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Cleaning up code.
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@schuemie
schuemie committed Dec 13, 2017
1 parent 5476282 commit c6ef2eb
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Showing 11 changed files with 55 additions and 330 deletions.
3 changes: 0 additions & 3 deletions PopEstMethodEvaluation/NAMESPACE
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Expand Up @@ -5,7 +5,6 @@ export(createCaseControlSettings)
export(createCaseCrossoverSettings)
export(createCohortMethodSettings)
export(createFiguresAndTables)
export(createIctpdSettings)
export(createMetaData)
export(createSccsSettings)
export(createSelfControlledCohortSettings)
Expand All @@ -14,7 +13,5 @@ export(packageResults)
export(runCaseControl)
export(runCaseCrossover)
export(runCohortMethod)
export(runIctpd)
export(runSelfControlledCaseSeries)
export(runSelfControlledCohort)
export(submitResults)
11 changes: 0 additions & 11 deletions PopEstMethodEvaluation/R/CaseCrossover.R
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Expand Up @@ -47,16 +47,6 @@ runCaseCrossover <- function(connectionDetails,
}
ccrAnalysisListFile <- system.file("settings", "ccrAnalysisSettings.txt", package = "PopEstMethodEvaluation")
ccrAnalysisList <- CaseCrossover::loadCcrAnalysisList(ccrAnalysisListFile)

mailSettings <- list(from = Sys.getenv("mailAddress"),
to = c(Sys.getenv("mailAddress")),
smtp = list(host.name = "smtp.gmail.com", port = 465,
user.name = Sys.getenv("mailAddress"),
passwd = Sys.getenv("mailPassword"), ssl = TRUE),
authenticate = TRUE,
send = TRUE)

result <- OhdsiRTools::runAndNotify({
ccrResult <- CaseCrossover::runCcrAnalyses(connectionDetails = connectionDetails,
cdmDatabaseSchema = cdmDatabaseSchema,
oracleTempSchema = oracleTempSchema,
Expand All @@ -72,7 +62,6 @@ runCaseCrossover <- function(connectionDetails,
selectSubjectsToIncludeThreads = min(5, maxCores),
getExposureStatusThreads = min(5, maxCores),
fitCaseCrossoverModelThreads = min(5, maxCores))
}, mailSettings = mailSettings, label = "wprdusmjtglay")
ccrSummary <- CaseCrossover::summarizeCcrAnalyses(ccrResult)
saveRDS(ccrSummary, ccrSummaryFile)
}
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31 changes: 13 additions & 18 deletions PopEstMethodEvaluation/R/CohortMethod.R
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Expand Up @@ -50,16 +50,6 @@ runCohortMethod <- function(connectionDetails,
}
cmAnalysisListFile <- system.file("settings", "cmAnalysisSettings.txt", package = "PopEstMethodEvaluation")
cmAnalysisList <- CohortMethod::loadCmAnalysisList(cmAnalysisListFile)
mailSettings <- list(from = Sys.getenv("mailAddress"),
to = c(Sys.getenv("mailAddress")),
smtp = list(host.name = "smtp.gmail.com", port = 465,
user.name = Sys.getenv("mailAddress"),
passwd = Sys.getenv("mailPassword"), ssl = TRUE),
authenticate = TRUE,
send = TRUE)

result <- OhdsiRTools::runAndNotify({

cmResult <- CohortMethod::runCmAnalyses(connectionDetails = connectionDetails,
cdmDatabaseSchema = cdmDatabaseSchema,
oracleTempSchema = oracleTempSchema,
Expand All @@ -76,11 +66,12 @@ runCohortMethod <- function(connectionDetails,
psCvThreads = min(10, floor(maxCores/3)),
computeCovarBalThreads = min(3, maxCores),
trimMatchStratifyThreads = min(10, maxCores),
fitOutcomeModelThreads = min(max(1, floor(maxCores/4)), 4),
outcomeCvThreads = min(4, maxCores),
fitOutcomeModelThreads = min(max(1, floor(maxCores/8)), 4),
outcomeCvThreads = min(10, maxCores),
refitPsForEveryOutcome = FALSE)
}, mailSettings = mailSettings, label = "wprdusmjtglaz")

cmSummary <- CohortMethod::summarizeAnalyses(cmResult)
# write.csv(cmSummary, file.path(workFolder, "cmSummary.csv"), row.names = FALSE)
saveRDS(cmSummary, cmSummaryFile)
}
delta <- Sys.time() - start
Expand All @@ -97,6 +88,7 @@ createCohortMethodSettings <- function(fileName) {
studyStartDate = "",
studyEndDate = "",
excludeDrugsFromCovariates = TRUE,
maxCohortSize = 250000,
covariateSettings = covariateSettings)

createStudyPopArgs1 <- CohortMethod::createCreateStudyPopulationArgs(removeSubjectsWithPriorOutcome = TRUE,
Expand All @@ -117,15 +109,16 @@ createCohortMethodSettings <- function(fileName) {
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)

createPsArgs <- CohortMethod::createCreatePsArgs(errorOnHighCorrelation = FALSE,
createPsArgs <- CohortMethod::createCreatePsArgs(errorOnHighCorrelation = TRUE,
stopOnError = FALSE,
maxCohortSizeForFitting = 150000,
control = Cyclops::createControl(cvType = "auto",
startingVariance = 0.01,
noiseLevel = "quiet",
tolerance = 2e-07,
cvRepetitions = 1))

matchOnPsArgs <- CohortMethod::createMatchOnPsArgs(maxRatio = 100)
matchOnPsArgs1 <- CohortMethod::createMatchOnPsArgs(maxRatio = 1)

cmAnalysis2 <- CohortMethod::createCmAnalysis(analysisId = 2,
description = "Matching plus simple outcome model",
Expand All @@ -134,7 +127,7 @@ createCohortMethodSettings <- function(fileName) {
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = matchOnPsArgs,
matchOnPsArgs = matchOnPsArgs1,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs1)

Expand All @@ -155,14 +148,16 @@ createCohortMethodSettings <- function(fileName) {
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)

matchOnPsArgs2 <- CohortMethod::createMatchOnPsArgs(maxRatio = 100)

cmAnalysis4 <- CohortMethod::createCmAnalysis(analysisId = 4,
description = "Matching plus stratified outcome model",
getDbCohortMethodDataArgs = getDbCmDataArgs,
createStudyPopArgs = createStudyPopArgs1,
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = matchOnPsArgs,
matchOnPsArgs = matchOnPsArgs2,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs2)

Expand All @@ -183,7 +178,7 @@ createCohortMethodSettings <- function(fileName) {
createPs = TRUE,
createPsArgs = createPsArgs,
matchOnPs = TRUE,
matchOnPsArgs = matchOnPsArgs,
matchOnPsArgs = matchOnPsArgs2,
fitOutcomeModel = TRUE,
fitOutcomeModelArgs = fitOutcomeModelArgs3)

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87 changes: 0 additions & 87 deletions PopEstMethodEvaluation/R/Ictpd.R
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This file was deleted.

18 changes: 3 additions & 15 deletions PopEstMethodEvaluation/R/SelfControlledCaseSeries.R
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Expand Up @@ -40,16 +40,6 @@ runSelfControlledCaseSeries <- function(connectionDetails,
}
sccsAnalysisListFile <- system.file("settings", "sccsAnalysisSettings.txt", package = "PopEstMethodEvaluation")
sccsAnalysisList <- SelfControlledCaseSeries::loadSccsAnalysisList(sccsAnalysisListFile)
mailSettings <- list(from = Sys.getenv("mailAddress"),
to = c(Sys.getenv("mailAddress")),
smtp = list(host.name = "smtp.gmail.com", port = 465,
user.name = Sys.getenv("mailAddress"),
passwd = Sys.getenv("mailPassword"), ssl = TRUE),
authenticate = TRUE,
send = TRUE)

result <- OhdsiRTools::runAndNotify({

sccsResult <- SelfControlledCaseSeries::runSccsAnalyses(connectionDetails = connectionDetails,
cdmDatabaseSchema = cdmDatabaseSchema,
oracleTempSchema = oracleTempSchema,
Expand All @@ -61,16 +51,14 @@ runSelfControlledCaseSeries <- function(connectionDetails,
cdmVersion = cdmVersion,
outputFolder = sccsFolder,
combineDataFetchAcrossOutcomes = TRUE,
compressSccsEraDataFiles = TRUE,
compressSccsEraDataFiles = FALSE,
getDbSccsDataThreads = 1,
createSccsEraDataThreads = 5,
fitSccsModelThreads = 5,
fitSccsModelThreads = 6,
cvThreads = 10)

sccsSummary <- SelfControlledCaseSeries::summarizeSccsAnalyses(sccsResult)
saveRDS(sccsSummary, sccsSummaryFile)
}, mailSettings = mailSettings, label = "wprdusmjtglaz")

}
delta <- Sys.time() - start
writeLines(paste("Completed SCCS analyses in", signif(delta, 3), attr(delta, "units")))
Expand All @@ -84,7 +72,7 @@ createSccsSettings <- function(fileName) {
studyStartDate = "",
studyEndDate = "",
exposureIds = c(),
maxCasesPerOutcome = 1000000)
maxCasesPerOutcome = 250000)

covarExposureOfInt <- SelfControlledCaseSeries::createCovariateSettings(label = "Exposure of interest",
includeCovariateIds = "exposureId",
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1 change: 0 additions & 1 deletion PopEstMethodEvaluation/R/SelfControlledCohort.R
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Expand Up @@ -53,7 +53,6 @@ runSelfControlledCohort <- function(connectionDetails,
cdmVersion = cdmVersion,
outputFolder = sccFolder,
analysisThreads = min(10, maxCores))

sccSummary <- SelfControlledCohort::summarizeAnalyses(sccResult)
saveRDS(sccSummary, sccSummaryFile)
}
Expand Down
47 changes: 0 additions & 47 deletions PopEstMethodEvaluation/R/SubmitResults.R
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This file was deleted.

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