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OHDSI · Aug 28, 2024 · e7a9bf7 · e7a9bf7
1 parent cec7f1e
commit e7a9bf7
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Showing 17 changed files with 309 additions and 611 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -2,7 +2,6 @@
 
 export(convertConceptSetDataFrameToExpression)
 export(convertConceptSetExpressionToDataFrame)
-export(createPheValuatorCohortsFromConceptSet)
 export(extractConceptSetsInCohortDefinition)
 export(extractConceptSetsInCohortDefinitionSet)
 export(findOrphanConcepts)

diff --git a/R/ConvertConceptSetDataFrameToExpression.R b/R/ConvertConceptSetDataFrameToExpression.R
@@ -140,7 +140,7 @@ convertConceptSetDataFrameToExpression <-
           )
         )
     }
-    
+
     if (selectAllDescendants) {
       conceptSetExpressionDataFrame <-
         dplyr::bind_rows(

diff --git a/R/ConvertConceptSetExpressionToDataFrame.R b/R/ConvertConceptSetExpressionToDataFrame.R
@@ -56,43 +56,41 @@ convertConceptSetExpressionToDataFrame <-
 
     items2 <- list()
 
-    errorMessage <-
-      "Given concept set expression R list object does not conform to expected structure. \n
-                      It is a vector that is more than 3 levels deep."
-
     for (i in (1:length(items))) {
       df <- as.data.frame(items[[i]]) |>
         dplyr::tibble()
-      names(df) <- stringr::str_replace(string = tolower(names(df)),
-                                        pattern = "concept.",
-                                        replacement = "")
-
-      if ('isExcluded' %in% names(df)) {
+      names(df) <- stringr::str_replace(
+        string = tolower(names(df)),
+        pattern = "concept.",
+        replacement = ""
+      )
+
+      if ("isExcluded" %in% names(df)) {
         df <- df |>
           dplyr::rename("is_excluded" = "isExcluded")
-      } else if ('isexcluded' %in% names(df)) {
+      } else if ("isexcluded" %in% names(df)) {
         df <- df |>
           dplyr::rename("is_excluded" = "isexcluded")
       } else {
         df <- df |>
           dplyr::mutate(is_excluded = FALSE)
       }
-      
-      if ('includeMapped' %in% names(df)) {
+
+      if ("includeMapped" %in% names(df)) {
         df <- df |>
           dplyr::rename("include_mapped" = "includeMapped")
-      } else if ('includemapped' %in% names(df)) {
+      } else if ("includemapped" %in% names(df)) {
         df <- df |>
           dplyr::rename("include_mapped" = "includemapped")
       } else {
         df <- df |>
           dplyr::mutate(include_mapped = FALSE)
       }
-      
-      if ('includeDescendants' %in% names(df)) {
+
+      if ("includeDescendants" %in% names(df)) {
         df <- df |>
           dplyr::rename("include_descendants" = "includeDescendants")
-      } else if ('includedescendants' %in% names(df)) {
+      } else if ("includedescendants" %in% names(df)) {
         df <- df |>
           dplyr::rename("include_descendants" = "includedescendants")
       } else {
@@ -101,9 +99,9 @@ convertConceptSetExpressionToDataFrame <-
       }
       items2[[i]] <- df
     }
-    
-    conceptSetExpressionDetails <- dplyr::bind_rows(items2) |> 
-      SqlRender::snakeCaseToCamelCaseNames() |> 
+
+    conceptSetExpressionDetails <- dplyr::bind_rows(items2) |>
+      SqlRender::snakeCaseToCamelCaseNames() |>
       tidyr::replace_na(
         replace = list(
           isExcluded = FALSE,
-Original file line number
+Diff line change
@@ Expand Up / @@ -140,7 +140,7 @@ convertConceptSetDataFrameToExpression <- @@
               )
             )
         }
         if (selectAllDescendants) {
           conceptSetExpressionDataFrame <-
             dplyr::bind_rows(
@@ Expand Down @@