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‎DESCRIPTION

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Package: CohortMethod
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Type: Package
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Title: New-User Cohort Method with Large Scale Propensity and Outcome Models
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Version: 5.2.0
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Date: 2023-12-21
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Version: 5.2.1
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Date: 2024-02-01
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Authors@R: c(
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person("Martijn", "Schuemie", , "[email protected]", role = c("aut", "cre")),
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person("Marc", "Suchard", role = c("aut")),
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ohdsi/ShinyAppBuilder
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LinkingTo: Rcpp
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NeedsCompilation: yes
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RoxygenNote: 7.2.3
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RoxygenNote: 7.3.1
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Roxygen: list(markdown = TRUE)
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Encoding: UTF-8

‎NEWS.md

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CohortMethod 5.2.1
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==================
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Changes:
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1. Ask to delete files in output folder when calling `runCmAnalyses()` with different analyses settings than those used to create the files. Also cleaning the cache.
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Bugfixes:
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1. Fixed bug in parsing covariate filter settings for balance.
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2. Updated vignettes to use latest `Capr` functions.
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CohortMethod 5.2.0
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==================
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‎R/Analyses.R

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# @file Analyses.R
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#
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# Copyright 2023 Observational Health Data Sciences and Informatics
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# Copyright 2024 Observational Health Data Sciences and Informatics
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#
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# This file is part of CohortMethod
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#

‎R/AttritionDiagram.R

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# @file AttritionDiagram.R
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#
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# Copyright 2023 Observational Health Data Sciences and Informatics
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# Copyright 2024 Observational Health Data Sciences and Informatics
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#
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# This file is part of CohortMethod
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#

‎R/Balance.R

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# Copyright 2023 Observational Health Data Sciences and Informatics
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# Copyright 2024 Observational Health Data Sciences and Informatics
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#
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# This file is part of CohortMethod
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#
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covariateIds2 <- covariateFilter %>%
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filter(!is.na(.data$covariateIds)) %>%
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pull(.data$covariateIds) %>%
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strsplit(",") %>%
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strsplit(",|;") %>%
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unlist() %>%
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as.numeric()
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covariates %>%

‎R/CohortMethod.R

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# @file CohortMethod.R
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#
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# Copyright 2023 Observational Health Data Sciences and Informatics
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# Copyright 2024 Observational Health Data Sciences and Informatics
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#
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# This file is part of CohortMethod
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#

‎R/CohortMethodData.R

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# Copyright 2023 Observational Health Data Sciences and Informatics
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# Copyright 2024 Observational Health Data Sciences and Informatics
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#
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# This file is part of CohortMethod
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#

‎R/DataLoadingSaving.R

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# Copyright 2023 Observational Health Data Sciences and Informatics
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# Copyright 2024 Observational Health Data Sciences and Informatics
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#
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# This file is part of CohortMethod
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#

‎R/Export.R

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# Copyright 2023 Observational Health Data Sciences and Informatics
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# Copyright 2024 Observational Health Data Sciences and Informatics
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#
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# This file is part of CohortMethod
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#

‎R/HelperFunctions.R

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# @file HelperFunctions.R
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#
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# Copyright 2023 Observational Health Data Sciences and Informatics
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# Copyright 2024 Observational Health Data Sciences and Informatics
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#
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# This file is part of CohortMethod
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#

‎R/KaplanMeier.R

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# @file KaplanMeier.R
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#
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# Copyright 2023 Observational Health Data Sciences and Informatics
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# Copyright 2024 Observational Health Data Sciences and Informatics
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#
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# This file is part of CohortMethod
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#

‎R/OutcomeModels.R

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# Copyright 2023 Observational Health Data Sciences and Informatics
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# Copyright 2024 Observational Health Data Sciences and Informatics
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#
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# This file is part of CohortMethod
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#

‎R/Power.R

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# @file Power.R
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#
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# Copyright 2023 Observational Health Data Sciences and Informatics
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# Copyright 2024 Observational Health Data Sciences and Informatics
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#
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# This file is part of CohortMethod
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#

‎R/PsFunctions.R

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# Copyright 2023 Observational Health Data Sciences and Informatics
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# Copyright 2024 Observational Health Data Sciences and Informatics
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#
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# This file is part of CohortMethod
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#

‎R/ResultsDataModel.R

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# Copyright 2023 Observational Health Data Sciences and Informatics
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# Copyright 2024 Observational Health Data Sciences and Informatics
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#
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# This file is part of CohortMethod
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#

‎R/RunAnalyses.R

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# Copyright 2023 Observational Health Data Sciences and Informatics
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# Copyright 2024 Observational Health Data Sciences and Informatics
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#
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# This file is part of CohortMethod
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#
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stop("Duplicate analysis IDs are not allowed")
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}
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outputFolder <- normalizePath(outputFolder, mustWork = FALSE)
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cmAnalysisListFile <- file.path(outputFolder, "cmAnalysisList.rds")
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if (file.exists(cmAnalysisListFile)) {
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oldCmAnalysisList <- readRDS(cmAnalysisListFile)
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if (!isTRUE(all.equal(oldCmAnalysisList, cmAnalysisList))) {
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rm(list=ls(envir = cache), envir = cache)
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message(sprintf("Output files already exist in '%s', but the analysis settings have changed.", outputFolder))
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response <- utils::askYesNo("Do you want to delete the old files before proceeding?")
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if (is.na(response)) {
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# Cancel:
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return()
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} else if (response == TRUE) {
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unlink(outputFolder, recursive = TRUE)
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}
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}
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}
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if (!file.exists(outputFolder)) {
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dir.create(outputFolder)
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}
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saveRDS(cmAnalysisList, cmAnalysisListFile)
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saveRDS(targetComparatorOutcomesList, file.path(outputFolder, "targetComparatorOutcomesList.rds"))
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referenceTable <- createReferenceTable(
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cmAnalysisList = cmAnalysisList,
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targetComparatorOutcomesList = targetComparatorOutcomesList,
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select(-"includedCovariateConceptIds", "excludedCovariateConceptIds") %>%
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saveRDS(file.path(outputFolder, "outcomeModelReference.rds"))
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saveRDS(cmAnalysisList, file.path(outputFolder, "cmAnalysisList.rds"))
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saveRDS(targetComparatorOutcomesList, file.path(outputFolder, "targetComparatorOutcomesList.rds"))
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# Create cohortMethodData objects -----------------------------
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subset <- referenceTable[!duplicated(referenceTable$cohortMethodDataFile), ]
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subset <- subset[subset$cohortMethodDataFile != "", ]

‎R/Simulation.R

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# Copyright 2023 Observational Health Data Sciences and Informatics
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# Copyright 2024 Observational Health Data Sciences and Informatics
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#
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# This file is part of CohortMethod
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#

‎R/StudyPopulation.R

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# Copyright 2023 Observational Health Data Sciences and Informatics
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# Copyright 2024 Observational Health Data Sciences and Informatics
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#
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# This file is part of CohortMethod
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#

‎R/Table1.R

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# @file Table1.R
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#
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# Copyright 2023 Observational Health Data Sciences and Informatics
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# Copyright 2024 Observational Health Data Sciences and Informatics
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#
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# This file is part of CohortMethod
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#

‎R/Viewer.R

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# Copyright 2023 Observational Health Data Sciences and Informatics
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# Copyright 2024 Observational Health Data Sciences and Informatics
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#
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# This file is part of CohortMethod
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#

‎docs/404.html

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