def_interventions_effects.RdThis function defines the survival and effects of interventions on the transition probabilities between the consecutive stages of the mosquito oviposition cycle. These values are given for a set of interpolation points which are uniformly distributed across the duration of the intervention. To define the effects, this function either uses the intervention models which are available in the AnophelesModel database, or directly receives the vectors with the intervention effects for interventions which are not present in the database. In the latter case, it is assumed that the provided intervention effects values are adjusted according to the mosquito bionomics, activity patterns of mosquitoes and humans, as well as human exposure to mosquitoes.
def_interventions_effects(
intervention_list,
model_p,
num_ip_points = 100,
verbose = TRUE
)list of intervention objects, where each object is itself a list with the following attributes:
id: string with the intervention ID; for intervention IDs
available in the package, check list_available_interventions()
description: short string with the description of
the intervention; can be used to differentiate between
interventions which have the same ID
parameterisation: string corresponding to the name of the
intervention parameterisation to be used to calculate the transition
probabilities. To use a parameterisation available in the
package database, this attribute needs to match one of the parameterisations
(column "Parameterisation") retrieved with list_intervention_models().
To use a new parameterisation which is
not present in the package database, this
argument can contain any name chosen by the user and the attribute
effects needs to be provided as well (see description below).
LLIN_type: a string containing the LLIN type,
only needed to be specified for LLINs interventions intending to use
the LLINs models parameters provided with the package
LLIN_insecticide: a string containing the LLIN insecticide type,
only needed for LLINs interventions intending to
use the LLIN models parameters provided with the package,
LLIN_country: a string containing the country where the LLIN
characteristics were measured, only provided for LLINs interventions
intending to use the LLIN models parameters provided with the package
effects: list of intervention survival and effects on the
mosquito oviposition cycle. This attribute allows defining intervention
effects which are not in the package database and is optional
if parameterisation matches one of the intervention parameterisations
available in the package database. These effects include, in addition to the
availability to mosquitoes and the proportion of infected mosquitoes, the
transition probabilities between the consecutive stages of the
oviposition cycle. The decay of the effects can also be specified if
generation of a <GVI> xml snippet for OpenMalaria simulations is envisaged.
The effects are defined through the following list attributes:
host_types: for reference only, vector of strings coding the
different types of hosts, must be equal to
{"protected humans", "unprotected humans", "animals"}. All the remaining
attributes of the effects object, except for survival
are represented by 3-column matrices, where each column,
j={1, 2, 3}, corresponds to values for the three types of hosts
defined in the same order as for host_types
Kvi: proportion of susceptible mosquitoes that become
infected after biting a host of type j, contains one row and 3 columns
alphai: availability of a host of type j to mosquitoes, contains
num_ip_points rows and 3 columns
PBi: probability that a mosquito bites a host of type j,
contains num_ip_points rows and 3 columns
PCi: probability that a mosquito finds a resting place after
biting a host of type j, contains num_ip_points rows and 3 columns
PDi: probability that a mosquito survives the resting phase
after biting a host of type j, contains num_ip_points
rows and 3 columns
PEi: probability that a mosquito lays eggs and
returns to host-seeking after biting a host of type j,
contains num_ip_points rows and 3 columns
survival: survival of the intervention,
vector of length num_ip_points
alphai_decay: decay of intervention effect on host availability
to mosquitoes, contains num_ip_points rows and 3 columns
PBi_decay: decay of intervention effect on
the probability that a mosquito bites a
host of type j, contains num_ip_points rows and 3 columns
PCi_decay: decay of intervention effect on
the probability that a mosquito finds a
resting place after biting a host of type j,
contains num_ip_points rows and 3 columns
For the above attributes with num_ip_points rows, the values are
provided for
consecutive time points equally distributed throughout the duration of the
intervention. The number of time points needs to match the provided argument
n_time_points.
model object
(generated with function build_model_obj())
number of interpolation points, default is 100. If
custom intervention effects are specified, the relevant effect attributes
need to have a number of rows equal to num_ip_points (see above)
boolean specifying whether any messages should be displayed during the execution of the function. Default value is TRUE.
list object with the following attributes:
id: string with the intervention ID
description: short string with the description of
the intervention
parameterisation: string corresponding to the name of the
intervention parameterisation
LLIN_type: only for LLINs, a string containing the LLIN type
LLIN_insecticide: only for LLINs, a string containing the
LLIN insecticide type
LLIN_country: only for LLINs, a string containing the country
where the LLIN characteristics were measured
model_p: model object provided as input