extras/CreateStudyAnalysisDetails.R
In ABMI/RanitidineCancerRisk: A Package to compare the risks of cancer between H2 blockers
# Copyright 2020 Observational Health Data Sciences and Informatics
#
# This file is part of RanitidineCancerRisk
#
# 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.
createAnalysesDetails <- function(workFolder) {
maxCohortSizeForFitting = 250000
covarSettings <- FeatureExtraction::createCovariateSettings(useDemographicsGender = TRUE,
useDemographicsAge = TRUE,
useDemographicsAgeGroup = TRUE,
useDemographicsRace = TRUE,
useDemographicsEthnicity = TRUE,
useDemographicsIndexYear = TRUE,
useDemographicsIndexMonth = TRUE,
useConditionOccurrenceAnyTimePrior = FALSE,
useConditionGroupEraAnyTimePrior = TRUE,
useConditionGroupEraLongTerm = TRUE,
useConditionGroupEraShortTerm = TRUE,
useDrugGroupEraLongTerm = TRUE,
useDrugGroupEraShortTerm = TRUE,
useDrugGroupEraOverlapping = TRUE,
useProcedureOccurrenceLongTerm = TRUE,
useMeasurementLongTerm = TRUE,
useMeasurementShortTerm = TRUE,
useMeasurementRangeGroupLongTerm = TRUE,
useObservationLongTerm = TRUE,
useCharlsonIndex = TRUE,
useVisitCountLongTerm = TRUE,
longTermStartDays = -365,
mediumTermStartDays = -180,
shortTermStartDays = -30,
endDays = 0,
excludedCovariateConceptIds = c(19011685,
961047,
950696,
43009003,
953076,
997276),
addDescendantsToExclude = TRUE,
includedCovariateIds = c()
)
# covarSettings <- FeatureExtraction::createDefaultCovariateSettings(excludedCovariateConceptIds = c(19011685,
# 961047,
# 950696,
# 43009003,
# 953076,
# 997276),
# addDescendantsToExclude = TRUE)
getDbCmDataArgs <- CohortMethod::createGetDbCohortMethodDataArgs(washoutPeriod = 365,
restrictToCommonPeriod = TRUE,
firstExposureOnly = FALSE,
removeDuplicateSubjects = "keep first",
studyStartDate = "",
studyEndDate = "",
excludeDrugsFromCovariates = FALSE,
covariateSettings = covarSettings)
OnTreatment1to0StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
minDaysAtRisk = 1,
riskWindowStart = 1,
startAnchor = "cohort start",
riskWindowEnd = 0,
endAnchor = "cohort end")
# OnTreatment30to0StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 30,
# startAnchor = "cohort start",
# riskWindowEnd = 0,
# endAnchor = "cohort end")
# OnTreatment365to0StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 365,
# startAnchor = "cohort start",
# riskWindowEnd = 0,
# endAnchor = "cohort end")
# OnTreatment1to365StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 1,
# startAnchor = "cohort start",
# riskWindowEnd = 365,
# endAnchor = "cohort end")
# OnTreatment30to365StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 30,
# startAnchor = "cohort start",
# riskWindowEnd = 365,
# endAnchor = "cohort end")
OnTreatment365to365StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
minDaysAtRisk = 1,
riskWindowStart = 365,
startAnchor = "cohort start",
riskWindowEnd = 365,
endAnchor = "cohort end")
# OnTreatment1to1095StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 1,
# startAnchor = "cohort start",
# riskWindowEnd = 1095,
# endAnchor = "cohort end")
# OnTreatment30to1095StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 30,
# startAnchor = "cohort start",
# riskWindowEnd = 1095,
# endAnchor = "cohort end")
# OnTreatment365to1095StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 365,
# startAnchor = "cohort start",
# riskWindowEnd = 1095,
# endAnchor = "cohort end")
ITTBlankingOf1StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
minDaysAtRisk = 1,
riskWindowStart = 1,
startAnchor = "cohort start",
riskWindowEnd = 9999,
endAnchor = "cohort end")
# ITTBlankingOf30StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 30,
# startAnchor = "cohort start",
# riskWindowEnd = 9999,
# endAnchor = "cohort end")
ITTBlankingOf365StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
minDaysAtRisk = 1,
riskWindowStart = 365,
startAnchor = "cohort start",
riskWindowEnd = 9999,
endAnchor = "cohort end")
createPsArgs <- CohortMethod::createCreatePsArgs(control = Cyclops::createControl(cvType = "auto",
startingVariance = 0.01,
noiseLevel = "quiet",
tolerance = 2e-07,
cvRepetitions = 10),
errorOnHighCorrelation = TRUE,
stopOnError = F,
maxCohortSizeForFitting = maxCohortSizeForFitting)
unConditionedCox <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = FALSE)
conditionedCox <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = TRUE)
oneToOneMatchOnPsArgs <- CohortMethod::createMatchOnPsArgs(maxRatio = 1)
variableRatioMatchOnPsArgs <- CohortMethod::createMatchOnPsArgs(maxRatio = 100)
stratificationMatchOnPsArgs <- CohortMethod::createStratifyByPsArgs(numberOfStrata = 10)
description1 = "No PS matching, on-treatment"
# description2 = "No PS matching, On-treatment, with blanking period of 30 days"
# description3 = "No PS matching, on-treatment, with 1-year blanking period"
description4 = "1:1 PS matching, on-treatment"
# description5 = "1:1 PS matching, On-treatment, with blanking period of 30 days"
# description6 = "1:1 PS matching, on-treatment, with 1-year blanking period"
description7 = "Variable-ratio PS matching, on-treatment"
# description8 = "Variable-ratio PS matching, with blanking period of 30 days"
# description9 = "Variable-ratio PS matching, on-treatment, with 1-year blanking period"
description10 = "PS stratification, On-treatment"
# description11 = "PS stratification, On-treatment, with blanking period of 30 days"
# description12 = "PS stratification, on-treatment, with 1-year blanking period"
# description13 = "No PS matching, on-treatment, with 1-year lag period"
# description14 = "No PS matching, 1 Year added to on-treatment, with blanking period of 30 days"
description15 = "No PS matching, on-treatment, with 1-year lag period"
# description16 = "1:1 PS matching, 1 Year added to on-treatment"
# description17 = "1:1 PS matching, 1 Year added to on-treatment, with blanking period of 30 days"
description18 = "1:1 PS matching, on-treatment, with 1-year lag period"
# description19 = "Variable-ratio PS matching, 1 Year added to on-treatment"
# description20 = "Variable-ratio PS matching, 1 Year added to on-treatment, with blanking period of 30 days"
description21 = "Variable-ratio PS matching, on-treatment, with 1-year lag period"
# description22 = "PS stratification, 1 Year added to on-treatment"
# description23 = "PS stratification, 1 Year added to on-treatment, with blanking period of 30 days"
description24 = "PS stratification, on-treatment, with 1-year lag period"
# description25 = "No PS matching, 3 Year added to on-treatment"
# description26 = "No PS matching, 3 Year added to on-treatment, with blanking period of 30 days"
# description27 = "No PS matching, 3 Year added to on-treatment, with blanking period of 1 year"
# description28 = "1:1 PS matching, 3 Year added to on-treatment"
# description29 = "1:1 PS matching, 3 Year added to on-treatment, with blanking period of 30 days"
# description30 = "1:1 PS matching, 3 Year added to on-treatment, with blanking period of 1 year"
# description31 = "Variable-ratio PS matching, 3 Year added to on-treatment"
# description32 = "Variable-ratio PS matching, 3 Year added to on-treatment, with blanking period of 30 days"
# description33 = "Variable-ratio PS matching, 3 Year added to on-treatment, with blanking period of 1 year"
# description34 = "PS stratification, 3 Year added to on-treatment"
# description35 = "PS stratification, 3 Year added to on-treatment, with blanking period of 30 days"
# description36 = "PS stratification, 3 Year added to on-treatment, with blanking period of 1 year"
description37 = "No PS matching, ITT"
# description38 = "No PS matching, ITT, with blanking period of 30 days"
description39 = "No PS matching, ITT, with 1-year lag period"
description40 = "1:1 PS matching, ITT"
# description41 = "1:1 PS matching, ITT, with blanking period of 30 days"
description42 = "1:1 PS matching, ITT, with 1-year lag period"
description43 = "Variable-ratio PS matching, ITT"
# description44 = "Variable-ratio PS matching, ITT, with blanking period of 30 days"
description45 = "Variable-ratio PS matching, ITT, with 1-year lag period"
description46 = "PS stratification, ITT"
# description47 = "PS stratification, ITT, with blanking period of 30 days"
description48 = "PS stratification, ITT, with 1-year lag period"
####1-12####
#Without matching
cmAnalysis1 <- CohortMethod::createCmAnalysis(analysisId = 1,
description = description1,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment1to0StudyPopArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis2 <- CohortMethod::createCmAnalysis(analysisId = 2,
# description = description2,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to0StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis3 <- CohortMethod::createCmAnalysis(analysisId = 3,
# description = description3,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment365to0StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
#1:1 PS matching
cmAnalysis4 <- CohortMethod::createCmAnalysis(analysisId = 4,
description = description4,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment1to0StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis5 <- CohortMethod::createCmAnalysis(analysisId = 5,
# description = description5,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to0StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = oneToOneMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis6 <- CohortMethod::createCmAnalysis(analysisId = 6,
# description = description6,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment365to0StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = oneToOneMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
#Variable-ratio PS matching
cmAnalysis7 <- CohortMethod::createCmAnalysis(analysisId = 7,
description = description7,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment1to0StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = variableRatioMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = conditionedCox)
# cmAnalysis8 <- CohortMethod::createCmAnalysis(analysisId = 8,
# description = description8,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to0StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = variableRatioMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
# cmAnalysis9 <- CohortMethod::createCmAnalysis(analysisId = 9,
# description = description9,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment365to0StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = variableRatioMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
#PS stratification
cmAnalysis10 <- CohortMethod::createCmAnalysis(analysisId = 10,
description = description10,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment1to0StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratificationMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = conditionedCox)
# cmAnalysis11 <- CohortMethod::createCmAnalysis(analysisId = 11,
# description = description11,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to0StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# stratifyByPs = TRUE,
# stratifyByPsArgs = stratificationMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
# cmAnalysis12 <- CohortMethod::createCmAnalysis(analysisId = 12,
# description = description12,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment365to0StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# stratifyByPs = TRUE,
# stratifyByPsArgs = stratificationMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
####13-24####
#Without matching
# cmAnalysis13 <- CohortMethod::createCmAnalysis(analysisId = 13,
# description = description13,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment1to365StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis14 <- CohortMethod::createCmAnalysis(analysisId = 14,
# description = description14,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to365StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
cmAnalysis15 <- CohortMethod::createCmAnalysis(analysisId = 15,
description = description15,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment365to365StudyPopArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = unConditionedCox)
#1:1 PS matching
# cmAnalysis16 <- CohortMethod::createCmAnalysis(analysisId = 16,
# description = description16,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment1to365StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = oneToOneMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis17 <- CohortMethod::createCmAnalysis(analysisId = 17,
# description = description17,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to365StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = oneToOneMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
cmAnalysis18 <- CohortMethod::createCmAnalysis(analysisId = 18,
description = description18,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment365to365StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = unConditionedCox)
#Variable-ratio PS matching
# cmAnalysis19 <- CohortMethod::createCmAnalysis(analysisId = 19,
# description = description19,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment1to365StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = variableRatioMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
# cmAnalysis20 <- CohortMethod::createCmAnalysis(analysisId = 20,
# description = description20,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to365StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = variableRatioMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
cmAnalysis21 <- CohortMethod::createCmAnalysis(analysisId = 21,
description = description21,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment365to365StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = variableRatioMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = conditionedCox)
#PS stratification
# cmAnalysis22 <- CohortMethod::createCmAnalysis(analysisId = 22,
# description = description22,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment1to365StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# stratifyByPs = TRUE,
# stratifyByPsArgs = stratificationMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
# cmAnalysis23 <- CohortMethod::createCmAnalysis(analysisId = 23,
# description = description23,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to365StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# stratifyByPs = TRUE,
# stratifyByPsArgs = stratificationMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
cmAnalysis24 <- CohortMethod::createCmAnalysis(analysisId = 24,
description = description24,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment365to365StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratificationMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = conditionedCox)
# ####25-36####
# #Without matching
# cmAnalysis25 <- CohortMethod::createCmAnalysis(analysisId = 25,
# description = description25,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment1to1095StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis26 <- CohortMethod::createCmAnalysis(analysisId = 26,
# description = description26,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to1095StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis27 <- CohortMethod::createCmAnalysis(analysisId = 27,
# description = description27,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment365to1095StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# #1:1 PS matching
# cmAnalysis28 <- CohortMethod::createCmAnalysis(analysisId = 28,
# description = description28,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment1to1095StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = oneToOneMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis29 <- CohortMethod::createCmAnalysis(analysisId = 29,
# description = description29,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to1095StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = oneToOneMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis30 <- CohortMethod::createCmAnalysis(analysisId = 30,
# description = description30,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment365to1095StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = oneToOneMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# #Variable-ratio PS matching
# cmAnalysis31 <- CohortMethod::createCmAnalysis(analysisId = 31,
# description = description31,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment1to1095StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = variableRatioMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
# cmAnalysis32 <- CohortMethod::createCmAnalysis(analysisId = 32,
# description = description32,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to1095StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = variableRatioMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
# cmAnalysis33 <- CohortMethod::createCmAnalysis(analysisId = 33,
# description = description33,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment365to1095StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = variableRatioMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
#
# #PS stratification
# cmAnalysis34 <- CohortMethod::createCmAnalysis(analysisId = 34,
# description = description34,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment1to1095StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# stratifyByPs = TRUE,
# stratifyByPsArgs = stratificationMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
# cmAnalysis35 <- CohortMethod::createCmAnalysis(analysisId = 35,
# description = description35,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to1095StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# stratifyByPs = TRUE,
# stratifyByPsArgs = stratificationMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
# cmAnalysis36 <- CohortMethod::createCmAnalysis(analysisId = 36,
# description = description36,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment365to1095StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# stratifyByPs = TRUE,
# stratifyByPsArgs = stratificationMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
####37-48####
#Without matching
cmAnalysis37 <- CohortMethod::createCmAnalysis(analysisId = 37,
description = description37,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf1StudyPopArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis38 <- CohortMethod::createCmAnalysis(analysisId = 38,
# description = description38,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = ITTBlankingOf30StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
cmAnalysis39 <- CohortMethod::createCmAnalysis(analysisId = 39,
description = description39,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = unConditionedCox)
#1:1 PS matching
cmAnalysis40 <- CohortMethod::createCmAnalysis(analysisId = 40,
description = description40,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf1StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis41 <- CohortMethod::createCmAnalysis(analysisId = 41,
# description = description41,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = ITTBlankingOf30StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = oneToOneMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
cmAnalysis42 <- CohortMethod::createCmAnalysis(analysisId = 42,
description = description42,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = unConditionedCox)
#Variable-ratio PS matching
cmAnalysis43 <- CohortMethod::createCmAnalysis(analysisId = 43,
description = description43,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf1StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = variableRatioMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = conditionedCox)
# cmAnalysis44 <- CohortMethod::createCmAnalysis(analysisId = 44,
# description = description44,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = ITTBlankingOf30StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = variableRatioMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
cmAnalysis45 <- CohortMethod::createCmAnalysis(analysisId = 45,
description = description45,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = variableRatioMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = conditionedCox)
#PS stratification
cmAnalysis46 <- CohortMethod::createCmAnalysis(analysisId = 46,
description = description46,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf1StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratificationMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = conditionedCox)
# cmAnalysis47 <- CohortMethod::createCmAnalysis(analysisId = 47,
# description = description47,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = ITTBlankingOf30StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# stratifyByPs = TRUE,
# stratifyByPsArgs = stratificationMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
cmAnalysis48 <- CohortMethod::createCmAnalysis(analysisId = 48,
description = description48,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratificationMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = conditionedCox)
####Interaction terms####
subGroupCovariateSettings <- RanitidineCancerRisk::createSubgroupCovariateSettings(windowStart = -365,
windowEnd = -1,
shortTermWindowStart = -7,
MaintenanceWindowEnd = 365,
analysisId = 998)
interactionDbCmDataArgs <- CohortMethod::createGetDbCohortMethodDataArgs(washoutPeriod = 365,
restrictToCommonPeriod = TRUE,
firstExposureOnly = FALSE,
removeDuplicateSubjects = "keep first",
studyStartDate = "",
studyEndDate = "",
excludeDrugsFromCovariates = FALSE,
covariateSettings = list(covarSettings, subGroupCovariateSettings))
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)
cmAnalysis1998 <- CohortMethod::createCmAnalysis(analysisId = 1998,
description = paste0(description42,", interaction:female"),
getDbCohortMethodDataArgs = interactionDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgsI1998,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs)
cmAnalysis2998 <- CohortMethod::createCmAnalysis(analysisId = 2998,
description = paste0(description42,", interaction:elderly (age >= 65)"),
getDbCohortMethodDataArgs = interactionDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgsI2998,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs)
cmAnalysis3998 <- CohortMethod::createCmAnalysis(analysisId = 3998,
description = paste0(description42,", interaction:cumulative drug dose than 365 unit"),
getDbCohortMethodDataArgs = interactionDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgsI3998,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs)
cmAnalysis4998 <- CohortMethod::createCmAnalysis(analysisId = 4998,
description = paste0(description42,", interaction:cumulative drug dose than 730 unit"),
getDbCohortMethodDataArgs = interactionDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgsI4998,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs)
cmAnalysis5998 <- CohortMethod::createCmAnalysis(analysisId = 5998,
description = paste0(description42,", interaction:cumulative drug dose than 1095 unit"),
getDbCohortMethodDataArgs = interactionDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgsI5998,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs)
# interactionCovariateIds <- c(8532001, 201826210, 21600960413) # Female, T2DM, concurent use of antithrombotic agents
#
# fitOutcomeModelArgs3 <- CohortMethod::createFitOutcomeModelArgs(modelType = "cox",
# stratified = TRUE,
# useCovariates = FALSE,
# interactionCovariateIds = interactionCovariateIds)
#
# cmAnalysis5 <- CohortMethod::createCmAnalysis(analysisId = 5,
# description = "Stratification with interaction terms",
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = createOnTreatmentStudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# stratifyByPs = TRUE,
# stratifyByPsArgs = stratifyByPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = fitOutcomeModelArgs3)
#paste0("cmAnalysis",1:48,collapse=", ")
cmAnalysisList <- list(cmAnalysis1, #cmAnalysis2, cmAnalysis3,
cmAnalysis4, #cmAnalysis5, cmAnalysis6,
cmAnalysis7, #cmAnalysis8, cmAnalysis9,
cmAnalysis10, #cmAnalysis11, cmAnalysis12,
#cmAnalysis13, #cmAnalysis14,
cmAnalysis15, #cmAnalysis16, cmAnalysis17,
cmAnalysis18, #cmAnalysis19, cmAnalysis20,
cmAnalysis21, #cmAnalysis22, cmAnalysis23,
cmAnalysis24,
#cmAnalysis25, cmAnalysis26, cmAnalysis27, cmAnalysis28, cmAnalysis29, cmAnalysis30, cmAnalysis31, cmAnalysis32, cmAnalysis33, cmAnalysis34, cmAnalysis35, cmAnalysis36,
cmAnalysis37, #cmAnalysis38,
cmAnalysis39, cmAnalysis40, #cmAnalysis41,
cmAnalysis42, cmAnalysis43,
#cmAnalysis44,
cmAnalysis45, cmAnalysis46, #cmAnalysis47,
cmAnalysis48,
cmAnalysis1998, cmAnalysis2998, cmAnalysis3998, cmAnalysis4998, cmAnalysis5998)
CohortMethod::saveCmAnalysisList(cmAnalysisList, file.path(workFolder, "cmAnalysisList.json"))
}
createPositiveControlSynthesisArgs <- function(workFolder) {
settings <- list(
outputIdOffset = 10000,
firstExposureOnly = TRUE,
firstOutcomeOnly = TRUE,
removePeopleWithPriorOutcomes = TRUE,
modelType = "survival",
washoutPeriod = 365,
riskWindowStart = 0,
riskWindowEnd = 30,
addExposureDaysToEnd = TRUE,
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(useDemographicsAgeGroup = TRUE,
useDemographicsGender = TRUE,
useDemographicsIndexYear = TRUE,
useDemographicsIndexMonth = TRUE,
useConditionGroupEraLongTerm = TRUE,
useDrugGroupEraLongTerm = TRUE,
useProcedureOccurrenceLongTerm = TRUE,
useMeasurementLongTerm = TRUE,
useObservationLongTerm = TRUE,
useCharlsonIndex = TRUE,
useDcsi = TRUE,
useChads2Vasc = TRUE,
longTermStartDays = -365,
endDays = 0)
)
ParallelLogger::saveSettingsToJson(settings, file.path(workFolder, "positiveControlSynthArgs.json"))
}
# createFeasibilityAnalysesDetails <- function(workFolder) {
# maxCohortSizeForFitting = 1000
# minCovarSettings <- FeatureExtraction::createCovariateSettings(useDemographicsGender = TRUE,
# useDemographicsAge = TRUE,
# useDemographicsAgeGroup = TRUE,
# useDemographicsRace = TRUE,
# useDemographicsEthnicity = TRUE,
# useDemographicsIndexYear = TRUE,
# useDemographicsPriorObservationTime = TRUE,
# useDemographicsPostObservationTime = TRUE,
# useDemographicsTimeInCohort = TRUE)
#
#
# minDbCmDataArgs <- CohortMethod::createGetDbCohortMethodDataArgs(washoutPeriod = 365,
# restrictToCommonPeriod = TRUE,
# firstExposureOnly = FALSE,
# removeDuplicateSubjects = "keep first",
# studyStartDate = "",
# studyEndDate = "",
# excludeDrugsFromCovariates = FALSE,
# covariateSettings = minCovarSettings)
#
# OnTreatment1to0StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 1,
# startAnchor = "cohort start",
# riskWindowEnd = 0,
# endAnchor = "cohort end")
#
# # OnTreatment30to0StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# # minDaysAtRisk = 1,
# # riskWindowStart = 30,
# # startAnchor = "cohort start",
# # riskWindowEnd = 0,
# # endAnchor = "cohort end")
#
# OnTreatment365to0StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 365,
# startAnchor = "cohort start",
# riskWindowEnd = 0,
# endAnchor = "cohort end")
#
# OnTreatment1to365StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 1,
# startAnchor = "cohort start",
# riskWindowEnd = 365,
# endAnchor = "cohort end")
#
# # OnTreatment30to365StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# # minDaysAtRisk = 1,
# # riskWindowStart = 30,
# # startAnchor = "cohort start",
# # riskWindowEnd = 365,
# # endAnchor = "cohort end")
#
# OnTreatment365to365StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 365,
# startAnchor = "cohort start",
# riskWindowEnd = 365,
# endAnchor = "cohort end")
#
# # OnTreatment1to1095StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# # minDaysAtRisk = 1,
# # riskWindowStart = 1,
# # startAnchor = "cohort start",
# # riskWindowEnd = 1095,
# # endAnchor = "cohort end")
#
# # OnTreatment30to1095StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# # minDaysAtRisk = 1,
# # riskWindowStart = 30,
# # startAnchor = "cohort start",
# # riskWindowEnd = 1095,
# # endAnchor = "cohort end")
#
# # OnTreatment365to1095StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# # minDaysAtRisk = 1,
# # riskWindowStart = 365,
# # startAnchor = "cohort start",
# # riskWindowEnd = 1095,
# # endAnchor = "cohort end")
#
# ITTBlankingOf1StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 1,
# startAnchor = "cohort start",
# riskWindowEnd = 9999,
# endAnchor = "cohort end")
#
# # ITTBlankingOf30StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# # minDaysAtRisk = 1,
# # riskWindowStart = 30,
# # startAnchor = "cohort start",
# # riskWindowEnd = 9999,
# # endAnchor = "cohort end")
#
# ITTBlankingOf365StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 365,
# startAnchor = "cohort start",
# riskWindowEnd = 9999,
# endAnchor = "cohort end")
#
#
# # createPsArgs <- CohortMethod::createCreatePsArgs(control = Cyclops::createControl(cvType = "auto",
# # startingVariance = 0.01,
# # noiseLevel = "quiet",
# # tolerance = 2e-07,
# # cvRepetitions = 10),
# # errorOnHighCorrelation = TRUE,
# # stopOnError = F,
# # maxCohortSizeForFitting = maxCohortSizeForFitting)
#
#
# unConditionedCox <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
# modelType = "cox",
# stratified = FALSE)
#
# conditionedCox <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
# modelType = "cox",
# stratified = TRUE)
#
# oneToOneMatchOnPsArgs <- CohortMethod::createMatchOnPsArgs(maxRatio = 1)
#
# variableRatioMatchOnPsArgs <- CohortMethod::createMatchOnPsArgs(maxRatio = 100)
#
# stratificationMatchOnPsArgs <- CohortMethod::createStratifyByPsArgs(numberOfStrata = 10)
#
# description1 = "No PS matching, On-treatment"
# #description2 = "No PS matching, On-treatment, with blanking period of 30 days"
# description3 = "No PS matching, On-treatment, with 1-year blanking period"
#
# description13 = "No PS matching, On-treatment with 1-year lag period"
# #description14 = "No PS matching, 1 Year added to on-treatment, with blanking period of 30 days"
# description15 = "No PS matching, On-treatment, with 1-year lag period, with 1-year blanking period"
#
# #description25 = "No PS matching, 3 Year added to on-treatment"
# #description26 = "No PS matching, 3 Year added to on-treatment, with blanking period of 30 days"
# #description27 = "No PS matching, 3 Year added to on-treatment, with blanking period of 1 year"
#
# description37 = "No PS matching, ITT"
# #description38 = "No PS matching, ITT, with blanking period of 30 days"
# description39 = "No PS matching, ITT, with 1-year blanking period"
#
#
# ####1-12####
# #Without matching
# cmAnalysis991 <- CohortMethod::createCmAnalysis(analysisId = 991,
# description = description1,
# getDbCohortMethodDataArgs = minDbCmDataArgs,
# createStudyPopArgs = OnTreatment1to0StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# # cmAnalysis992 <- CohortMethod::createCmAnalysis(analysisId = 992,
# # description = description2,
# # getDbCohortMethodDataArgs = minDbCmDataArgs,
# # createStudyPopArgs = OnTreatment30to0StudyPopArgs,
# # fitOutcomeModel = TRUE,
# # fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis993 <- CohortMethod::createCmAnalysis(analysisId = 993,
# description = description3,
# getDbCohortMethodDataArgs = minDbCmDataArgs,
# createStudyPopArgs = OnTreatment365to0StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
#
# ####13-24####
# #Without matching
# cmAnalysis913 <- CohortMethod::createCmAnalysis(analysisId = 913,
# description = description13,
# getDbCohortMethodDataArgs = minDbCmDataArgs,
# createStudyPopArgs = OnTreatment1to365StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# # cmAnalysis914 <- CohortMethod::createCmAnalysis(analysisId = 914,
# # description = description14,
# # getDbCohortMethodDataArgs = minDbCmDataArgs,
# # createStudyPopArgs = OnTreatment30to365StudyPopArgs,
# # fitOutcomeModel = TRUE,
# # fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis915 <- CohortMethod::createCmAnalysis(analysisId = 915,
# description = description15,
# getDbCohortMethodDataArgs = minDbCmDataArgs,
# createStudyPopArgs = OnTreatment365to365StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# ####25-36####
# #Without matching
# # cmAnalysis925 <- CohortMethod::createCmAnalysis(analysisId = 925,
# # description = description25,
# # getDbCohortMethodDataArgs = minDbCmDataArgs,
# # createStudyPopArgs = OnTreatment1to1095StudyPopArgs,
# # fitOutcomeModel = TRUE,
# # fitOutcomeModelArgs = unConditionedCox)
# # cmAnalysis926 <- CohortMethod::createCmAnalysis(analysisId = 926,
# # description = description26,
# # getDbCohortMethodDataArgs = minDbCmDataArgs,
# # createStudyPopArgs = OnTreatment30to1095StudyPopArgs,
# # fitOutcomeModel = TRUE,
# # fitOutcomeModelArgs = unConditionedCox)
# # cmAnalysis927 <- CohortMethod::createCmAnalysis(analysisId = 927,
# # description = description27,
# # getDbCohortMethodDataArgs = minDbCmDataArgs,
# # createStudyPopArgs = OnTreatment365to1095StudyPopArgs,
# # fitOutcomeModel = TRUE,
# # fitOutcomeModelArgs = unConditionedCox)
# ####37-48####
# #Without matching
# cmAnalysis937 <- CohortMethod::createCmAnalysis(analysisId = 937,
# description = description37,
# getDbCohortMethodDataArgs = minDbCmDataArgs,
# createStudyPopArgs = ITTBlankingOf1StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# # cmAnalysis938 <- CohortMethod::createCmAnalysis(analysisId = 938,
# # description = description38,
# # getDbCohortMethodDataArgs = minDbCmDataArgs,
# # createStudyPopArgs = ITTBlankingOf30StudyPopArgs,
# # fitOutcomeModel = TRUE,
# # fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis939 <- CohortMethod::createCmAnalysis(analysisId = 939,
# description = description39,
# getDbCohortMethodDataArgs = minDbCmDataArgs,
# createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
#
# ####Interaction terms####
# subGroupCovariateSettings <- RanitidineCancerRisk::createSubgroupCovariateSettings(windowStart = -365,
# windowEnd = -1,
# shortTermWindowStart = -7,
# MaintenanceWindowEnd = 365,
# analysisId = 998)
#
# interactionDbCmDataArgs <- CohortMethod::createGetDbCohortMethodDataArgs(washoutPeriod = 365,
# restrictToCommonPeriod = TRUE,
# firstExposureOnly = FALSE,
# removeDuplicateSubjects = "keep first",
# studyStartDate = "",
# studyEndDate = "",
# excludeDrugsFromCovariates = FALSE,
# covariateSettings = list(minCovarSettings, subGroupCovariateSettings))
#
# 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)
#
# cmAnalysis1998 <- CohortMethod::createCmAnalysis(analysisId = 1998,
# description = paste0(description39,", interaction:female"),
# getDbCohortMethodDataArgs = interactionDbCmDataArgs,
# createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = fitOutcomeModelArgsI1998)
#
# cmAnalysis2998 <- CohortMethod::createCmAnalysis(analysisId = 2998,
# description = paste0(description39,", interaction:elderly (age >= 65)"),
# getDbCohortMethodDataArgs = interactionDbCmDataArgs,
# createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = fitOutcomeModelArgsI2998)
#
# cmAnalysis3998 <- CohortMethod::createCmAnalysis(analysisId = 3998,
# description = paste0(description39,", interaction:cumulative drug dose than 365 unit"),
# getDbCohortMethodDataArgs = interactionDbCmDataArgs,
# createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = fitOutcomeModelArgsI3998)
#
# cmAnalysis4998 <- CohortMethod::createCmAnalysis(analysisId = 4998,
# description = paste0(description39,", interaction:cumulative drug dose than 730 unit"),
# getDbCohortMethodDataArgs = interactionDbCmDataArgs,
# createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = fitOutcomeModelArgsI4998)
#
# cmAnalysis5998 <- CohortMethod::createCmAnalysis(analysisId = 5998,
# description = paste0(description39,", interaction:cumulative drug dose than 1095 unit"),
# getDbCohortMethodDataArgs = interactionDbCmDataArgs,
# createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = fitOutcomeModelArgsI5998)
#
# # cmAnalysis6998 <- CohortMethod::createCmAnalysis(analysisId = 6998,
# # description = paste0(description39,", interaction:gastric ulcer history within previous 1 year"),
# # getDbCohortMethodDataArgs = interactionDbCmDataArgs,
# # createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
# # fitOutcomeModel = TRUE,
# # fitOutcomeModelArgs = fitOutcomeModelArgsI6998)
#
# cmAnalysisFeasibilityList <- list(cmAnalysis991, cmAnalysis993,
# cmAnalysis913, cmAnalysis915,
# cmAnalysis937, cmAnalysis939,
# cmAnalysis1998, cmAnalysis2998, cmAnalysis3998, cmAnalysis4998, cmAnalysis5998#, cmAnalysis6998
# )
#
# CohortMethod::saveCmAnalysisList(cmAnalysisFeasibilityList, file.path(workFolder, "cmAnalysisFeasibilityList.json"))
# }
ABMI/RanitidineCancerRisk documentation built on March 11, 2021, 9:02 p.m.
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# Copyright 2020 Observational Health Data Sciences and Informatics
#
# This file is part of RanitidineCancerRisk
#
# 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.
createAnalysesDetails <- function(workFolder) {
maxCohortSizeForFitting = 250000
covarSettings <- FeatureExtraction::createCovariateSettings(useDemographicsGender = TRUE,
useDemographicsAge = TRUE,
useDemographicsAgeGroup = TRUE,
useDemographicsRace = TRUE,
useDemographicsEthnicity = TRUE,
useDemographicsIndexYear = TRUE,
useDemographicsIndexMonth = TRUE,
useConditionOccurrenceAnyTimePrior = FALSE,
useConditionGroupEraAnyTimePrior = TRUE,
useConditionGroupEraLongTerm = TRUE,
useConditionGroupEraShortTerm = TRUE,
useDrugGroupEraLongTerm = TRUE,
useDrugGroupEraShortTerm = TRUE,
useDrugGroupEraOverlapping = TRUE,
useProcedureOccurrenceLongTerm = TRUE,
useMeasurementLongTerm = TRUE,
useMeasurementShortTerm = TRUE,
useMeasurementRangeGroupLongTerm = TRUE,
useObservationLongTerm = TRUE,
useCharlsonIndex = TRUE,
useVisitCountLongTerm = TRUE,
longTermStartDays = -365,
mediumTermStartDays = -180,
shortTermStartDays = -30,
endDays = 0,
excludedCovariateConceptIds = c(19011685,
961047,
950696,
43009003,
953076,
997276),
addDescendantsToExclude = TRUE,
includedCovariateIds = c()
)
# covarSettings <- FeatureExtraction::createDefaultCovariateSettings(excludedCovariateConceptIds = c(19011685,
# 961047,
# 950696,
# 43009003,
# 953076,
# 997276),
# addDescendantsToExclude = TRUE)
getDbCmDataArgs <- CohortMethod::createGetDbCohortMethodDataArgs(washoutPeriod = 365,
restrictToCommonPeriod = TRUE,
firstExposureOnly = FALSE,
removeDuplicateSubjects = "keep first",
studyStartDate = "",
studyEndDate = "",
excludeDrugsFromCovariates = FALSE,
covariateSettings = covarSettings)
OnTreatment1to0StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
minDaysAtRisk = 1,
riskWindowStart = 1,
startAnchor = "cohort start",
riskWindowEnd = 0,
endAnchor = "cohort end")
# OnTreatment30to0StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 30,
# startAnchor = "cohort start",
# riskWindowEnd = 0,
# endAnchor = "cohort end")
# OnTreatment365to0StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 365,
# startAnchor = "cohort start",
# riskWindowEnd = 0,
# endAnchor = "cohort end")
# OnTreatment1to365StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 1,
# startAnchor = "cohort start",
# riskWindowEnd = 365,
# endAnchor = "cohort end")
# OnTreatment30to365StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 30,
# startAnchor = "cohort start",
# riskWindowEnd = 365,
# endAnchor = "cohort end")
OnTreatment365to365StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
minDaysAtRisk = 1,
riskWindowStart = 365,
startAnchor = "cohort start",
riskWindowEnd = 365,
endAnchor = "cohort end")
# OnTreatment1to1095StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 1,
# startAnchor = "cohort start",
# riskWindowEnd = 1095,
# endAnchor = "cohort end")
# OnTreatment30to1095StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 30,
# startAnchor = "cohort start",
# riskWindowEnd = 1095,
# endAnchor = "cohort end")
# OnTreatment365to1095StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 365,
# startAnchor = "cohort start",
# riskWindowEnd = 1095,
# endAnchor = "cohort end")
ITTBlankingOf1StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
minDaysAtRisk = 1,
riskWindowStart = 1,
startAnchor = "cohort start",
riskWindowEnd = 9999,
endAnchor = "cohort end")
# ITTBlankingOf30StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 30,
# startAnchor = "cohort start",
# riskWindowEnd = 9999,
# endAnchor = "cohort end")
ITTBlankingOf365StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
minDaysAtRisk = 1,
riskWindowStart = 365,
startAnchor = "cohort start",
riskWindowEnd = 9999,
endAnchor = "cohort end")
createPsArgs <- CohortMethod::createCreatePsArgs(control = Cyclops::createControl(cvType = "auto",
startingVariance = 0.01,
noiseLevel = "quiet",
tolerance = 2e-07,
cvRepetitions = 10),
errorOnHighCorrelation = TRUE,
stopOnError = F,
maxCohortSizeForFitting = maxCohortSizeForFitting)
unConditionedCox <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = FALSE)
conditionedCox <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = TRUE)
oneToOneMatchOnPsArgs <- CohortMethod::createMatchOnPsArgs(maxRatio = 1)
variableRatioMatchOnPsArgs <- CohortMethod::createMatchOnPsArgs(maxRatio = 100)
stratificationMatchOnPsArgs <- CohortMethod::createStratifyByPsArgs(numberOfStrata = 10)
description1 = "No PS matching, on-treatment"
# description2 = "No PS matching, On-treatment, with blanking period of 30 days"
# description3 = "No PS matching, on-treatment, with 1-year blanking period"
description4 = "1:1 PS matching, on-treatment"
# description5 = "1:1 PS matching, On-treatment, with blanking period of 30 days"
# description6 = "1:1 PS matching, on-treatment, with 1-year blanking period"
description7 = "Variable-ratio PS matching, on-treatment"
# description8 = "Variable-ratio PS matching, with blanking period of 30 days"
# description9 = "Variable-ratio PS matching, on-treatment, with 1-year blanking period"
description10 = "PS stratification, On-treatment"
# description11 = "PS stratification, On-treatment, with blanking period of 30 days"
# description12 = "PS stratification, on-treatment, with 1-year blanking period"
# description13 = "No PS matching, on-treatment, with 1-year lag period"
# description14 = "No PS matching, 1 Year added to on-treatment, with blanking period of 30 days"
description15 = "No PS matching, on-treatment, with 1-year lag period"
# description16 = "1:1 PS matching, 1 Year added to on-treatment"
# description17 = "1:1 PS matching, 1 Year added to on-treatment, with blanking period of 30 days"
description18 = "1:1 PS matching, on-treatment, with 1-year lag period"
# description19 = "Variable-ratio PS matching, 1 Year added to on-treatment"
# description20 = "Variable-ratio PS matching, 1 Year added to on-treatment, with blanking period of 30 days"
description21 = "Variable-ratio PS matching, on-treatment, with 1-year lag period"
# description22 = "PS stratification, 1 Year added to on-treatment"
# description23 = "PS stratification, 1 Year added to on-treatment, with blanking period of 30 days"
description24 = "PS stratification, on-treatment, with 1-year lag period"
# description25 = "No PS matching, 3 Year added to on-treatment"
# description26 = "No PS matching, 3 Year added to on-treatment, with blanking period of 30 days"
# description27 = "No PS matching, 3 Year added to on-treatment, with blanking period of 1 year"
# description28 = "1:1 PS matching, 3 Year added to on-treatment"
# description29 = "1:1 PS matching, 3 Year added to on-treatment, with blanking period of 30 days"
# description30 = "1:1 PS matching, 3 Year added to on-treatment, with blanking period of 1 year"
# description31 = "Variable-ratio PS matching, 3 Year added to on-treatment"
# description32 = "Variable-ratio PS matching, 3 Year added to on-treatment, with blanking period of 30 days"
# description33 = "Variable-ratio PS matching, 3 Year added to on-treatment, with blanking period of 1 year"
# description34 = "PS stratification, 3 Year added to on-treatment"
# description35 = "PS stratification, 3 Year added to on-treatment, with blanking period of 30 days"
# description36 = "PS stratification, 3 Year added to on-treatment, with blanking period of 1 year"
description37 = "No PS matching, ITT"
# description38 = "No PS matching, ITT, with blanking period of 30 days"
description39 = "No PS matching, ITT, with 1-year lag period"
description40 = "1:1 PS matching, ITT"
# description41 = "1:1 PS matching, ITT, with blanking period of 30 days"
description42 = "1:1 PS matching, ITT, with 1-year lag period"
description43 = "Variable-ratio PS matching, ITT"
# description44 = "Variable-ratio PS matching, ITT, with blanking period of 30 days"
description45 = "Variable-ratio PS matching, ITT, with 1-year lag period"
description46 = "PS stratification, ITT"
# description47 = "PS stratification, ITT, with blanking period of 30 days"
description48 = "PS stratification, ITT, with 1-year lag period"
####1-12####
#Without matching
cmAnalysis1 <- CohortMethod::createCmAnalysis(analysisId = 1,
description = description1,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment1to0StudyPopArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis2 <- CohortMethod::createCmAnalysis(analysisId = 2,
# description = description2,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to0StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis3 <- CohortMethod::createCmAnalysis(analysisId = 3,
# description = description3,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment365to0StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
#1:1 PS matching
cmAnalysis4 <- CohortMethod::createCmAnalysis(analysisId = 4,
description = description4,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment1to0StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis5 <- CohortMethod::createCmAnalysis(analysisId = 5,
# description = description5,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to0StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = oneToOneMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis6 <- CohortMethod::createCmAnalysis(analysisId = 6,
# description = description6,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment365to0StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = oneToOneMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
#Variable-ratio PS matching
cmAnalysis7 <- CohortMethod::createCmAnalysis(analysisId = 7,
description = description7,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment1to0StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = variableRatioMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = conditionedCox)
# cmAnalysis8 <- CohortMethod::createCmAnalysis(analysisId = 8,
# description = description8,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to0StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = variableRatioMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
# cmAnalysis9 <- CohortMethod::createCmAnalysis(analysisId = 9,
# description = description9,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment365to0StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = variableRatioMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
#PS stratification
cmAnalysis10 <- CohortMethod::createCmAnalysis(analysisId = 10,
description = description10,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment1to0StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratificationMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = conditionedCox)
# cmAnalysis11 <- CohortMethod::createCmAnalysis(analysisId = 11,
# description = description11,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to0StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# stratifyByPs = TRUE,
# stratifyByPsArgs = stratificationMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
# cmAnalysis12 <- CohortMethod::createCmAnalysis(analysisId = 12,
# description = description12,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment365to0StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# stratifyByPs = TRUE,
# stratifyByPsArgs = stratificationMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
####13-24####
#Without matching
# cmAnalysis13 <- CohortMethod::createCmAnalysis(analysisId = 13,
# description = description13,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment1to365StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis14 <- CohortMethod::createCmAnalysis(analysisId = 14,
# description = description14,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to365StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
cmAnalysis15 <- CohortMethod::createCmAnalysis(analysisId = 15,
description = description15,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment365to365StudyPopArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = unConditionedCox)
#1:1 PS matching
# cmAnalysis16 <- CohortMethod::createCmAnalysis(analysisId = 16,
# description = description16,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment1to365StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = oneToOneMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis17 <- CohortMethod::createCmAnalysis(analysisId = 17,
# description = description17,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to365StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = oneToOneMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
cmAnalysis18 <- CohortMethod::createCmAnalysis(analysisId = 18,
description = description18,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment365to365StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = unConditionedCox)
#Variable-ratio PS matching
# cmAnalysis19 <- CohortMethod::createCmAnalysis(analysisId = 19,
# description = description19,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment1to365StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = variableRatioMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
# cmAnalysis20 <- CohortMethod::createCmAnalysis(analysisId = 20,
# description = description20,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to365StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = variableRatioMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
cmAnalysis21 <- CohortMethod::createCmAnalysis(analysisId = 21,
description = description21,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment365to365StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = variableRatioMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = conditionedCox)
#PS stratification
# cmAnalysis22 <- CohortMethod::createCmAnalysis(analysisId = 22,
# description = description22,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment1to365StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# stratifyByPs = TRUE,
# stratifyByPsArgs = stratificationMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
# cmAnalysis23 <- CohortMethod::createCmAnalysis(analysisId = 23,
# description = description23,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to365StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# stratifyByPs = TRUE,
# stratifyByPsArgs = stratificationMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
cmAnalysis24 <- CohortMethod::createCmAnalysis(analysisId = 24,
description = description24,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = OnTreatment365to365StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratificationMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = conditionedCox)
# ####25-36####
# #Without matching
# cmAnalysis25 <- CohortMethod::createCmAnalysis(analysisId = 25,
# description = description25,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment1to1095StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis26 <- CohortMethod::createCmAnalysis(analysisId = 26,
# description = description26,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to1095StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis27 <- CohortMethod::createCmAnalysis(analysisId = 27,
# description = description27,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment365to1095StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# #1:1 PS matching
# cmAnalysis28 <- CohortMethod::createCmAnalysis(analysisId = 28,
# description = description28,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment1to1095StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = oneToOneMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis29 <- CohortMethod::createCmAnalysis(analysisId = 29,
# description = description29,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to1095StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = oneToOneMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis30 <- CohortMethod::createCmAnalysis(analysisId = 30,
# description = description30,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment365to1095StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = oneToOneMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# #Variable-ratio PS matching
# cmAnalysis31 <- CohortMethod::createCmAnalysis(analysisId = 31,
# description = description31,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment1to1095StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = variableRatioMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
# cmAnalysis32 <- CohortMethod::createCmAnalysis(analysisId = 32,
# description = description32,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to1095StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = variableRatioMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
# cmAnalysis33 <- CohortMethod::createCmAnalysis(analysisId = 33,
# description = description33,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment365to1095StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = variableRatioMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
#
# #PS stratification
# cmAnalysis34 <- CohortMethod::createCmAnalysis(analysisId = 34,
# description = description34,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment1to1095StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# stratifyByPs = TRUE,
# stratifyByPsArgs = stratificationMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
# cmAnalysis35 <- CohortMethod::createCmAnalysis(analysisId = 35,
# description = description35,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment30to1095StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# stratifyByPs = TRUE,
# stratifyByPsArgs = stratificationMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
# cmAnalysis36 <- CohortMethod::createCmAnalysis(analysisId = 36,
# description = description36,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = OnTreatment365to1095StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# stratifyByPs = TRUE,
# stratifyByPsArgs = stratificationMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
####37-48####
#Without matching
cmAnalysis37 <- CohortMethod::createCmAnalysis(analysisId = 37,
description = description37,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf1StudyPopArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis38 <- CohortMethod::createCmAnalysis(analysisId = 38,
# description = description38,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = ITTBlankingOf30StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
cmAnalysis39 <- CohortMethod::createCmAnalysis(analysisId = 39,
description = description39,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = unConditionedCox)
#1:1 PS matching
cmAnalysis40 <- CohortMethod::createCmAnalysis(analysisId = 40,
description = description40,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf1StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis41 <- CohortMethod::createCmAnalysis(analysisId = 41,
# description = description41,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = ITTBlankingOf30StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = oneToOneMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
cmAnalysis42 <- CohortMethod::createCmAnalysis(analysisId = 42,
description = description42,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = unConditionedCox)
#Variable-ratio PS matching
cmAnalysis43 <- CohortMethod::createCmAnalysis(analysisId = 43,
description = description43,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf1StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = variableRatioMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = conditionedCox)
# cmAnalysis44 <- CohortMethod::createCmAnalysis(analysisId = 44,
# description = description44,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = ITTBlankingOf30StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# matchOnPs = TRUE,
# matchOnPsArgs = variableRatioMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
cmAnalysis45 <- CohortMethod::createCmAnalysis(analysisId = 45,
description = description45,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = variableRatioMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = conditionedCox)
#PS stratification
cmAnalysis46 <- CohortMethod::createCmAnalysis(analysisId = 46,
description = description46,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf1StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratificationMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = conditionedCox)
# cmAnalysis47 <- CohortMethod::createCmAnalysis(analysisId = 47,
# description = description47,
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = ITTBlankingOf30StudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# stratifyByPs = TRUE,
# stratifyByPsArgs = stratificationMatchOnPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = conditionedCox)
cmAnalysis48 <- CohortMethod::createCmAnalysis(analysisId = 48,
description = description48,
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
createPs = TRUE,
createPsArgs = createPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratificationMatchOnPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = conditionedCox)
####Interaction terms####
subGroupCovariateSettings <- RanitidineCancerRisk::createSubgroupCovariateSettings(windowStart = -365,
windowEnd = -1,
shortTermWindowStart = -7,
MaintenanceWindowEnd = 365,
analysisId = 998)
interactionDbCmDataArgs <- CohortMethod::createGetDbCohortMethodDataArgs(washoutPeriod = 365,
restrictToCommonPeriod = TRUE,
firstExposureOnly = FALSE,
removeDuplicateSubjects = "keep first",
studyStartDate = "",
studyEndDate = "",
excludeDrugsFromCovariates = FALSE,
covariateSettings = list(covarSettings, subGroupCovariateSettings))
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)
cmAnalysis1998 <- CohortMethod::createCmAnalysis(analysisId = 1998,
description = paste0(description42,", interaction:female"),
getDbCohortMethodDataArgs = interactionDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgsI1998,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs)
cmAnalysis2998 <- CohortMethod::createCmAnalysis(analysisId = 2998,
description = paste0(description42,", interaction:elderly (age >= 65)"),
getDbCohortMethodDataArgs = interactionDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgsI2998,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs)
cmAnalysis3998 <- CohortMethod::createCmAnalysis(analysisId = 3998,
description = paste0(description42,", interaction:cumulative drug dose than 365 unit"),
getDbCohortMethodDataArgs = interactionDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgsI3998,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs)
cmAnalysis4998 <- CohortMethod::createCmAnalysis(analysisId = 4998,
description = paste0(description42,", interaction:cumulative drug dose than 730 unit"),
getDbCohortMethodDataArgs = interactionDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgsI4998,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs)
cmAnalysis5998 <- CohortMethod::createCmAnalysis(analysisId = 5998,
description = paste0(description42,", interaction:cumulative drug dose than 1095 unit"),
getDbCohortMethodDataArgs = interactionDbCmDataArgs,
createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgsI5998,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = oneToOneMatchOnPsArgs)
# interactionCovariateIds <- c(8532001, 201826210, 21600960413) # Female, T2DM, concurent use of antithrombotic agents
#
# fitOutcomeModelArgs3 <- CohortMethod::createFitOutcomeModelArgs(modelType = "cox",
# stratified = TRUE,
# useCovariates = FALSE,
# interactionCovariateIds = interactionCovariateIds)
#
# cmAnalysis5 <- CohortMethod::createCmAnalysis(analysisId = 5,
# description = "Stratification with interaction terms",
# getDbCohortMethodDataArgs = getDbCmDataArgs,
# createStudyPopArgs = createOnTreatmentStudyPopArgs,
# createPs = TRUE,
# createPsArgs = createPsArgs,
# stratifyByPs = TRUE,
# stratifyByPsArgs = stratifyByPsArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = fitOutcomeModelArgs3)
#paste0("cmAnalysis",1:48,collapse=", ")
cmAnalysisList <- list(cmAnalysis1, #cmAnalysis2, cmAnalysis3,
cmAnalysis4, #cmAnalysis5, cmAnalysis6,
cmAnalysis7, #cmAnalysis8, cmAnalysis9,
cmAnalysis10, #cmAnalysis11, cmAnalysis12,
#cmAnalysis13, #cmAnalysis14,
cmAnalysis15, #cmAnalysis16, cmAnalysis17,
cmAnalysis18, #cmAnalysis19, cmAnalysis20,
cmAnalysis21, #cmAnalysis22, cmAnalysis23,
cmAnalysis24,
#cmAnalysis25, cmAnalysis26, cmAnalysis27, cmAnalysis28, cmAnalysis29, cmAnalysis30, cmAnalysis31, cmAnalysis32, cmAnalysis33, cmAnalysis34, cmAnalysis35, cmAnalysis36,
cmAnalysis37, #cmAnalysis38,
cmAnalysis39, cmAnalysis40, #cmAnalysis41,
cmAnalysis42, cmAnalysis43,
#cmAnalysis44,
cmAnalysis45, cmAnalysis46, #cmAnalysis47,
cmAnalysis48,
cmAnalysis1998, cmAnalysis2998, cmAnalysis3998, cmAnalysis4998, cmAnalysis5998)
CohortMethod::saveCmAnalysisList(cmAnalysisList, file.path(workFolder, "cmAnalysisList.json"))
}
createPositiveControlSynthesisArgs <- function(workFolder) {
settings <- list(
outputIdOffset = 10000,
firstExposureOnly = TRUE,
firstOutcomeOnly = TRUE,
removePeopleWithPriorOutcomes = TRUE,
modelType = "survival",
washoutPeriod = 365,
riskWindowStart = 0,
riskWindowEnd = 30,
addExposureDaysToEnd = TRUE,
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(useDemographicsAgeGroup = TRUE,
useDemographicsGender = TRUE,
useDemographicsIndexYear = TRUE,
useDemographicsIndexMonth = TRUE,
useConditionGroupEraLongTerm = TRUE,
useDrugGroupEraLongTerm = TRUE,
useProcedureOccurrenceLongTerm = TRUE,
useMeasurementLongTerm = TRUE,
useObservationLongTerm = TRUE,
useCharlsonIndex = TRUE,
useDcsi = TRUE,
useChads2Vasc = TRUE,
longTermStartDays = -365,
endDays = 0)
)
ParallelLogger::saveSettingsToJson(settings, file.path(workFolder, "positiveControlSynthArgs.json"))
}
# createFeasibilityAnalysesDetails <- function(workFolder) {
# maxCohortSizeForFitting = 1000
# minCovarSettings <- FeatureExtraction::createCovariateSettings(useDemographicsGender = TRUE,
# useDemographicsAge = TRUE,
# useDemographicsAgeGroup = TRUE,
# useDemographicsRace = TRUE,
# useDemographicsEthnicity = TRUE,
# useDemographicsIndexYear = TRUE,
# useDemographicsPriorObservationTime = TRUE,
# useDemographicsPostObservationTime = TRUE,
# useDemographicsTimeInCohort = TRUE)
#
#
# minDbCmDataArgs <- CohortMethod::createGetDbCohortMethodDataArgs(washoutPeriod = 365,
# restrictToCommonPeriod = TRUE,
# firstExposureOnly = FALSE,
# removeDuplicateSubjects = "keep first",
# studyStartDate = "",
# studyEndDate = "",
# excludeDrugsFromCovariates = FALSE,
# covariateSettings = minCovarSettings)
#
# OnTreatment1to0StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 1,
# startAnchor = "cohort start",
# riskWindowEnd = 0,
# endAnchor = "cohort end")
#
# # OnTreatment30to0StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# # minDaysAtRisk = 1,
# # riskWindowStart = 30,
# # startAnchor = "cohort start",
# # riskWindowEnd = 0,
# # endAnchor = "cohort end")
#
# OnTreatment365to0StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 365,
# startAnchor = "cohort start",
# riskWindowEnd = 0,
# endAnchor = "cohort end")
#
# OnTreatment1to365StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 1,
# startAnchor = "cohort start",
# riskWindowEnd = 365,
# endAnchor = "cohort end")
#
# # OnTreatment30to365StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# # minDaysAtRisk = 1,
# # riskWindowStart = 30,
# # startAnchor = "cohort start",
# # riskWindowEnd = 365,
# # endAnchor = "cohort end")
#
# OnTreatment365to365StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 365,
# startAnchor = "cohort start",
# riskWindowEnd = 365,
# endAnchor = "cohort end")
#
# # OnTreatment1to1095StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# # minDaysAtRisk = 1,
# # riskWindowStart = 1,
# # startAnchor = "cohort start",
# # riskWindowEnd = 1095,
# # endAnchor = "cohort end")
#
# # OnTreatment30to1095StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# # minDaysAtRisk = 1,
# # riskWindowStart = 30,
# # startAnchor = "cohort start",
# # riskWindowEnd = 1095,
# # endAnchor = "cohort end")
#
# # OnTreatment365to1095StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# # minDaysAtRisk = 1,
# # riskWindowStart = 365,
# # startAnchor = "cohort start",
# # riskWindowEnd = 1095,
# # endAnchor = "cohort end")
#
# ITTBlankingOf1StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 1,
# startAnchor = "cohort start",
# riskWindowEnd = 9999,
# endAnchor = "cohort end")
#
# # ITTBlankingOf30StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# # minDaysAtRisk = 1,
# # riskWindowStart = 30,
# # startAnchor = "cohort start",
# # riskWindowEnd = 9999,
# # endAnchor = "cohort end")
#
# ITTBlankingOf365StudyPopArgs <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
# minDaysAtRisk = 1,
# riskWindowStart = 365,
# startAnchor = "cohort start",
# riskWindowEnd = 9999,
# endAnchor = "cohort end")
#
#
# # createPsArgs <- CohortMethod::createCreatePsArgs(control = Cyclops::createControl(cvType = "auto",
# # startingVariance = 0.01,
# # noiseLevel = "quiet",
# # tolerance = 2e-07,
# # cvRepetitions = 10),
# # errorOnHighCorrelation = TRUE,
# # stopOnError = F,
# # maxCohortSizeForFitting = maxCohortSizeForFitting)
#
#
# unConditionedCox <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
# modelType = "cox",
# stratified = FALSE)
#
# conditionedCox <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
# modelType = "cox",
# stratified = TRUE)
#
# oneToOneMatchOnPsArgs <- CohortMethod::createMatchOnPsArgs(maxRatio = 1)
#
# variableRatioMatchOnPsArgs <- CohortMethod::createMatchOnPsArgs(maxRatio = 100)
#
# stratificationMatchOnPsArgs <- CohortMethod::createStratifyByPsArgs(numberOfStrata = 10)
#
# description1 = "No PS matching, On-treatment"
# #description2 = "No PS matching, On-treatment, with blanking period of 30 days"
# description3 = "No PS matching, On-treatment, with 1-year blanking period"
#
# description13 = "No PS matching, On-treatment with 1-year lag period"
# #description14 = "No PS matching, 1 Year added to on-treatment, with blanking period of 30 days"
# description15 = "No PS matching, On-treatment, with 1-year lag period, with 1-year blanking period"
#
# #description25 = "No PS matching, 3 Year added to on-treatment"
# #description26 = "No PS matching, 3 Year added to on-treatment, with blanking period of 30 days"
# #description27 = "No PS matching, 3 Year added to on-treatment, with blanking period of 1 year"
#
# description37 = "No PS matching, ITT"
# #description38 = "No PS matching, ITT, with blanking period of 30 days"
# description39 = "No PS matching, ITT, with 1-year blanking period"
#
#
# ####1-12####
# #Without matching
# cmAnalysis991 <- CohortMethod::createCmAnalysis(analysisId = 991,
# description = description1,
# getDbCohortMethodDataArgs = minDbCmDataArgs,
# createStudyPopArgs = OnTreatment1to0StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# # cmAnalysis992 <- CohortMethod::createCmAnalysis(analysisId = 992,
# # description = description2,
# # getDbCohortMethodDataArgs = minDbCmDataArgs,
# # createStudyPopArgs = OnTreatment30to0StudyPopArgs,
# # fitOutcomeModel = TRUE,
# # fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis993 <- CohortMethod::createCmAnalysis(analysisId = 993,
# description = description3,
# getDbCohortMethodDataArgs = minDbCmDataArgs,
# createStudyPopArgs = OnTreatment365to0StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
#
# ####13-24####
# #Without matching
# cmAnalysis913 <- CohortMethod::createCmAnalysis(analysisId = 913,
# description = description13,
# getDbCohortMethodDataArgs = minDbCmDataArgs,
# createStudyPopArgs = OnTreatment1to365StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# # cmAnalysis914 <- CohortMethod::createCmAnalysis(analysisId = 914,
# # description = description14,
# # getDbCohortMethodDataArgs = minDbCmDataArgs,
# # createStudyPopArgs = OnTreatment30to365StudyPopArgs,
# # fitOutcomeModel = TRUE,
# # fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis915 <- CohortMethod::createCmAnalysis(analysisId = 915,
# description = description15,
# getDbCohortMethodDataArgs = minDbCmDataArgs,
# createStudyPopArgs = OnTreatment365to365StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# ####25-36####
# #Without matching
# # cmAnalysis925 <- CohortMethod::createCmAnalysis(analysisId = 925,
# # description = description25,
# # getDbCohortMethodDataArgs = minDbCmDataArgs,
# # createStudyPopArgs = OnTreatment1to1095StudyPopArgs,
# # fitOutcomeModel = TRUE,
# # fitOutcomeModelArgs = unConditionedCox)
# # cmAnalysis926 <- CohortMethod::createCmAnalysis(analysisId = 926,
# # description = description26,
# # getDbCohortMethodDataArgs = minDbCmDataArgs,
# # createStudyPopArgs = OnTreatment30to1095StudyPopArgs,
# # fitOutcomeModel = TRUE,
# # fitOutcomeModelArgs = unConditionedCox)
# # cmAnalysis927 <- CohortMethod::createCmAnalysis(analysisId = 927,
# # description = description27,
# # getDbCohortMethodDataArgs = minDbCmDataArgs,
# # createStudyPopArgs = OnTreatment365to1095StudyPopArgs,
# # fitOutcomeModel = TRUE,
# # fitOutcomeModelArgs = unConditionedCox)
# ####37-48####
# #Without matching
# cmAnalysis937 <- CohortMethod::createCmAnalysis(analysisId = 937,
# description = description37,
# getDbCohortMethodDataArgs = minDbCmDataArgs,
# createStudyPopArgs = ITTBlankingOf1StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
# # cmAnalysis938 <- CohortMethod::createCmAnalysis(analysisId = 938,
# # description = description38,
# # getDbCohortMethodDataArgs = minDbCmDataArgs,
# # createStudyPopArgs = ITTBlankingOf30StudyPopArgs,
# # fitOutcomeModel = TRUE,
# # fitOutcomeModelArgs = unConditionedCox)
# cmAnalysis939 <- CohortMethod::createCmAnalysis(analysisId = 939,
# description = description39,
# getDbCohortMethodDataArgs = minDbCmDataArgs,
# createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = unConditionedCox)
#
# ####Interaction terms####
# subGroupCovariateSettings <- RanitidineCancerRisk::createSubgroupCovariateSettings(windowStart = -365,
# windowEnd = -1,
# shortTermWindowStart = -7,
# MaintenanceWindowEnd = 365,
# analysisId = 998)
#
# interactionDbCmDataArgs <- CohortMethod::createGetDbCohortMethodDataArgs(washoutPeriod = 365,
# restrictToCommonPeriod = TRUE,
# firstExposureOnly = FALSE,
# removeDuplicateSubjects = "keep first",
# studyStartDate = "",
# studyEndDate = "",
# excludeDrugsFromCovariates = FALSE,
# covariateSettings = list(minCovarSettings, subGroupCovariateSettings))
#
# 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)
#
# cmAnalysis1998 <- CohortMethod::createCmAnalysis(analysisId = 1998,
# description = paste0(description39,", interaction:female"),
# getDbCohortMethodDataArgs = interactionDbCmDataArgs,
# createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = fitOutcomeModelArgsI1998)
#
# cmAnalysis2998 <- CohortMethod::createCmAnalysis(analysisId = 2998,
# description = paste0(description39,", interaction:elderly (age >= 65)"),
# getDbCohortMethodDataArgs = interactionDbCmDataArgs,
# createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = fitOutcomeModelArgsI2998)
#
# cmAnalysis3998 <- CohortMethod::createCmAnalysis(analysisId = 3998,
# description = paste0(description39,", interaction:cumulative drug dose than 365 unit"),
# getDbCohortMethodDataArgs = interactionDbCmDataArgs,
# createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = fitOutcomeModelArgsI3998)
#
# cmAnalysis4998 <- CohortMethod::createCmAnalysis(analysisId = 4998,
# description = paste0(description39,", interaction:cumulative drug dose than 730 unit"),
# getDbCohortMethodDataArgs = interactionDbCmDataArgs,
# createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = fitOutcomeModelArgsI4998)
#
# cmAnalysis5998 <- CohortMethod::createCmAnalysis(analysisId = 5998,
# description = paste0(description39,", interaction:cumulative drug dose than 1095 unit"),
# getDbCohortMethodDataArgs = interactionDbCmDataArgs,
# createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
# fitOutcomeModel = TRUE,
# fitOutcomeModelArgs = fitOutcomeModelArgsI5998)
#
# # cmAnalysis6998 <- CohortMethod::createCmAnalysis(analysisId = 6998,
# # description = paste0(description39,", interaction:gastric ulcer history within previous 1 year"),
# # getDbCohortMethodDataArgs = interactionDbCmDataArgs,
# # createStudyPopArgs = ITTBlankingOf365StudyPopArgs,
# # fitOutcomeModel = TRUE,
# # fitOutcomeModelArgs = fitOutcomeModelArgsI6998)
#
# cmAnalysisFeasibilityList <- list(cmAnalysis991, cmAnalysis993,
# cmAnalysis913, cmAnalysis915,
# cmAnalysis937, cmAnalysis939,
# cmAnalysis1998, cmAnalysis2998, cmAnalysis3998, cmAnalysis4998, cmAnalysis5998#, cmAnalysis6998
# )
#
# CohortMethod::saveCmAnalysisList(cmAnalysisFeasibilityList, file.path(workFolder, "cmAnalysisFeasibilityList.json"))
# }
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