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0.1 version document for Febuxostat Study
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Signed-off-by: chandryou <applegna@gmail.com>
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@chandryou
chandryou committed Sep 26, 2018
1 parent dac2499 commit 8b988b3
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115 changes: 97 additions & 18 deletions FebuxostatVsAllopurinolCVD/extras/CreateStudyAnalysisDetailsEurope.R
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Original file line number Diff line number Diff line change
Expand Up @@ -148,17 +148,38 @@ createAnalysesDetails <- function(workFolder) {
riskWindowEnd = 9999,
addExposureDaysToEnd = FALSE)

createStudyPopArgs3 <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
minDaysAtRisk = 1095,
riskWindowStart = 1,
addExposureDaysToStart = FALSE,
riskWindowEnd = 30,
addExposureDaysToEnd = TRUE)

fitOutcomeModelArgs1 <- CohortMethod::createFitOutcomeModelArgs(useCovariates = FALSE,
modelType = "cox",
stratified = FALSE)

cmAnalysis1 <- CohortMethod::createCmAnalysis(analysisId = 1,
description = "No matching",
description = "No matching On Treatment",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = createStudyPopArgs1,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)

cmAnalysis2 <- CohortMethod::createCmAnalysis(analysisId = 2,
description = "No matching ITT",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = createStudyPopArgs2,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)

cmAnalysis3 <- CohortMethod::createCmAnalysis(analysisId = 3,
description = "No matching with minDaysAtRisk more than 3yr",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = createStudyPopArgs3,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)

createPsArgs <- CohortMethod::createCreatePsArgs(control = Cyclops::createControl(cvType = "auto",
startingVariance = 0.01,
noiseLevel = "quiet",
Expand All @@ -171,8 +192,8 @@ createAnalysesDetails <- function(workFolder) {
modelType = "cox",
stratified = TRUE)

cmAnalysis2 <- CohortMethod::createCmAnalysis(analysisId = 2,
description = "One-on-one matching",
cmAnalysis4 <- CohortMethod::createCmAnalysis(analysisId = 4,
description = "One-on-one matching on Treatment",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = createStudyPopArgs1,
createPs = TRUE,
Expand All @@ -182,44 +203,102 @@ createAnalysesDetails <- function(workFolder) {
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)

matchOnPsArgs2 <- CohortMethod::createMatchOnPsArgs(maxRatio = 100)
cmAnalysis5 <- CohortMethod::createCmAnalysis(analysisId = 5,
description = "One-on-one matching ITT",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = createStudyPopArgs2,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = matchOnPsArgs1,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)

cmAnalysis3 <- CohortMethod::createCmAnalysis(analysisId = 3,
description = "Variable ratio matching",
cmAnalysis6 <- CohortMethod::createCmAnalysis(analysisId = 6,
description = "One-on-one matching with minDaysAtRisk more than 3yr",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = createStudyPopArgs1,
createStudyPopArgs = createStudyPopArgs3,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = matchOnPsArgs2,
matchOnPsArgs = matchOnPsArgs1,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)

stratifyByPsArgs <- CohortMethod::createStratifyByPsArgs(numberOfStrata = 5)
matchOnPsArgs2 <- CohortMethod::createMatchOnPsArgs(maxRatio = 100)

cmAnalysis4 <- CohortMethod::createCmAnalysis(analysisId = 4,
description = "Stratification",
cmAnalysis7 <- CohortMethod::createCmAnalysis(analysisId = 7,
description = "Variable ratio matching on Treatmet",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = createStudyPopArgs1,
createPs = TRUE,
createPsArgs = createPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratifyByPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = matchOnPsArgs2,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)

cmAnalysis5 <- CohortMethod::createCmAnalysis(analysisId = 5,
description = "One-on-one matching until observation end",
cmAnalysis8 <- CohortMethod::createCmAnalysis(analysisId = 8,
description = "Variable ratio matching ITT",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = createStudyPopArgs2,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = matchOnPsArgs1,
matchOnPsArgs = matchOnPsArgs2,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)

cmAnalysis9 <- CohortMethod::createCmAnalysis(analysisId = 9,
description = "Variable ratio matching with minDaysAtRisk more than 3yr",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = createStudyPopArgs3,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = matchOnPsArgs2,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)

cmAnalysisList <- list(cmAnalysis1, cmAnalysis2, cmAnalysis3, cmAnalysis4,cmAnalysis5)

stratifyByPsArgs <- CohortMethod::createStratifyByPsArgs(numberOfStrata = 10)

cmAnalysis10 <- CohortMethod::createCmAnalysis(analysisId = 10,
description = "Stratification on Treatment",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = createStudyPopArgs1,
createPs = TRUE,
createPsArgs = createPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratifyByPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)

cmAnalysis11 <- CohortMethod::createCmAnalysis(analysisId = 11,
description = "Stratification ITT",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = createStudyPopArgs2,
createPs = TRUE,
createPsArgs = createPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratifyByPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)

cmAnalysis12 <- CohortMethod::createCmAnalysis(analysisId = 12,
description = "Stratification with minDaysAtRisk more than 3y",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = createStudyPopArgs3,
createPs = TRUE,
createPsArgs = createPsArgs,
stratifyByPs = TRUE,
stratifyByPsArgs = stratifyByPsArgs,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)



cmAnalysisList <- list(cmAnalysis1, cmAnalysis2, cmAnalysis3, cmAnalysis4,cmAnalysis5, cmAnalysis6,
cmAnalysis7, cmAnalysis8, cmAnalysis9, cmAnalysis10, cmAnalysis11, cmAnalysis12)

CohortMethod::saveCmAnalysisList(cmAnalysisList, file.path(workFolder, "cmAnalysisListEurope.json"))
}
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