Merge pull request #281 from OHDSI/issue_268

name changed to summariseConceptIdCounts

NAMESPACE

@@ -9,18 +9,18 @@ export(plotInObservation)
 export(plotObservationPeriod)
 export(plotRecordCount)
 export(settings)
-export(summariseAllConceptCounts)
 export(summariseClinicalRecords)
 export(summariseConceptCounts)
+export(summariseConceptIdCounts)
 export(summariseConceptSetCounts)
 export(summariseInObservation)
 export(summariseMissingData)
 export(summariseObservationPeriod)
 export(summariseOmopSnapshot)
 export(summariseRecordCount)
 export(suppress)
-export(tableAllConceptCounts)
 export(tableClinicalRecords)
+export(tableConceptIdCounts)
 export(tableMissingData)
 export(tableObservationPeriod)
 export(tableOmopSnapshot)

R/plotRecordCount.R

@@ -82,7 +82,6 @@ plotRecordCount <- function(result,
         plot.margin = ggplot2::margin(t = 5, r = 5, b = 30, l = 5)
       )
 
-
   }else{
     p <- result |>
       visOmopResults::barPlot(x = "variable_name",

R/summariseAllConceptCounts.R → R/summariseConceptIdCounts.R

@@ -30,10 +30,10 @@
 #' con <- dbConnect(duckdb(), eunomiaDir())
 #' cdm <- cdmFromCon(con = con, cdmSchema = "main", writeSchema = "main")
 #'
-#' summariseAllConceptCounts(cdm, "condition_occurrence")
+#' summariseConceptIdCounts(cdm, "condition_occurrence")
 #' }
 #'
-summariseAllConceptCounts <- function(cdm,
+summariseConceptIdCounts <- function(cdm,
                                       omopTableName,
                                       countBy = "record",
                                       year = FALSE,
@@ -108,7 +108,7 @@ summariseAllConceptCounts <- function(cdm,
 
     omopgenerics::dropSourceTable(cdm = cdm, name = dplyr::starts_with(prefix))
 
-  return(result)
+    return(result)
   }) |>
     purrr::compact()
 

R/tableAllConceptCounts.R → R/tableConceptIdCounts.R

@@ -1,11 +1,11 @@
-#' Create a visual table from a summariseAllConceptCounts() result.
+#' Create a visual table from a summariseConceptIdCounts() result.
 #' @param result A summarised_result object.
 #' @param type Type of formatting output table, either "gt" or "flextable".
 #' @return A gt or flextable object with the summarised data.
 #' @export
 #'
 #'
-tableAllConceptCounts <- function(result,
+tableConceptIdCounts <- function(result,
                              type = "gt") {
   # initial checks
   rlang::check_installed("visOmopResults")

_pkgdown.yml

@@ -30,8 +30,8 @@ reference:
 - contents:
   - summariseConceptSetCounts
   - plotConceptSetCounts
-  - summariseAllConceptCounts
-  - tableAllConceptCounts
+  - summariseConceptIdCounts
+  - tableConceptIdCounts
 - subtitle: Mock Database
   desc: Create a mock database to test the OmopSketch package
 - contents: