Merge branch 'develop'

OHDSI · Feb 2, 2024 · 6d8d51d · 6d8d51d
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: CohortMethod
 Type: Package
 Title: New-User Cohort Method with Large Scale Propensity and Outcome Models
-Version: 5.2.0
-Date: 2023-12-21
+Version: 5.2.1
+Date: 2024-02-01
 Authors@R: c(
 	person("Martijn", "Schuemie", , "schuemie@ohdsi.org", role = c("aut", "cre")),
 	person("Marc", "Suchard", role = c("aut")),
@@ -70,6 +70,6 @@ Remotes:
 	ohdsi/ShinyAppBuilder
 LinkingTo: Rcpp
 NeedsCompilation: yes
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
 Encoding: UTF-8
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,17 @@
+CohortMethod 5.2.1
+==================
+
+Changes:
+
+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.
+
+Bugfixes:
+
+1. Fixed bug in parsing covariate filter settings for balance.
+
+2. Updated vignettes to use latest `Capr` functions.
+
+
 CohortMethod 5.2.0
 ==================
 

diff --git a/R/Analyses.R b/R/Analyses.R
@@ -1,6 +1,6 @@
 # @file Analyses.R
 #
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortMethod
 #

diff --git a/R/AttritionDiagram.R b/R/AttritionDiagram.R
@@ -1,6 +1,6 @@
 # @file AttritionDiagram.R
 #
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortMethod
 #

diff --git a/R/Balance.R b/R/Balance.R
@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortMethod
 #
@@ -36,7 +36,7 @@ filterCovariates <- function(covariates, covariateRef, covariateFilter) {
     covariateIds2 <- covariateFilter %>%
       filter(!is.na(.data$covariateIds)) %>%
       pull(.data$covariateIds) %>%
-      strsplit(",") %>%
+      strsplit(",|;") %>%
       unlist() %>%
       as.numeric()
     covariates %>%

diff --git a/R/CohortMethod.R b/R/CohortMethod.R
@@ -1,6 +1,6 @@
 # @file CohortMethod.R
 #
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortMethod
 #

diff --git a/R/CohortMethodData.R b/R/CohortMethodData.R
@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortMethod
 #

diff --git a/R/DataLoadingSaving.R b/R/DataLoadingSaving.R
@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortMethod
 #

diff --git a/R/Export.R b/R/Export.R
@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortMethod
 #

diff --git a/R/HelperFunctions.R b/R/HelperFunctions.R
@@ -1,6 +1,6 @@
 # @file HelperFunctions.R
 #
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortMethod
 #

diff --git a/R/KaplanMeier.R b/R/KaplanMeier.R
@@ -1,6 +1,6 @@
 # @file KaplanMeier.R
 #
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortMethod
 #

diff --git a/R/OutcomeModels.R b/R/OutcomeModels.R
@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortMethod
 #

diff --git a/R/Power.R b/R/Power.R
@@ -1,6 +1,6 @@
 # @file Power.R
 #
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortMethod
 #

diff --git a/R/PsFunctions.R b/R/PsFunctions.R
@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortMethod
 #

diff --git a/R/ResultsDataModel.R b/R/ResultsDataModel.R
@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortMethod
 #

diff --git a/R/RunAnalyses.R b/R/RunAnalyses.R
@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortMethod
 #
@@ -259,10 +259,26 @@ runCmAnalyses <- function(connectionDetails,
     stop("Duplicate analysis IDs are not allowed")
   }
   outputFolder <- normalizePath(outputFolder, mustWork = FALSE)
+  cmAnalysisListFile <- file.path(outputFolder, "cmAnalysisList.rds")
+  if (file.exists(cmAnalysisListFile)) {
+    oldCmAnalysisList <- readRDS(cmAnalysisListFile)
+    if (!isTRUE(all.equal(oldCmAnalysisList, cmAnalysisList))) {
+      rm(list=ls(envir = cache), envir = cache)
+      message(sprintf("Output files already exist in '%s', but the analysis settings have changed.", outputFolder))
+      response <- utils::askYesNo("Do you want to delete the old files before proceeding?")
+      if (is.na(response)) {
+        # Cancel:
+        return()
+      } else if (response == TRUE) {
+        unlink(outputFolder, recursive = TRUE)
+      }
+    }
+  }
   if (!file.exists(outputFolder)) {
     dir.create(outputFolder)
   }
-
+  saveRDS(cmAnalysisList, cmAnalysisListFile)
+  saveRDS(targetComparatorOutcomesList, file.path(outputFolder, "targetComparatorOutcomesList.rds"))
   referenceTable <- createReferenceTable(
     cmAnalysisList = cmAnalysisList,
     targetComparatorOutcomesList = targetComparatorOutcomesList,
@@ -275,9 +291,6 @@ runCmAnalyses <- function(connectionDetails,
     select(-"includedCovariateConceptIds", "excludedCovariateConceptIds") %>%
     saveRDS(file.path(outputFolder, "outcomeModelReference.rds"))
 
-  saveRDS(cmAnalysisList, file.path(outputFolder, "cmAnalysisList.rds"))
-  saveRDS(targetComparatorOutcomesList, file.path(outputFolder, "targetComparatorOutcomesList.rds"))
-
   # Create cohortMethodData objects -----------------------------
   subset <- referenceTable[!duplicated(referenceTable$cohortMethodDataFile), ]
   subset <- subset[subset$cohortMethodDataFile != "", ]

diff --git a/R/Simulation.R b/R/Simulation.R
@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortMethod
 #

diff --git a/R/StudyPopulation.R b/R/StudyPopulation.R
@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortMethod
 #

diff --git a/R/Table1.R b/R/Table1.R
@@ -1,6 +1,6 @@
 # @file Table1.R
 #
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortMethod
 #

diff --git a/R/Viewer.R b/R/Viewer.R
@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortMethod
 #

diff --git a/docs/404.html b/docs/404.html