Merge pull request #218 from darwin-eu/v3.2

cran v3.2.0

Author: edward-burn

DESCRIPTION

@@ -1,16 +1,18 @@
 Package: CodelistGenerator
 Title: Identify Relevant Clinical Codes and Evaluate Their Use
-Version: 3.1.0.900
+Version: 3.2.0
 Authors@R: c(
     person("Edward", "Burn", email = "[email protected]", 
     role = c("aut", "cre"),
     comment = c(ORCID = "0000-0002-9286-1128")),
     person("Marti", "Catala", email = "[email protected]", 
     role = c("ctb"), 
     comment = c(ORCID = "0000-0003-3308-9905")),
-    person("Xihang", " Chen", email = "[email protected]", 
-    role = c("ctb"), 
+    person("Xihang", "Chen", email = "[email protected]", 
+    role = c("aut"), 
     comment = c(ORCID = "0009-0001-8112-8959")),
+    person("Nuria", "Mercade-Besora", email = "[email protected]", 
+    role = c("aut"), comment = c(ORCID = "0009-0006-7948-3747")),
     person("Mike", "Du", email = "[email protected]", 
     role = c("ctb"), 
     comment = c(ORCID = "0000-0002-9517-8834")),

NAMESPACE

@@ -1,6 +1,9 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
+export(availableATC)
+export(availableICD10)
+export(availableIngredients)
 export(codesFromCohort)
 export(codesFromConceptSet)
 export(codesInUse)

R/summariseAchillesCodeUse.R

@@ -189,6 +189,6 @@ fetchAchillesCounts <- function(cdm, analysisId, conceptId = NULL){
   # the same code might appear in multiple tables so we will sum them
   analyses %>%
     dplyr::group_by(.data$concept_id) |>
-    dplyr::summarise(n = sum(n, na.rm = TRUE)) |>
+    dplyr::summarise(n = sum(.data$n, na.rm = TRUE)) |>
     dplyr::mutate(n = as.integer(.data$n))
 }

R/vocabUtilities.R

@@ -518,10 +518,10 @@ filterOnDoseForm <- function(concepts, conceptDoseForms, doseForm){
 }
 
 addIngredientCount <- function(cdm, concepts) {
-
  ingredient_ancestor <- cdm$concept_ancestor %>%
     dplyr::inner_join(cdm$concept %>%
-                        dplyr::filter(.data$concept_class_id == "Ingredient") %>%
+                        dplyr::filter(.data$concept_class_id == "Ingredient",
+                                      .data$standard_concept == "S") %>%
                         dplyr::select("concept_id"),
                by = c("ancestor_concept_id" = "concept_id"))
 

_pkgdown.yml

@@ -28,7 +28,7 @@ reference:
   - matches("codesInUse|compareCodelists|subsetToCodesInUse|restrictToCodesInUse|subsetOnRouteCategory|stratifyByRouteCategory|stratifyByDoseUnit|stratifyByConcept|subsetOnDoseUnit")
 - subtitle: Vocabulary utility functions
 - contents:
-  - matches("getVocabVersion|getVocabularies|getConceptClassId|getDomains|getDescendants|getDoseForm|doseFormToRoute|getRouteCategories|getRoutes|getDoseUnit|getRelationshipId|getMappings|sourceCodesInUse")
+  - matches("getVocabVersion|getVocabularies|getConceptClassId|getDomains|getDescendants|getDoseForm|doseFormToRoute|getRouteCategories|getRoutes|getDoseUnit|getRelationshipId|getMappings|sourceCodesInUse|availableATC|availableICD10|availableIngredients")
 - subtitle: Create a mock dataset that contains vocabulary tables
 - contents:
   - matches("mockVocabRef")

cran-comments.md

@@ -1,3 +1,3 @@
 ## R CMD check results
 
-This is a new release.
+This release addresses a breaking change in a dependency.