Function reference • openMalariaUtilities

All functions

BEN: Demographic data from Benin

CMR: Demographic data from Cameroon

GHA: Demographic data from Ghana

HTI: Demographic data from Haiti

MOZ: Demographic data from Mozambique

TZA: Demographic data from Tanzania

UGA: Demographic data from Uganda

ageGroupsGen(): Generate list for 'demography/ageGroup'

changeHSCFRGen(): Generate list for 'changeHS/CFR'

changeHSpSeqInGen(): Generate list for 'changeHS/SpSeq'

cleanLogs() clean_logs(): Clean log directories

cleanupExperiment(): Cleanup an experiment

clearCache() clear_cache(): Remove all objects from cache.

collectResults() collect_results(): Collect Open Malaria results into a database

createBaseXml() create_base_xml(): Create a base XML file and folder structure

defineChangeHS() define_changeHS(): Write the case management deployments

defineDemography() define_demography(): Define and write demography input to baseList

defineEntomology() define_entomology(): Defines entomology setting

defineHealthSystem() define_health_system(): Writes the health system part

defineIRS() define_IRS(): Adds the IRS intervention parameterisation

defineITN() define_ITN(): Writes the ITN intervention parameterisation xml chunk

defineImportedInfections() define_importedInfections(): Writes importation intervention

defineLarv() define_larv(): Function that writes the larviciding component

defineNothing() define_nothing(): Writes an intervention parameterisation xml chunk that does nothing

defineTreatSimple() define_treatSimple() define_treatSimple_compat(): SMC, MDA parameterization section

defineVaccine() define_vaccine(): Adds vaccine intervention parameterisation to baseList

defineVectorControl() define_vector_control(): Adds vector control intervention parameterisation to baseList

define_IRS_compat(): Adds the IRS intervention parameterisation. Compatibility version.

define_ITN_compat(): Writes the ITN intervention parameterisation xml chunk. Compatibility version.

define_changeHS_compat(): Function to write the case management deployments

define_importedInfections_compat(): Writes importation intervention

define_larv_compat(): Function that writes the larviciding component xml chunk

define_nothing_compat(): Writes an intervention parameterisation xml chunk that does nothing. Compatibility version.

deleteLogs() delete_logs(): Remove all files from the log directory

deployIT() deploy_IT(): Writes the deployment of an intervention.

deploy_cont_compat(): Deployment of an continuous intervention

deploy_it_compat(): Writes the deployment of an intervention. Compatibility version.

.calculateSmoothCompact(): Calculate smooth compact decay parameters

.calculateSmoothCompactHalflife(): Calculate smooth compact halflife

.deployTime_compat(): Basic function used for deploying interventions

.placeholderCollect(): Collect if current value is a placeholder

.xmlTimeBlockSeq(): Generate date sequence based on specified days, months and years

expInfo(): Collect information about current experiment

extractList(): Extract sublist which matches input

finalizeScenarios() finalize_scenarios(): Generate scenarios from a base xml file

getCache() get_cache(): Get cached object from cache.

listCache() list_cache(): List objects and values in cache.

loadExperiment() load_experiment() loadCache() load_cache(): Load cached data from experiment

make_ento_compat(): Write entomology

monitoringCohortsGen(): Generate list for 'monitoring/Cohorts'

monitoringContinuousGen(): Generate list for 'monitoring/continuous/options'

monitoringSurveyOptionsGen(): Generate list for 'monitoring/continuous/options'

monitoringSurveyTimesGen(): Generate list for 'monitoring/surveys/surveyTime'

omOutputDict(): Open Malaria output dictionary

processFile(): Read file line by line

putCache() put_cache(): Store object in cache.

readOutputFile(): Read Open Malaria output file

readResults(): Collect Open Malaria results into a database

readScenarios() read_scenarios(): Return cached scenarios

runSimulations() run_simulations(): Run openMalaria scenarios

setupDirs() setup_dirs(): Create folder structure

setupOM() setup_om(): Download required Open Malaria files

setupScenarios() setup_scenarios(): Generate scenarios from a base xml file

splitSeq(): Divide a sequence x into chunks of size n. Any rest is appended.

storeScenarios() store_scenarios(): Store scenarios in cache folder

surveyAgeGroupsGen(): Generate list for 'monitoring/ageGroup'

syncCache() sync_cache(): Synchronized cached data from experiment

toggleDebug(): Toggle debug messages

toggleVerbose(): Toggle verbose messages

validateXML() validate_xml(): Validate the XML file

writeCache() write_cache(): Write cached data from experiment

write_demography_compat(): Write xml chunk for demography

write_end_compat(): Write the underlying transmission dynamics

write_healthsys_compat(): Writes the health system part of the xml file

write_monitoring_compat(): Writes the monitoring measures xml chunk

xmlTimeGen(): Generate date sequence based on start and end date