekingDeathRate=double
    mosqSeekingDuration=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
  />

mosqRestDuration=int

mosqSeekingDeathRate

mosqSeekingDeathRate=double

mosqSeekingDuration

mosqSeekingDuration=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

mosqProbOvipositing

mosqProbOvipositing=double

MDA

→ scenario → interventions → timed → intervention → MDA

<MDA
    maxAge=double
    minAge=double
    coverage=double
  />

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IRS

→ scenario → interventions → timed → intervention → IRS

<IRS/>

vaccinate

→ scenario → interventions → timed → intervention → vaccinate

<vaccinate
    maxAge=double
    minAge=double
    coverage=double
  />

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

→ scenario → interventions → timed → intervention → ITN

<ITN
    maxAge=double
    minAge=double
    coverage=double
  />

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

→ scenario → interventions → timed → intervention → ipti

<ipti
    maxAge=double
    minAge=double
    coverage=double
  />

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

caseManagements

<caseManagements
    name=string
  >
IN THIS ORDER:
| ( <caseManagement ... /> )+
</caseManagements>

caseManagement

name=string

Units: string

Name of age specific intervention

caseManagement