Merge pull request #104 from darwin-eu/device

support device concepts in summarise code use

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: CodelistGenerator
 Title: Generate Code Lists for the OMOP Common Data Model
-Version: 2.0.0
+Version: 2.1.0
 Authors@R: c(
     person("Edward", "Burn", email = "[email protected]", 
     role = c("aut", "cre"),

R/codesFromConceptSet.R

@@ -184,8 +184,10 @@ extractCodes <- function(file, unknown) {
 appendDescendants <- function(codelistTibble, cdm) {
   cdm[["concept_ancestor"]] %>%
     dplyr::select("ancestor_concept_id", "descendant_concept_id") %>%
+    dplyr::mutate(ancestor_concept_id = as.integer(.data$ancestor_concept_id)) %>%
     dplyr::inner_join(
-      codelistTibble %>%
+      codelistTibble%>%
+        dplyr::mutate(concept_id = as.integer(.data$concept_id)) %>%
         dplyr::filter(.data$include_descendants == TRUE) %>%
         dplyr::rename("ancestor_concept_id" = "concept_id"),
       by = "ancestor_concept_id",
@@ -283,14 +285,16 @@ addDetails <- function(conceptList, cdm){
 formatConceptList <- function(conceptList, cdm) {
   conceptList <- conceptList %>%
     dplyr::filter(.data$include_descendants == FALSE) %>%
-    dplyr::union(
+    dplyr::union_all(
       cdm[["concept_ancestor"]] %>%
         dplyr::select(
           "concept_id" = "ancestor_concept_id",
           "descendant_concept_id"
         ) %>%
+        dplyr::mutate(concept_id = as.integer(.data$concept_id)) %>%
         dplyr::inner_join(
           conceptList %>%
+            dplyr::mutate(concept_id = as.integer(.data$concept_id)) %>%
             dplyr::filter(.data$include_descendants == TRUE),
           copy = TRUE,
           by = "concept_id"

R/drugCodes.R

@@ -25,12 +25,15 @@
 #' @param doseForm Only descendants codes with the specified dose form
 #' will be returned. If NULL, descendant codes will be returned regardless
 #' of dose form.
-#' @param withConceptDetails If FALSE a vector of concept IDs will be returned
-#' for each ATC group If TRUE a tibble will be returned with additional
+#' @param withConceptDetails If FALSE, each item in the list of results (one per
+#' ATC group) will contain a vector of concept IDs for each ingredient. If
+#' TRUE each item in the list of results will contain a tibble with additional
 #' information on the identified concepts.
 #'
-#' @return A named list, with each element containing the descendant
-#' concepts for a particular ATC group
+#' @return A named list, with each item containing a vector of descendant
+#' concepts of an ATC group (if withConceptDetails was set as FALSE) or a
+#' tibble with the descendant concepts along with additional details about them
+#' (if withConceptDetails was set as TRUE).
 #' @export
 #'
 #' @examples
@@ -159,12 +162,15 @@ getATCCodes <- function(cdm,
 #' @param doseForm Only descendants codes with the specified dose form
 #' will be returned. If NULL, descendant codes will be returned regardless
 #' of dose form.
-#' @param withConceptDetails If FALSE a vector of concept IDs will be returned
-#' for each ingredient. If TRUE a tibble will be returned with additional
+#' @param withConceptDetails If FALSE, each item in the list of results (one per
+#' ingredient) will contain a vector of concept IDs for each ingredient. If
+#' TRUE each item in the list of results will contain a tibble with additional
 #' information on the identified concepts.
 #'
-#' @return A named list, with each item containing descendant concepts of
-#' an ingredient
+#' @return A named list, with each item containing a vector of descendant
+#' concepts of an ingredient (if withConceptDetails was set as FALSE) or a
+#' tibble with the descendant concepts along with additional details about them
+#' (if withConceptDetails was set as TRUE).
 #' @export
 #'
 #' @examples