extras/CreateStudyAnalysisDetailsWithoutOntreatmentWithBlankingPeriod.R
In chandryou/TicagrelorVsClopidogrel: A Package Skeleton for Comparative Effectiveness Studies
# Copyright 2018 Observational Health Data Sciences and Informatics
#
# This file is part of TicagrelorVsClopidogrel
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#' Create the analyses details
#'
#' @details
#' This function creates files specifying the analyses that will be performed.
#'
#' @param workFolder Name of local folder to place results; make sure to use forward slashes
#' (/)
#'
#' @export
createAnalysesDetails <- function(workFolder) {
defaultPrior <- Cyclops::createPrior("laplace",
exclude = c(0),
useCrossValidation = TRUE)
defaultControl <- Cyclops::createControl(cvType = "auto",
startingVariance = 0.01,
noiseLevel = "quiet",
tolerance = 2e-07,
maxIterations = 2500,
cvRepetitions = 10,
seed = 1234)
defaultCovariateSettings <- 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 = TRUE,
#useConditionOccurrenceMediumTerm = TRUE,
useConditionOccurrenceShortTerm = TRUE,
#useConditionOccurrencePrimaryInpatientAnyTimePrior = FALSE,
#useConditionOccurrencePrimaryInpatientLongTerm = FALSE,
#useConditionOccurrencePrimaryInpatientMediumTerm = TRUE,
#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 = TRUE,
useDrugExposureShortTerm = TRUE,
#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 = TRUE,
#useDrugGroupEraStartLongTerm = FALSE,
#useDrugGroupEraStartMediumTerm = FALSE,
#useDrugGroupEraStartShortTerm = FALSE,
#useProcedureOccurrenceAnyTimePrior = FALSE,
useProcedureOccurrenceLongTerm = TRUE,
#useProcedureOccurrenceMediumTerm = FALSE,
useProcedureOccurrenceShortTerm = TRUE,
#useDeviceExposureAnyTimePrior = FALSE,
#useDeviceExposureLongTerm = TRUE,
#useDeviceExposureMediumTerm = FALSE,
useDeviceExposureShortTerm = TRUE,
#useMeasurementAnyTimePrior = FALSE,
#useMeasurementLongTerm = FALSE,
#useMeasurementMediumTerm = TRUE,
useMeasurementShortTerm = TRUE,
#useMeasurementValueAnyTimePrior = FALSE,
#useMeasurementValueLongTerm = FALSE,
#useMeasurementValueMediumTerm = TRUE,
useMeasurementValueShortTerm = TRUE,
#useMeasurementRangeGroupAnyTimePrior = FALSE,
#useMeasurementRangeGroupLongTerm = FALSE,
#useMeasurementRangeGroupMediumTerm = FALSE,
#useMeasurementRangeGroupShortTerm = FALSE,
#useObservationAnyTimePrior = FALSE,
#useObservationLongTerm = FALSE,
#useObservationMediumTerm = FALSE,
#useObservationShortTerm = FALSE,
#useCharlsonIndex = FALSE,
#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 = FALSE,
#useVisitConceptCountLongTerm = FALSE,
#useVisitConceptCountMediumTerm = FALSE,
#useVisitConceptCountShortTerm = FALSE,
longTermStartDays = -365,
mediumTermStartDays = -30,
shortTermStartDays = -7,
endDays = 0,
includedCovariateConceptIds = c(),
addDescendantsToInclude = FALSE,
excludedCovariateConceptIds = c(1322184,
40241186),
addDescendantsToExclude = TRUE,
includedCovariateIds = c())
# defaultCovariateSettings <- FeatureExtraction::createCovariateSettings(useDemographicsGender = TRUE,
# useDemographicsAge = FALSE,
# useDemographicsAgeGroup = TRUE,
# useConditionOccurrenceLongTerm = FALSE,
# useConditionOccurrenceMediumTerm = FALSE,
# useConditionOccurrenceShortTerm = TRUE,
# addDescendantsToInclude = FALSE,
# excludedCovariateConceptIds = c(1322184,
# 40241186),
# addDescendantsToExclude = TRUE,
# includedCovariateIds = c())
subGroupCovariateSettings <- createSubgroupCovariateSettings(windowStart = -365, windowEnd = -1,
shortTermWindowStart = -7,
MaintenanceWindowEnd = 365,
analysisId = 998)
covariateSettings <- list(defaultCovariateSettings ,subGroupCovariateSettings
)
getDbCmDataArgs <- CohortMethod::createGetDbCohortMethodDataArgs(washoutPeriod = 0,
firstExposureOnly = FALSE,
removeDuplicateSubjects = 'keep first',
restrictToCommonPeriod = TRUE,
maxCohortSize = 0,
excludeDrugsFromCovariates = FALSE,
covariateSettings = covariateSettings)
OneYearOutcome <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = FALSE,
firstExposureOnly = FALSE,
washoutPeriod = 0,
removeDuplicateSubjects = 'keep first',
minDaysAtRisk = 1,
riskWindowStart = 1,
addExposureDaysToStart = FALSE,
riskWindowEnd = 365,
addExposureDaysToEnd = FALSE,
censorAtNewRiskWindow = FALSE)
OneYearOutcomeWithBlanking <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = FALSE,
firstExposureOnly = FALSE,
washoutPeriod = 0,
removeDuplicateSubjects = 'keep first',
minDaysAtRisk = 1,
riskWindowStart = 29,
addExposureDaysToStart = FALSE,
riskWindowEnd = 365,
addExposureDaysToEnd = FALSE,
censorAtNewRiskWindow = FALSE)
# OneYearOutcomeWithMinTAR <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = FALSE,
# firstExposureOnly = FALSE,
# washoutPeriod = 0,
# removeDuplicateSubjects = 'keep first',
# minDaysAtRisk = 364,
# riskWindowStart = 1,
# addExposureDaysToStart = FALSE,
# riskWindowEnd = 365,
# addExposureDaysToEnd = FALSE,
# censorAtNewRiskWindow = FALSE)
OnTreatment <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = FALSE,
firstExposureOnly = FALSE,
washoutPeriod = 0,
removeDuplicateSubjects = 'keep first',
minDaysAtRisk = 1,
riskWindowStart = 1,
addExposureDaysToStart = FALSE,
riskWindowEnd = 0,
addExposureDaysToEnd = TRUE,
censorAtNewRiskWindow = FALSE)
OnTreatmentWithBlanking <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = FALSE,
firstExposureOnly = FALSE,
washoutPeriod = 0,
removeDuplicateSubjects = 'keep first',
minDaysAtRisk = 1,
riskWindowStart = 29,
addExposureDaysToStart = FALSE,
riskWindowEnd = 0,
addExposureDaysToEnd = TRUE,
censorAtNewRiskWindow = FALSE)
ITT <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = FALSE,
firstExposureOnly = FALSE,
washoutPeriod = 0,
removeDuplicateSubjects = 'keep first',
minDaysAtRisk = 1,
riskWindowStart = 1,
addExposureDaysToStart = FALSE,
riskWindowEnd = 9999,
addExposureDaysToEnd = FALSE,
censorAtNewRiskWindow = FALSE)
ITTwithBlanking <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = FALSE,
firstExposureOnly = FALSE,
washoutPeriod = 0,
removeDuplicateSubjects = 'keep first',
minDaysAtRisk = 1,
riskWindowStart = 29,
addExposureDaysToStart = FALSE,
riskWindowEnd = 9999,
addExposureDaysToEnd = FALSE,
censorAtNewRiskWindow = FALSE)
# timeToFirstPostIndexEvent7DaysFromTreatment <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = FALSE,
# firstExposureOnly = FALSE,
# washoutPeriod = 0,
# removeDuplicateSubjects = 'keep first',
# minDaysAtRisk = 1,
# riskWindowStart = 1,
# addExposureDaysToStart = FALSE,
# riskWindowEnd = 7,
# addExposureDaysToEnd = TRUE,
# censorAtNewRiskWindow = FALSE)
# timeToFirstPostIndexEventModifiedITT <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = FALSE,
# firstExposureOnly = FALSE,
# washoutPeriod = 0,
# removeDuplicateSubjects = FALSE,
# minDaysAtRisk = 1,
# riskWindowStart = 1,
# addExposureDaysToStart = FALSE,
# riskWindowEnd = 9999,
# addExposureDaysToEnd = FALSE,
# censorAtNewRiskWindow = TRUE)
subgroupCovariateIds <- c(1000, 2000, 3000, 4000, 5000, 6000)+subGroupCovariateSettings$analysisId #c(1998, 2998, 3998, 4998, 5998, 6998)
createPsArgs1 <- CohortMethod::createCreatePsArgs(control = defaultControl,
errorOnHighCorrelation = FALSE,
excludeCovariateIds = subgroupCovariateIds,
stopOnError = FALSE)
#trimByPsArgs<- CohortMethod::createTrimByPsArgs(trimFraction = 0.05)
oneToOneMatchOnPsArgs <- CohortMethod::createMatchOnPsArgs(maxRatio = 1,
caliper = 0.2,
caliperScale = "standardized logit")
variableRatioMatchOnPsArgs <- CohortMethod::createMatchOnPsArgs(maxRatio = 10,
caliper = 0.2,
caliperScale = "standardized logit")
# variableRatioMatchOnPsArgs <- CohortMethod::createMatchOnPsArgs(maxRatio = 100,
# caliper = 0.2,
# caliperScale = "standardized logit")
stratifyByPsArgs <- CohortMethod::createStratifyByPsArgs(numberOfStrata = 10)
#without matching arg
fitOutcomeModelArgs0 <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = FALSE,
prior = defaultPrior,
control = defaultControl)
#conditioning
fitOutcomeModelArgs1 <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = TRUE,
prior = defaultPrior,
control = defaultControl)
#Without conditioning
fitOutcomeModelArgs2 <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = FALSE,
prior = defaultPrior,
control = defaultControl)
a1 <- CohortMethod::createCmAnalysis(analysisId = 1,
description = "One-year outcome, one-to-one matching",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcome,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)
a2 <- CohortMethod::createCmAnalysis(analysisId = 2,
description = "One-year outcome, variable-ratio matching",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcome,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = variableRatioMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
a3 <- CohortMethod::createCmAnalysis(analysisId = 3,
description = "One-year outcome, stratification",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcome,
createPs = TRUE,
createPsArgs = createPsArgs1,
#trimByPs = TRUE,
#trimByPsArgs = trimByPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratifyByPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
a4 <- CohortMethod::createCmAnalysis(analysisId = 4,
description = "One-year outcome, without matching",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcome,
createPs = FALSE,
createPsArgs = NULL,
#trimByPs = TRUE,
#trimByPsArgs = trimByPsArgs,
stratifyByPs = FALSE,
stratifyByPsArgs = NULL,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs0)
a5 <- CohortMethod::createCmAnalysis(analysisId = 5,
description = "One-year outcome with blanking period, one-to-one matching ",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcomeWithBlanking,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)
a6 <- CohortMethod::createCmAnalysis(analysisId = 6,
description = "One-year outcome with blanking period, variable-ratio matchingg",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcomeWithBlanking,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = variableRatioMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
a7 <- CohortMethod::createCmAnalysis(analysisId = 7,
description = "One-year outcome with blanking period, stratification",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcomeWithBlanking,
createPs = TRUE,
createPsArgs = createPsArgs1,
#trimByPs = TRUE,
#trimByPsArgs = trimByPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratifyByPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
#####################################################
a8 <- CohortMethod::createCmAnalysis(analysisId = 8,
description = "On-treatment outcome, one-to-one matching",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)
a9 <- CohortMethod::createCmAnalysis(analysisId = 9,
description = "On-treatment outcome, variable-ratio matching",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = variableRatioMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
a10 <- CohortMethod::createCmAnalysis(analysisId = 10,
description = "On-treatment outcome, stratification",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment,
createPs = TRUE,
createPsArgs = createPsArgs1,
#trimByPs = TRUE,
#trimByPsArgs = trimByPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratifyByPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
a11 <- CohortMethod::createCmAnalysis(analysisId = 11,
description = "On-treatment outcome, without matching",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment,
createPs = FALSE,
createPsArgs = NULL,
#trimByPs = TRUE,
#trimByPsArgs = trimByPsArgs,
stratifyByPs = FALSE,
stratifyByPsArgs = NULL,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs0)
a12 <- CohortMethod::createCmAnalysis(analysisId = 12,
description = "On-treatment outcome with blanking period, one-to-one matching ",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatmentWithBlanking,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)
a13 <- CohortMethod::createCmAnalysis(analysisId = 13,
description = "On-treatment outcome with blanking period, variable-ratio matchingg",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatmentWithBlanking,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = variableRatioMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
a14 <- CohortMethod::createCmAnalysis(analysisId = 14,
description = "On-treatment outcome with blanking period, stratification",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatmentWithBlanking,
createPs = TRUE,
createPsArgs = createPsArgs1,
#trimByPs = TRUE,
#trimByPsArgs = trimByPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratifyByPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
###########################################
a15 <- CohortMethod::createCmAnalysis(analysisId = 15,
description = "ITT, one-to-one matching",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITT,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)
a16 <- CohortMethod::createCmAnalysis(analysisId = 16,
description = "ITT, variable-ratio matching",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITT,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = variableRatioMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
a17 <- CohortMethod::createCmAnalysis(analysisId = 17,
description = "ITT, stratification",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITT,
createPs = TRUE,
createPsArgs = createPsArgs1,
#trimByPs = TRUE,
#trimByPsArgs = trimByPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratifyByPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
a18 <- CohortMethod::createCmAnalysis(analysisId = 18,
description = "ITT, without matching",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITT,
createPs = FALSE,
createPsArgs = NULL,
#trimByPs = TRUE,
#trimByPsArgs = trimByPsArgs,
stratifyByPs = FALSE,
stratifyByPsArgs = NULL,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs0)
a19 <- CohortMethod::createCmAnalysis(analysisId = 19,
description = "ITT with blanking period, one-to-one matching ",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITTwithBlanking,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)
a20 <- CohortMethod::createCmAnalysis(analysisId = 20,
description = "ITT with blanking period, variable-ratio matchingg",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITTwithBlanking,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = variableRatioMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
a21 <- CohortMethod::createCmAnalysis(analysisId = 21,
description = "ITT with blanking period, stratification",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITTwithBlanking,
createPs = TRUE,
createPsArgs = createPsArgs1,
#trimByPs = TRUE,
#trimByPsArgs = trimByPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratifyByPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
##Interaction terms
fitOutcomeModelArgsI1998 <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = FALSE,
prior = defaultPrior,
interactionCovariateIds = 1998)
fitOutcomeModelArgsI2998 <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = FALSE,
prior = defaultPrior,
interactionCovariateIds = 2998)
fitOutcomeModelArgsI3998 <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = FALSE,
prior = defaultPrior,
interactionCovariateIds = 3998)
fitOutcomeModelArgsI4998 <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = FALSE,
prior = defaultPrior,
interactionCovariateIds = 4998)
fitOutcomeModelArgsI5998 <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = FALSE,
prior = defaultPrior,
interactionCovariateIds = 5998)
fitOutcomeModelArgsI6998 <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = FALSE,
prior = defaultPrior,
interactionCovariateIds = 6998)
fitOutcomeModelArgsI9998 <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = FALSE,
prior = defaultPrior,
interactionCovariateIds = subgroupCovariateIds)
a79 <- CohortMethod::createCmAnalysis(analysisId = 79,
description = "One-year outcome, matching, femal interaction",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcome,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgsI1998)
a29 <- CohortMethod::createCmAnalysis(analysisId = 29,
description = "One-year outcome, matching, elderly interaction",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcome,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgsI2998)
a39 <- CohortMethod::createCmAnalysis(analysisId = 39,
description = "One-year outcome, matching, black or aftrican race interaction",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcome,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgsI3998)
a49 <- CohortMethod::createCmAnalysis(analysisId = 49,
description = "One-year outcome, matching, short-term MI interaction",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcome,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgsI4998)
a59 <- CohortMethod::createCmAnalysis(analysisId = 59,
description = "One-year outcome, matching, concomitant PPI use interaction",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcome,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgsI5998)
a69 <- CohortMethod::createCmAnalysis(analysisId = 69,
description = "One-year outcome, matching, maintenance aspirin dosage interaction",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcome,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgsI6998)
# a99 <- CohortMethod::createCmAnalysis(analysisId = 99,
# description = "Time to First Post Index Event within 1 year, With 1 to 1 Matching, all interaction",
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = timeToFirstPostIndexEvent1Year,
# createPs = TRUE,
# createPsArgs = createPsArgs1,
# matchOnPs = TRUE,
# matchOnPsArgs = oneToOneMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = fitOutcomeModelArgsI6998)
cmAnalysisList <- list(a1, a2, a3, a4, a5, a6, a7,
a8, a9, a10, a11, #a12, a13, a14,
a15, a16, a17, a18, a19, a20, a21,
a79, a29, a39, a49, a59, a69#, a99
)
#cmAnalysisList <- list(a1)
CohortMethod::saveCmAnalysisList(cmAnalysisList, file.path(workFolder, "cmAnalysisListWithoutOnTreatmentWithBlankingPeriod.json"))
}
chandryou/TicagrelorVsClopidogrel documentation built on Oct. 9, 2020, 6:22 a.m.
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# Copyright 2018 Observational Health Data Sciences and Informatics
#
# This file is part of TicagrelorVsClopidogrel
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#' Create the analyses details
#'
#' @details
#' This function creates files specifying the analyses that will be performed.
#'
#' @param workFolder Name of local folder to place results; make sure to use forward slashes
#' (/)
#'
#' @export
createAnalysesDetails <- function(workFolder) {
defaultPrior <- Cyclops::createPrior("laplace",
exclude = c(0),
useCrossValidation = TRUE)
defaultControl <- Cyclops::createControl(cvType = "auto",
startingVariance = 0.01,
noiseLevel = "quiet",
tolerance = 2e-07,
maxIterations = 2500,
cvRepetitions = 10,
seed = 1234)
defaultCovariateSettings <- 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 = TRUE,
#useConditionOccurrenceMediumTerm = TRUE,
useConditionOccurrenceShortTerm = TRUE,
#useConditionOccurrencePrimaryInpatientAnyTimePrior = FALSE,
#useConditionOccurrencePrimaryInpatientLongTerm = FALSE,
#useConditionOccurrencePrimaryInpatientMediumTerm = TRUE,
#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 = TRUE,
useDrugExposureShortTerm = TRUE,
#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 = TRUE,
#useDrugGroupEraStartLongTerm = FALSE,
#useDrugGroupEraStartMediumTerm = FALSE,
#useDrugGroupEraStartShortTerm = FALSE,
#useProcedureOccurrenceAnyTimePrior = FALSE,
useProcedureOccurrenceLongTerm = TRUE,
#useProcedureOccurrenceMediumTerm = FALSE,
useProcedureOccurrenceShortTerm = TRUE,
#useDeviceExposureAnyTimePrior = FALSE,
#useDeviceExposureLongTerm = TRUE,
#useDeviceExposureMediumTerm = FALSE,
useDeviceExposureShortTerm = TRUE,
#useMeasurementAnyTimePrior = FALSE,
#useMeasurementLongTerm = FALSE,
#useMeasurementMediumTerm = TRUE,
useMeasurementShortTerm = TRUE,
#useMeasurementValueAnyTimePrior = FALSE,
#useMeasurementValueLongTerm = FALSE,
#useMeasurementValueMediumTerm = TRUE,
useMeasurementValueShortTerm = TRUE,
#useMeasurementRangeGroupAnyTimePrior = FALSE,
#useMeasurementRangeGroupLongTerm = FALSE,
#useMeasurementRangeGroupMediumTerm = FALSE,
#useMeasurementRangeGroupShortTerm = FALSE,
#useObservationAnyTimePrior = FALSE,
#useObservationLongTerm = FALSE,
#useObservationMediumTerm = FALSE,
#useObservationShortTerm = FALSE,
#useCharlsonIndex = FALSE,
#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 = FALSE,
#useVisitConceptCountLongTerm = FALSE,
#useVisitConceptCountMediumTerm = FALSE,
#useVisitConceptCountShortTerm = FALSE,
longTermStartDays = -365,
mediumTermStartDays = -30,
shortTermStartDays = -7,
endDays = 0,
includedCovariateConceptIds = c(),
addDescendantsToInclude = FALSE,
excludedCovariateConceptIds = c(1322184,
40241186),
addDescendantsToExclude = TRUE,
includedCovariateIds = c())
# defaultCovariateSettings <- FeatureExtraction::createCovariateSettings(useDemographicsGender = TRUE,
# useDemographicsAge = FALSE,
# useDemographicsAgeGroup = TRUE,
# useConditionOccurrenceLongTerm = FALSE,
# useConditionOccurrenceMediumTerm = FALSE,
# useConditionOccurrenceShortTerm = TRUE,
# addDescendantsToInclude = FALSE,
# excludedCovariateConceptIds = c(1322184,
# 40241186),
# addDescendantsToExclude = TRUE,
# includedCovariateIds = c())
subGroupCovariateSettings <- createSubgroupCovariateSettings(windowStart = -365, windowEnd = -1,
shortTermWindowStart = -7,
MaintenanceWindowEnd = 365,
analysisId = 998)
covariateSettings <- list(defaultCovariateSettings ,subGroupCovariateSettings
)
getDbCmDataArgs <- CohortMethod::createGetDbCohortMethodDataArgs(washoutPeriod = 0,
firstExposureOnly = FALSE,
removeDuplicateSubjects = 'keep first',
restrictToCommonPeriod = TRUE,
maxCohortSize = 0,
excludeDrugsFromCovariates = FALSE,
covariateSettings = covariateSettings)
OneYearOutcome <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = FALSE,
firstExposureOnly = FALSE,
washoutPeriod = 0,
removeDuplicateSubjects = 'keep first',
minDaysAtRisk = 1,
riskWindowStart = 1,
addExposureDaysToStart = FALSE,
riskWindowEnd = 365,
addExposureDaysToEnd = FALSE,
censorAtNewRiskWindow = FALSE)
OneYearOutcomeWithBlanking <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = FALSE,
firstExposureOnly = FALSE,
washoutPeriod = 0,
removeDuplicateSubjects = 'keep first',
minDaysAtRisk = 1,
riskWindowStart = 29,
addExposureDaysToStart = FALSE,
riskWindowEnd = 365,
addExposureDaysToEnd = FALSE,
censorAtNewRiskWindow = FALSE)
# OneYearOutcomeWithMinTAR <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = FALSE,
# firstExposureOnly = FALSE,
# washoutPeriod = 0,
# removeDuplicateSubjects = 'keep first',
# minDaysAtRisk = 364,
# riskWindowStart = 1,
# addExposureDaysToStart = FALSE,
# riskWindowEnd = 365,
# addExposureDaysToEnd = FALSE,
# censorAtNewRiskWindow = FALSE)
OnTreatment <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = FALSE,
firstExposureOnly = FALSE,
washoutPeriod = 0,
removeDuplicateSubjects = 'keep first',
minDaysAtRisk = 1,
riskWindowStart = 1,
addExposureDaysToStart = FALSE,
riskWindowEnd = 0,
addExposureDaysToEnd = TRUE,
censorAtNewRiskWindow = FALSE)
OnTreatmentWithBlanking <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = FALSE,
firstExposureOnly = FALSE,
washoutPeriod = 0,
removeDuplicateSubjects = 'keep first',
minDaysAtRisk = 1,
riskWindowStart = 29,
addExposureDaysToStart = FALSE,
riskWindowEnd = 0,
addExposureDaysToEnd = TRUE,
censorAtNewRiskWindow = FALSE)
ITT <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = FALSE,
firstExposureOnly = FALSE,
washoutPeriod = 0,
removeDuplicateSubjects = 'keep first',
minDaysAtRisk = 1,
riskWindowStart = 1,
addExposureDaysToStart = FALSE,
riskWindowEnd = 9999,
addExposureDaysToEnd = FALSE,
censorAtNewRiskWindow = FALSE)
ITTwithBlanking <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = FALSE,
firstExposureOnly = FALSE,
washoutPeriod = 0,
removeDuplicateSubjects = 'keep first',
minDaysAtRisk = 1,
riskWindowStart = 29,
addExposureDaysToStart = FALSE,
riskWindowEnd = 9999,
addExposureDaysToEnd = FALSE,
censorAtNewRiskWindow = FALSE)
# timeToFirstPostIndexEvent7DaysFromTreatment <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = FALSE,
# firstExposureOnly = FALSE,
# washoutPeriod = 0,
# removeDuplicateSubjects = 'keep first',
# minDaysAtRisk = 1,
# riskWindowStart = 1,
# addExposureDaysToStart = FALSE,
# riskWindowEnd = 7,
# addExposureDaysToEnd = TRUE,
# censorAtNewRiskWindow = FALSE)
# timeToFirstPostIndexEventModifiedITT <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = FALSE,
# firstExposureOnly = FALSE,
# washoutPeriod = 0,
# removeDuplicateSubjects = FALSE,
# minDaysAtRisk = 1,
# riskWindowStart = 1,
# addExposureDaysToStart = FALSE,
# riskWindowEnd = 9999,
# addExposureDaysToEnd = FALSE,
# censorAtNewRiskWindow = TRUE)
subgroupCovariateIds <- c(1000, 2000, 3000, 4000, 5000, 6000)+subGroupCovariateSettings$analysisId #c(1998, 2998, 3998, 4998, 5998, 6998)
createPsArgs1 <- CohortMethod::createCreatePsArgs(control = defaultControl,
errorOnHighCorrelation = FALSE,
excludeCovariateIds = subgroupCovariateIds,
stopOnError = FALSE)
#trimByPsArgs<- CohortMethod::createTrimByPsArgs(trimFraction = 0.05)
oneToOneMatchOnPsArgs <- CohortMethod::createMatchOnPsArgs(maxRatio = 1,
caliper = 0.2,
caliperScale = "standardized logit")
variableRatioMatchOnPsArgs <- CohortMethod::createMatchOnPsArgs(maxRatio = 10,
caliper = 0.2,
caliperScale = "standardized logit")
# variableRatioMatchOnPsArgs <- CohortMethod::createMatchOnPsArgs(maxRatio = 100,
# caliper = 0.2,
# caliperScale = "standardized logit")
stratifyByPsArgs <- CohortMethod::createStratifyByPsArgs(numberOfStrata = 10)
#without matching arg
fitOutcomeModelArgs0 <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = FALSE,
prior = defaultPrior,
control = defaultControl)
#conditioning
fitOutcomeModelArgs1 <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = TRUE,
prior = defaultPrior,
control = defaultControl)
#Without conditioning
fitOutcomeModelArgs2 <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = FALSE,
prior = defaultPrior,
control = defaultControl)
a1 <- CohortMethod::createCmAnalysis(analysisId = 1,
description = "One-year outcome, one-to-one matching",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcome,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)
a2 <- CohortMethod::createCmAnalysis(analysisId = 2,
description = "One-year outcome, variable-ratio matching",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcome,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = variableRatioMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
a3 <- CohortMethod::createCmAnalysis(analysisId = 3,
description = "One-year outcome, stratification",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcome,
createPs = TRUE,
createPsArgs = createPsArgs1,
#trimByPs = TRUE,
#trimByPsArgs = trimByPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratifyByPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
a4 <- CohortMethod::createCmAnalysis(analysisId = 4,
description = "One-year outcome, without matching",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcome,
createPs = FALSE,
createPsArgs = NULL,
#trimByPs = TRUE,
#trimByPsArgs = trimByPsArgs,
stratifyByPs = FALSE,
stratifyByPsArgs = NULL,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs0)
a5 <- CohortMethod::createCmAnalysis(analysisId = 5,
description = "One-year outcome with blanking period, one-to-one matching ",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcomeWithBlanking,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)
a6 <- CohortMethod::createCmAnalysis(analysisId = 6,
description = "One-year outcome with blanking period, variable-ratio matchingg",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcomeWithBlanking,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = variableRatioMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
a7 <- CohortMethod::createCmAnalysis(analysisId = 7,
description = "One-year outcome with blanking period, stratification",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcomeWithBlanking,
createPs = TRUE,
createPsArgs = createPsArgs1,
#trimByPs = TRUE,
#trimByPsArgs = trimByPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratifyByPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
#####################################################
a8 <- CohortMethod::createCmAnalysis(analysisId = 8,
description = "On-treatment outcome, one-to-one matching",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)
a9 <- CohortMethod::createCmAnalysis(analysisId = 9,
description = "On-treatment outcome, variable-ratio matching",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = variableRatioMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
a10 <- CohortMethod::createCmAnalysis(analysisId = 10,
description = "On-treatment outcome, stratification",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment,
createPs = TRUE,
createPsArgs = createPsArgs1,
#trimByPs = TRUE,
#trimByPsArgs = trimByPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratifyByPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
a11 <- CohortMethod::createCmAnalysis(analysisId = 11,
description = "On-treatment outcome, without matching",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment,
createPs = FALSE,
createPsArgs = NULL,
#trimByPs = TRUE,
#trimByPsArgs = trimByPsArgs,
stratifyByPs = FALSE,
stratifyByPsArgs = NULL,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs0)
a12 <- CohortMethod::createCmAnalysis(analysisId = 12,
description = "On-treatment outcome with blanking period, one-to-one matching ",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatmentWithBlanking,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)
a13 <- CohortMethod::createCmAnalysis(analysisId = 13,
description = "On-treatment outcome with blanking period, variable-ratio matchingg",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatmentWithBlanking,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = variableRatioMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
a14 <- CohortMethod::createCmAnalysis(analysisId = 14,
description = "On-treatment outcome with blanking period, stratification",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatmentWithBlanking,
createPs = TRUE,
createPsArgs = createPsArgs1,
#trimByPs = TRUE,
#trimByPsArgs = trimByPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratifyByPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
###########################################
a15 <- CohortMethod::createCmAnalysis(analysisId = 15,
description = "ITT, one-to-one matching",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITT,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)
a16 <- CohortMethod::createCmAnalysis(analysisId = 16,
description = "ITT, variable-ratio matching",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITT,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = variableRatioMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
a17 <- CohortMethod::createCmAnalysis(analysisId = 17,
description = "ITT, stratification",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITT,
createPs = TRUE,
createPsArgs = createPsArgs1,
#trimByPs = TRUE,
#trimByPsArgs = trimByPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratifyByPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
a18 <- CohortMethod::createCmAnalysis(analysisId = 18,
description = "ITT, without matching",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITT,
createPs = FALSE,
createPsArgs = NULL,
#trimByPs = TRUE,
#trimByPsArgs = trimByPsArgs,
stratifyByPs = FALSE,
stratifyByPsArgs = NULL,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs0)
a19 <- CohortMethod::createCmAnalysis(analysisId = 19,
description = "ITT with blanking period, one-to-one matching ",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITTwithBlanking,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)
a20 <- CohortMethod::createCmAnalysis(analysisId = 20,
description = "ITT with blanking period, variable-ratio matchingg",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITTwithBlanking,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = variableRatioMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
a21 <- CohortMethod::createCmAnalysis(analysisId = 21,
description = "ITT with blanking period, stratification",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITTwithBlanking,
createPs = TRUE,
createPsArgs = createPsArgs1,
#trimByPs = TRUE,
#trimByPsArgs = trimByPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratifyByPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)
##Interaction terms
fitOutcomeModelArgsI1998 <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = FALSE,
prior = defaultPrior,
interactionCovariateIds = 1998)
fitOutcomeModelArgsI2998 <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = FALSE,
prior = defaultPrior,
interactionCovariateIds = 2998)
fitOutcomeModelArgsI3998 <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = FALSE,
prior = defaultPrior,
interactionCovariateIds = 3998)
fitOutcomeModelArgsI4998 <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = FALSE,
prior = defaultPrior,
interactionCovariateIds = 4998)
fitOutcomeModelArgsI5998 <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = FALSE,
prior = defaultPrior,
interactionCovariateIds = 5998)
fitOutcomeModelArgsI6998 <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = FALSE,
prior = defaultPrior,
interactionCovariateIds = 6998)
fitOutcomeModelArgsI9998 <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = FALSE,
prior = defaultPrior,
interactionCovariateIds = subgroupCovariateIds)
a79 <- CohortMethod::createCmAnalysis(analysisId = 79,
description = "One-year outcome, matching, femal interaction",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcome,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgsI1998)
a29 <- CohortMethod::createCmAnalysis(analysisId = 29,
description = "One-year outcome, matching, elderly interaction",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcome,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgsI2998)
a39 <- CohortMethod::createCmAnalysis(analysisId = 39,
description = "One-year outcome, matching, black or aftrican race interaction",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcome,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgsI3998)
a49 <- CohortMethod::createCmAnalysis(analysisId = 49,
description = "One-year outcome, matching, short-term MI interaction",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcome,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgsI4998)
a59 <- CohortMethod::createCmAnalysis(analysisId = 59,
description = "One-year outcome, matching, concomitant PPI use interaction",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcome,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgsI5998)
a69 <- CohortMethod::createCmAnalysis(analysisId = 69,
description = "One-year outcome, matching, maintenance aspirin dosage interaction",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OneYearOutcome,
createPs = TRUE,
createPsArgs = createPsArgs1,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgsI6998)
# a99 <- CohortMethod::createCmAnalysis(analysisId = 99,
# description = "Time to First Post Index Event within 1 year, With 1 to 1 Matching, all interaction",
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = timeToFirstPostIndexEvent1Year,
# createPs = TRUE,
# createPsArgs = createPsArgs1,
# matchOnPs = TRUE,
# matchOnPsArgs = oneToOneMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = fitOutcomeModelArgsI6998)
cmAnalysisList <- list(a1, a2, a3, a4, a5, a6, a7,
a8, a9, a10, a11, #a12, a13, a14,
a15, a16, a17, a18, a19, a20, a21,
a79, a29, a39, a49, a59, a69#, a99
)
#cmAnalysisList <- list(a1)
CohortMethod::saveCmAnalysisList(cmAnalysisList, file.path(workFolder, "cmAnalysisListWithoutOnTreatmentWithBlankingPeriod.json"))
}
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