cohort_codelist attribute (#412)

include cohort_codelist attribute in generate concept cohort set
darwin-eu · Mar 7, 2024 · c8fdedd · c8fdedd
1 parent e3a9b99
commit c8fdedd
Show file tree

Hide file tree

Showing 2 changed files with 18 additions and 1 deletion.
diff --git a/R/generateConceptCohortSet.R b/R/generateConceptCohortSet.R
@@ -350,11 +350,28 @@ generateConceptCohortSet <- function(cdm,
       excluded_records = 0,
       excluded_subjects = 0)
 
+  if(utils::packageVersion("omopgenerics") < 0.1){
   cdm[[name]] <- omopgenerics::newCohortTable(
     table = cohortRef,
     cohortSetRef = cohortSetRef,
     cohortAttritionRef = cohortAttritionRef
   )
+  } else {
+
+    cohortCodelistRef <-df  %>%
+      dplyr::mutate(type = "index event") %>%
+      dplyr::select("cohort_definition_id",
+                    "codelist_name" = "cohort_name",
+                    "concept_id",
+                    "type")
+
+    cdm[[name]] <- omopgenerics::newCohortTable(
+      table = cohortRef,
+      cohortSetRef = cohortSetRef,
+      cohortAttritionRef = cohortAttritionRef,
+      cohortCodelistRef = cohortCodelistRef
+    )
+  }
 
   return(cdm)
 }

diff --git a/man/cdm_from_con.Rd b/man/cdm_from_con.Rd