Merge pull request #270 from OHDSI/issue_262

summariseConceptCount changes name

DESCRIPTION

@@ -62,6 +62,7 @@ Imports:
     clock,
     CohortConstructor (>= 0.3.1),
     dplyr,
+    lifecycle,
     omopgenerics (>= 0.3.1),
     PatientProfiles (>= 1.2.1),
     purrr,

NAMESPACE

@@ -4,14 +4,15 @@ export(bind)
 export(exportSummarisedResult)
 export(importSummarisedResult)
 export(mockOmopSketch)
-export(plotConceptCounts)
+export(plotConceptSetCounts)
 export(plotInObservation)
 export(plotObservationPeriod)
 export(plotRecordCount)
 export(settings)
 export(summariseAllConceptCounts)
 export(summariseClinicalRecords)
 export(summariseConceptCounts)
+export(summariseConceptSetCounts)
 export(summariseInObservation)
 export(summariseMissingData)
 export(summariseObservationPeriod)

R/plotConceptCounts.R → R/plotConceptSetCounts.R

@@ -1,6 +1,6 @@
-#' Plot the concept counts of a summariseConceptCounts output.
+#' Plot the concept counts of a summariseConceptSetCounts output.
 #'
-#' @param result A summarised_result object (output of summariseConceptCounts).
+#' @param result A summarised_result object (output of summariseConceptSetCounts).
 #' @param facet Columns to face by. Formula format can be provided. See possible
 #' columns to face by with: `visOmopResults::tidyColumns()`.
 #' @param colour Columns to colour by. See possible columns to colour by with:
@@ -14,20 +14,20 @@
 #' cdm <- mockOmopSketch()
 #'
 #' result <- cdm |>
-#'   summariseConceptCounts(
-#'     conceptId = list(
+#'   summariseConceptSetCounts(
+#'     conceptSet= list(
 #'       "Renal agenesis" = 194152,
 #'       "Manic mood" = c(4226696, 4304866, 37110496, 40371897)
 #'     )
 #'   )
 #'
 #' result |>
 #'   filter(variable_name == "Number subjects") |>
-#'   plotConceptCounts(facet = "codelist_name", colour = "standard_concept_name")
+#'   plotConceptSetCounts(facet = "codelist_name", colour = "standard_concept_name")
 #'
 #' PatientProfiles::mockDisconnect(cdm)
 #' }
-plotConceptCounts <- function(result,
+plotConceptSetCounts <- function(result,
                               facet = NULL,
                               colour = NULL){
 
@@ -39,10 +39,10 @@ plotConceptCounts <- function(result,
 
   # subset to results of interest
   result <- result |>
-    omopgenerics::filterSettings(.data$result_type == "summarise_concept_counts")
+    omopgenerics::filterSettings(.data$result_type == "summarise_concept_set_counts")
 
   if (nrow(result) == 0) {
-    cli::cli_abort(c("!" = "No records found with result_type == summarise_concept_counts"))
+    cli::cli_abort(c("!" = "No records found with result_type == summarise_concept_set_counts"))
   }
 
   # check only one estimate is contained