createPositiveControlSynthesisArgs <- function(workFolder) {
settings <- list(
outputIdOffset = 10000,
firstExposureOnly = TRUE,
firstOutcomeOnly = TRUE,
removePeopleWithPriorOutcomes = TRUE,
modelType = "survival",
washoutPeriod = 30,
riskWindowStart = 1,
riskWindowEnd = 365,
addExposureDaysToEnd = FALSE,
effectSizes = c(1.5, 2, 4),
precision = 0.01,
prior = Cyclops::createPrior("laplace", exclude = 0, useCrossValidation = TRUE),
control = Cyclops::createControl(cvType = "auto",
startingVariance = 0.01,
noiseLevel = "quiet",
cvRepetitions = 1,
threads = 1),
maxSubjectsForModel = 250000,
minOutcomeCountForModel = 50,
minOutcomeCountForInjection = 25,
covariateSettings = FeatureExtraction::createCovariateSettings(useDemographicsGender = TRUE,
useDemographicsAge = FALSE,
useDemographicsAgeGroup = TRUE,
useDemographicsRace = TRUE,
useDemographicsEthnicity = FALSE,
useDemographicsIndexYear = TRUE,
useDemographicsIndexMonth = TRUE,
useDemographicsPriorObservationTime = FALSE,
useDemographicsPostObservationTime = FALSE,
useDemographicsTimeInCohort = FALSE,
useDemographicsIndexYearMonth = FALSE,
useConditionOccurrenceAnyTimePrior = FALSE,
useConditionOccurrenceLongTerm = FALSE,
useConditionOccurrenceMediumTerm = FALSE,
useConditionOccurrenceShortTerm = TRUE,
useConditionOccurrencePrimaryInpatientAnyTimePrior = FALSE,
useConditionOccurrencePrimaryInpatientLongTerm = FALSE,
useConditionOccurrencePrimaryInpatientMediumTerm = FALSE,
useConditionOccurrencePrimaryInpatientShortTerm = FALSE,
useConditionEraAnyTimePrior = FALSE,
useConditionEraLongTerm = FALSE,
useConditionEraMediumTerm = FALSE,
useConditionEraShortTerm = FALSE,
useConditionEraOverlapping = FALSE,
useConditionEraStartLongTerm = FALSE,
useConditionEraStartMediumTerm = FALSE,
useConditionEraStartShortTerm = FALSE,
useConditionGroupEraAnyTimePrior = TRUE,
useConditionGroupEraLongTerm = TRUE,
useConditionGroupEraMediumTerm = FALSE,
useConditionGroupEraShortTerm = TRUE,
useConditionGroupEraOverlapping = FALSE,
useConditionGroupEraStartLongTerm = FALSE,
useConditionGroupEraStartMediumTerm = FALSE,
useConditionGroupEraStartShortTerm = FALSE,
useDrugExposureAnyTimePrior = FALSE,
useDrugExposureLongTerm = FALSE,
useDrugExposureMediumTerm = FALSE,
useDrugExposureShortTerm = FALSE,
useDrugEraAnyTimePrior = FALSE,
useDrugEraLongTerm = FALSE,
useDrugEraMediumTerm = FALSE,
useDrugEraShortTerm = FALSE,
useDrugEraOverlapping = FALSE,
useDrugEraStartLongTerm = FALSE,
useDrugEraStartMediumTerm = FALSE,
useDrugEraStartShortTerm = FALSE,
useDrugGroupEraAnyTimePrior = TRUE,
useDrugGroupEraLongTerm = TRUE,
useDrugGroupEraMediumTerm = FALSE,
useDrugGroupEraShortTerm = TRUE,
useDrugGroupEraOverlapping = FALSE,
useDrugGroupEraStartLongTerm = FALSE,
useDrugGroupEraStartMediumTerm = FALSE,
useDrugGroupEraStartShortTerm = FALSE,
useProcedureOccurrenceAnyTimePrior = TRUE,
useProcedureOccurrenceLongTerm = TRUE,
useProcedureOccurrenceMediumTerm = FALSE,
useProcedureOccurrenceShortTerm = TRUE,
useDeviceExposureAnyTimePrior = FALSE,
useDeviceExposureLongTerm = TRUE,
useDeviceExposureMediumTerm = FALSE,
useDeviceExposureShortTerm = TRUE,
useMeasurementAnyTimePrior = FALSE,
useMeasurementLongTerm = FALSE,
useMeasurementMediumTerm = FALSE,
useMeasurementShortTerm = FALSE,
useMeasurementValueAnyTimePrior = FALSE,
useMeasurementValueLongTerm = FALSE,
useMeasurementValueMediumTerm = FALSE,
useMeasurementValueShortTerm = FALSE,
useMeasurementRangeGroupAnyTimePrior = FALSE,
useMeasurementRangeGroupLongTerm = FALSE,
useMeasurementRangeGroupMediumTerm = FALSE,
useMeasurementRangeGroupShortTerm = FALSE,
useObservationAnyTimePrior = FALSE,
useObservationLongTerm = FALSE,
useObservationMediumTerm = FALSE,
useObservationShortTerm = FALSE,
useCharlsonIndex = TRUE,
useDcsi = FALSE,
useChads2 = FALSE,
useChads2Vasc = FALSE,
useDistinctConditionCountLongTerm = FALSE,
useDistinctConditionCountMediumTerm = FALSE,
useDistinctConditionCountShortTerm = FALSE,
useDistinctIngredientCountLongTerm = FALSE,
useDistinctIngredientCountMediumTerm = FALSE,
useDistinctIngredientCountShortTerm = FALSE,
useDistinctProcedureCountLongTerm = FALSE,
useDistinctProcedureCountMediumTerm = FALSE,
useDistinctProcedureCountShortTerm = FALSE,
useDistinctMeasurementCountLongTerm = FALSE,
useDistinctMeasurementCountMediumTerm = FALSE,
useDistinctMeasurementCountShortTerm = FALSE,
useDistinctObservationCountLongTerm = FALSE,
useDistinctObservationCountMediumTerm = FALSE,
useDistinctObservationCountShortTerm = FALSE,
useVisitCountLongTerm = TRUE,
useVisitCountMediumTerm = FALSE,
useVisitCountShortTerm = TRUE,
useVisitConceptCountLongTerm = FALSE,
useVisitConceptCountMediumTerm = FALSE,
useVisitConceptCountShortTerm = FALSE,
longTermStartDays = -365,
mediumTermStartDays = -180,
shortTermStartDays = -7,
endDays = 0,
includedCovariateConceptIds = c(),
addDescendantsToInclude = FALSE,
excludedCovariateConceptIds = c(1322184,40241186),
addDescendantsToExclude = TRUE,
includedCovariateIds = c())
)
ParallelLogger::saveSettingsToJson(settings, file.path(workFolder, "positiveControlSynthArgs.json"))
}
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