Man pages for SwissTPH/r-openMalariaUtilities
Helper functions to provide easier usage of Open Malaria from R
| ageGroupsGen | Generate list for 'demography/ageGroup' |
| BEN | Demographic data from Benin |
| changeHSCFRGen | Generate list for 'changeHS/CFR' |
| changeHSpSeqInGen | Generate list for 'changeHS/SpSeq' |
| cleanLogs | Clean log directories |
| cleanupExperiment | Cleanup an experiment |
| clearCache | Remove all objects from cache. |
| CMR | Demographic data from Cameroon |
| collectResults | Collect Open Malaria results into a database |
| createBaseXml | Create a base XML file and folder structure |
| defineChangeHS | Write the case management deployments |
| define_changeHS_compat | Function to write the case management deployments |
| defineDemography | Define and write demography input to baseList |
| defineEntomology | Defines entomology setting |
| defineHealthSystem | Writes the health system part |
| defineImportedInfections | Writes importation intervention |
| define_importedInfections_compat | Writes importation intervention |
| defineIRS | Adds the IRS intervention parameterisation |
| define_IRS_compat | Adds the IRS intervention parameterisation. Compatibility... |
| defineITN | Writes the ITN intervention parameterisation xml chunk |
| define_ITN_compat | Writes the ITN intervention parameterisation xml chunk.... |
| defineLarv | Function that writes the larviciding component |
| define_larv_compat | Function that writes the larviciding component xml chunk |
| defineNothing | Writes an intervention parameterisation xml chunk that does... |
| define_nothing_compat | Writes an intervention parameterisation xml chunk that does... |
| defineTreatSimple | SMC, MDA parameterization section |
| defineVaccine | Adds vaccine intervention parameterisation to baseList |
| defineVectorControl | Adds vector control intervention parameterisation to baseList |
| deleteLogs | Remove all files from the log directory |
| deploy_cont_compat | Deployment of an continuous intervention |
| deployIT | Writes the deployment of an intervention. |
| deploy_it_compat | Writes the deployment of an intervention. Compatibility... |
| dot-addExpToDB | Add data to experiments table in DB |
| dot-addPlaceholdersToDB | Add data to placeholders table in DB |
| dot-addResultsToDB | Add data to results table in DB |
| dot-addScenToDB | Add data to scenarios and scenarios_metadata table in DB |
| dot-calculateSmoothCompact | Calculate smooth compact decay parameters |
| dot-calculateSmoothCompactHalflife | Calculate smooth compact halflife |
| dot-compressFiles | Compress files into zip archive |
| dot-createDB | Create a database connection |
| dot-createFolders | Create folder structure |
| dot-createResultsTable | Create the DB result table |
| dot-createTables | Create the DB table layout, except the results table |
| dot-defineInterventionsHeader | Make sure required elements are declared |
| dot-deployTime_compat | Basic function used for deploying interventions |
| dot-equalizePlaceholders | Equalize length of placeholder sequences |
| dot-getIndex | Search for name and/or value |
| dot-indexList | Build index of a list recursively |
| dot-makeXmlRoot | Generate XML root |
| dot-placeholderCollect | Collect if current value is a placeholder |
| dot-placeholderseqGen | Generate placeholder sequence |
| dot-printDebug | Print debug messages |
| dot-printVerbose | Print verbose messages |
| dot-recXML | Recursively create XML |
| dot-scenariosFilenames | Add a filename column to scenarios |
| dot-scenariosGenFiles | Generate scenario xml files |
| dot-scenariosRowSelect | Select rows for scenario creation |
| dot-setFunArgs | Override default function arguments |
| dot-syncBoth | Synchronize diskCache and memCache |
| dot-syncDisk | Writes .pkgcache to disk |
| dot-synchronizeCache | Synchronize the Cache |
| dot-syncMem | Assign values from diskCache to .pkgcache |
| dot-unqouteExpr | Unqoute expression |
| dot-useDir | Create a folder and return the path |
| dot-xmlAddChunks | Generate XML chunks |
| dot-xmlAddList | Add sublist to list |
| dot-xmlMakeDocRec | Create xml entries recursively |
| dot-xmlMonitoringTimeRegularSeq | Generate a date sequence |
| dot-xmlTimeBlockSeq | Generate date sequence based on specified days, months and... |
| dot-xmlTimeRegularSeq | Generate date sequence based on start and end date |
| expInfo | Collect information about current experiment |
| extractList | Extract sublist which matches input |
| finalizeScenarios | Generate scenarios from a base xml file |
| getCache | Get cached object from cache. |
| GHA | Demographic data from Ghana |
| HTI | Demographic data from Haiti |
| listCache | List objects and values in cache. |
| loadExperiment | 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' |
| MOZ | Demographic data from Mozambique |
| omOutputDict | Open Malaria output dictionary |
| processFile | Read file line by line |
| putCache | Store object in cache. |
| readOutputFile | Read Open Malaria output file |
| readResults | Collect Open Malaria results into a database |
| readScenarios | Return cached scenarios |
| runSimulations | Run openMalaria scenarios |
| setupDirs | Create folder structure |
| setupOM | Download required Open Malaria files |
| setupScenarios | Generate scenarios from a base xml file |
| splitSeq | Divide a sequence x into chunks of size n. Any rest is... |
| storeScenarios | Store scenarios in cache folder |
| surveyAgeGroupsGen | Generate list for 'monitoring/ageGroup' |
| syncCache | Synchronized cached data from experiment |
| toggleDebug | Toggle debug messages |
| toggleVerbose | Toggle verbose messages |
| TZA | Demographic data from Tanzania |
| UGA | Demographic data from Uganda |
| validateXML | Validate the XML file |
| writeCache | 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 |
