Files in SwissTPH/r-openMalariaUtilities

Helper functions to provide easier usage of Open Malaria from R

.github/workflows/example.R CONTRIBUTING.md LICENSE.md NEWS.md R/base.R R/cache.R R/data.R R/db.R R/directories.R R/logs.R R/om_output_dict.R R/pkg_setup.R R/printing.R R/scenarios.R R/simulation.R R/time.R R/utils.R R/xml.R R/xml_demography.R R/xml_entomology_define.R R/xml_healthSystem.R R/xml_interventions.R R/xml_interventions_changeHS.R R/xml_interventions_define.R R/xml_interventions_deploy.R R/xml_model.R R/xml_monitoring.R R/xml_root.R R/xml_validation.R README.md data-raw/demography.R man/BEN.Rd man/CMR.Rd man/GHA.Rd man/HTI.Rd man/MOZ.Rd man/TZA.Rd man/UGA.Rd man/ageGroupsGen.Rd man/changeHSCFRGen.Rd man/changeHSpSeqInGen.Rd man/cleanLogs.Rd man/cleanupExperiment.Rd man/clearCache.Rd man/collectResults.Rd man/createBaseXml.Rd man/defineChangeHS.Rd man/defineDemography.Rd man/defineEntomology.Rd man/defineHealthSystem.Rd man/defineIRS.Rd man/defineITN.Rd man/defineImportedInfections.Rd man/defineLarv.Rd man/defineNothing.Rd man/defineTreatSimple.Rd man/defineVaccine.Rd man/defineVectorControl.Rd man/define_IRS_compat.Rd man/define_ITN_compat.Rd man/define_changeHS_compat.Rd man/define_importedInfections_compat.Rd man/define_larv_compat.Rd man/define_nothing_compat.Rd man/deleteLogs.Rd man/deployIT.Rd man/deploy_cont_compat.Rd man/deploy_it_compat.Rd man/dot-addExpToDB.Rd man/dot-addPlaceholdersToDB.Rd man/dot-addResultsToDB.Rd man/dot-addScenToDB.Rd man/dot-calculateSmoothCompact.Rd man/dot-calculateSmoothCompactHalflife.Rd man/dot-compressFiles.Rd man/dot-createDB.Rd man/dot-createFolders.Rd man/dot-createResultsTable.Rd man/dot-createTables.Rd man/dot-defineInterventionsHeader.Rd man/dot-deployTime_compat.Rd man/dot-equalizePlaceholders.Rd man/dot-getIndex.Rd man/dot-indexList.Rd man/dot-makeXmlRoot.Rd man/dot-placeholderCollect.Rd man/dot-placeholderseqGen.Rd man/dot-printDebug.Rd man/dot-printVerbose.Rd man/dot-recXML.Rd man/dot-scenariosFilenames.Rd man/dot-scenariosGenFiles.Rd man/dot-scenariosRowSelect.Rd man/dot-setFunArgs.Rd man/dot-syncBoth.Rd man/dot-syncDisk.Rd man/dot-syncMem.Rd man/dot-synchronizeCache.Rd man/dot-unqouteExpr.Rd man/dot-useDir.Rd man/dot-xmlAddChunks.Rd man/dot-xmlAddList.Rd man/dot-xmlMakeDocRec.Rd man/dot-xmlMonitoringTimeRegularSeq.Rd man/dot-xmlTimeBlockSeq.Rd man/dot-xmlTimeRegularSeq.Rd man/expInfo.Rd man/extractList.Rd man/finalizeScenarios.Rd man/getCache.Rd man/listCache.Rd man/loadExperiment.Rd man/make_ento_compat.Rd man/monitoringCohortsGen.Rd man/monitoringContinuousGen.Rd man/monitoringSurveyOptionsGen.Rd man/monitoringSurveyTimesGen.Rd man/omOutputDict.Rd man/processFile.Rd man/putCache.Rd man/readOutputFile.Rd man/readResults.Rd man/readScenarios.Rd man/runSimulations.Rd man/setupDirs.Rd man/setupOM.Rd man/setupScenarios.Rd man/splitSeq.Rd man/storeScenarios.Rd man/surveyAgeGroupsGen.Rd man/syncCache.Rd man/toggleDebug.Rd man/toggleVerbose.Rd man/validateXML.Rd man/writeCache.Rd man/write_demography_compat.Rd man/write_end_compat.Rd man/write_healthsys_compat.Rd man/write_monitoring_compat.Rd man/xmlTimeGen.Rd tests/testthat.R tests/testthat/test-base.R tests/testthat/test-cache.R tests/testthat/test-db.R tests/testthat/test-directories.R tests/testthat/test-logs.R tests/testthat/test-printing.R tests/testthat/test-scenarios.R tests/testthat/test-simulation.R tests/testthat/test-time.R tests/testthat/test-utils.R tests/testthat/test-validation.R tests/testthat/test-xml.R tests/testthat/test-xml_demography.R tests/testthat/test-xml_entomology_define.R tests/testthat/test-xml_healthSystem.R tests/testthat/test-xml_interventions.R tests/testthat/test-xml_interventions_changeHS.R tests/testthat/test-xml_interventions_define.R tests/testthat/test-xml_interventions_deploy.R tests/testthat/test-xml_model.R tests/testthat/test-xml_monitoring.R tests/testthat/test-xml_root.R vignettes/collectResults.Rmd vignettes/faq.Rmd vignettes/om_example.R vignettes/openmalariautilities.Rmd vignettes/scenarios.Rmd