extras/CreatePositiveControlSynthesisDetails.R

In ohdsi-studies/TicagrelorVsClopidogrel: A Package Skeleton for Comparative Effectiveness Studies

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"))
}