From c653d94a3fd7b4eb800248d3cad8ca1f9bb43c74 Mon Sep 17 00:00:00 2001
From: Marta Alcalde-Herraiz <marta.alcalde@estudiantat.upc.edu>
Date: Tue, 5 Nov 2024 10:37:40 +0000
Subject: [PATCH 1/2] Move variable_level to additional_level in RecordCount
 and InObservation

---
 DESCRIPTION                                  |  2 +-
 R/plotInObservation.R                        |  8 +--
 R/plotRecordCount.R                          |  8 +--
 R/summariseInObservation.R                   | 42 +++++++------
 R/summariseRecordCount.R                     | 23 ++++---
 R/utilities.R                                |  9 ++-
 tests/testthat/test-summariseConceptCounts.R |  2 +-
 tests/testthat/test-summariseInObservation.R | 46 ++++++++------
 tests/testthat/test-summariseRecordCount.R   | 63 ++++++++++----------
 9 files changed, 111 insertions(+), 92 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 95671c2..2380e90 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: OmopSketch
 Title: Characterise Tables of an OMOP Common Data Model Instance
-Version: 0.1.1
+Version: 0.1.2
 Authors@R: c(
     person( 
         "Marta", "Alcalde-Herraiz", 
diff --git a/R/plotInObservation.R b/R/plotInObservation.R
index 9270555..7910f20 100644
--- a/R/plotInObservation.R
+++ b/R/plotInObservation.R
@@ -52,15 +52,15 @@ plotInObservation <- function(result,
   }
 
   # warn
-  warnFacetColour(result, list(facet = asCharacterFacet(facet), colour = colour, "variable_level"))
+  warnFacetColour(result, list(facet = asCharacterFacet(facet), colour = colour, "additional_level"))
 
   # plot
-  if(length(unique(result$variable_level)) > 1 ){
+  if(length(unique(result$additional_level)) > 1 ){
     result |>
-      dplyr::mutate(variable_level = as.Date(gsub(" to.*","",.data$variable_level))) |>
+      dplyr::mutate(additional_level = as.character(gsub("-01$","",as.Date(gsub(" to.*","",.data$additional_level))))) |>
       dplyr::filter(.data$estimate_name == "count") |>
       visOmopResults::scatterPlot(
-        x = "variable_level",
+        x = "time_interval",
         y = "count",
         line = TRUE,
         point = TRUE,
diff --git a/R/plotRecordCount.R b/R/plotRecordCount.R
index a42e1dd..f8b902e 100644
--- a/R/plotRecordCount.R
+++ b/R/plotRecordCount.R
@@ -38,12 +38,12 @@ plotRecordCount <- function(result,
   }
 
   # Detect if there are several time intervals
-  if(length(unique(result$variable_level)) > 1 ){
+  if(length(unique(result$additional_level)) > 1 ){
     # Line plot where each concept is a different line
     p <- result |>
-      dplyr::filter(.data$variable_level != "overall") |>
+      dplyr::filter(.data$additional_level != "overall") |>
       dplyr::filter(.data$estimate_name == "count") |>
-      visOmopResults::scatterPlot(x = "variable_level",
+      visOmopResults::scatterPlot(x = "time_interval",
                                   y = "count",
                                   line   = TRUE,
                                   point  = TRUE,
@@ -57,7 +57,7 @@ plotRecordCount <- function(result,
       )
   }else{
     p <- result |>
-      visOmopResults::barPlot(x = "variable_level",
+      visOmopResults::barPlot(x = "additional_level",
                               y = "count",
                               facet = facet,
                               colour = colour)  +
diff --git a/R/summariseInObservation.R b/R/summariseInObservation.R
index 5f1ea6c..e52d6b8 100644
--- a/R/summariseInObservation.R
+++ b/R/summariseInObservation.R
@@ -52,6 +52,7 @@ summariseInObservation <- function(observationPeriod,
   checkOutput(output)
   ageGroup <- omopgenerics::validateAgeGroupArgument(ageGroup, ageGroupName = "")[[1]]
   omopgenerics::assertLogical(sex, length = 1)
+  original_interval <- interval
   x <- validateIntervals(interval)
   interval <- x$interval
   unitInterval <- x$unitInterval
@@ -88,7 +89,7 @@ summariseInObservation <- function(observationPeriod,
   result <- addSexOverall(result, sex)
 
   # Create summarisedResult
-  result <- createSummarisedResultObservationPeriod(result, observationPeriod, name, denominator, interval, unitInterval)
+  result <- createSummarisedResultObservationPeriod(result, observationPeriod, name, denominator, original_interval)
 
   CDMConnector::dropTable(cdm, name = dplyr::starts_with(tablePrefix))
   return(result)
@@ -172,7 +173,7 @@ countRecords <- function(observationPeriod, cdm, start_date_name, end_date_name,
   if(output == "person-days" | output == "all"){
     if(interval != "overall"){
       x <- cdm[[paste0(tablePrefix, "interval")]] |>
-        dplyr::rename("variable_level" = "interval_group") |>
+        dplyr::rename("additional_level" = "interval_group") |>
         dplyr::cross_join(
           observationPeriod |>
             dplyr::select("start_date" = "observation_period_start_date",
@@ -188,14 +189,16 @@ countRecords <- function(observationPeriod, cdm, start_date_name, end_date_name,
       x <- observationPeriod |>
         dplyr::rename("start_date" = "observation_period_start_date",
                       "end_date"   = "observation_period_end_date") |>
-        dplyr::mutate("variable_level" = NA)
+        dplyr::mutate("additional_level" = "overall",
+                      "additional_name"  = "overall")
     }
 
     personDays <- x %>%
       dplyr::mutate(estimate_value = !!CDMConnector::datediff("start_date","end_date", interval = "day")+1) |>
-      dplyr::group_by(dplyr::across(dplyr::any_of(c("variable_level", "sex", "age_group")))) |>
+      dplyr::group_by(dplyr::across(dplyr::any_of(c("additional_level", "sex", "age_group")))) |>
       dplyr::summarise(estimate_value = sum(.data$estimate_value, na.rm = TRUE), .groups = "drop") |>
-      dplyr::mutate(variable_name = "Number person-days") |>
+      dplyr::mutate("variable_name" = "Number person-days",
+                    "additional_name" = "time_interval") |>
       dplyr::collect()
   }else{
     personDays <- createEmptyIntervalTable(interval)
@@ -212,20 +215,22 @@ if(output == "records" | output == "all"){
         dplyr::compute(temporary = FALSE, name = tablePrefix)
 
       records <- cdm[[paste0(tablePrefix, "interval")]] |>
-        dplyr::rename("variable_level" = "interval_group") |>
+        dplyr::rename("additional_level" = "interval_group") |>
         dplyr::cross_join(x) |>
         dplyr::filter((.data$start_date < .data$interval_start_date & .data$end_date >= .data$interval_start_date) |
                         (.data$start_date >= .data$interval_start_date & .data$start_date <= .data$interval_end_date)) |>
-        dplyr::group_by(.data$variable_level, .data$age_group, .data$sex) |>
+        dplyr::group_by(.data$additional_level, .data$age_group, .data$sex) |>
         dplyr::summarise(estimate_value = sum(.data$estimate_value, na.rm = TRUE), .groups = "drop") |>
-        dplyr::mutate(variable_name = "Number records in observation") |>
+        dplyr::mutate("variable_name" = "Number records in observation",
+                      "additional_name" = "time_interval") |>
         dplyr::collect()
     }else{
       records <- observationPeriod |>
         dplyr::group_by(.data$age_group, .data$sex) |>
         dplyr::summarise(estimate_value = dplyr::n(), .groups = "drop") |>
         dplyr::mutate("variable_name" = "Number records in observation",
-                      "variable_level" = NA) |>
+                      "additional_level" = "overall",
+                      "additional_name"  = "overall") |>
         dplyr::collect()
     }
   }else{
@@ -234,12 +239,12 @@ if(output == "records" | output == "all"){
 
   x <- personDays |>
     rbind(records) |>
-    dplyr::arrange(dplyr::across(dplyr::any_of("variable_level")))
+    dplyr::arrange(dplyr::across(dplyr::any_of("additional_level")))
 
   return(x)
 }
 
-createSummarisedResultObservationPeriod <- function(result, observationPeriod, name, denominator, interval, unitInterval){
+createSummarisedResultObservationPeriod <- function(result, observationPeriod, name, denominator, original_interval){
   result <- result |>
     dplyr::mutate("estimate_value" = as.character(.data$estimate_value)) |>
     visOmopResults::uniteStrata(cols = c("sex", "age_group")) |>
@@ -248,15 +253,14 @@ createSummarisedResultObservationPeriod <- function(result, observationPeriod, n
       "cdm_name" = omopgenerics::cdmName(omopgenerics::cdmReference(observationPeriod)),
       "group_name"  = "omop_table",
       "group_level" = name,
+      "variable_level" = as.character(NA),
       "estimate_name" = "count",
-      "estimate_type" = "integer",
-      "additional_name" = "overall",
-      "additional_level" = "overall"
+      "estimate_type" = "integer"
     )
 
   result <- result |>
     rbind(result) |>
-    dplyr::group_by(.data$variable_level, .data$strata_level, .data$variable_name) |>
+    dplyr::group_by(.data$additional_level, .data$strata_level, .data$variable_name) |>
     dplyr::mutate(estimate_type = dplyr::if_else(dplyr::row_number() == 2, "percentage", .data$estimate_type)) |>
     dplyr::inner_join(denominator, by = "variable_name") |>
     dplyr::mutate(estimate_value = dplyr::if_else(.data$estimate_type == "percentage", as.character(as.numeric(.data$estimate_value)/denominator*100), .data$estimate_value)) |>
@@ -267,8 +271,7 @@ createSummarisedResultObservationPeriod <- function(result, observationPeriod, n
       "result_type" = "summarise_in_observation",
       "package_name" = "OmopSketch",
       "package_version" = as.character(utils::packageVersion("OmopSketch")),
-      "interval" = .env$interval,
-      "unitInterval" = .env$unitInterval
+      "interval" = .env$original_interval
     ))
 
   return(result)
@@ -332,9 +335,10 @@ addSexOverall <- function(result, sex){
   if(sex){
     result <- result |> rbind(
       result |>
-        dplyr::group_by(.data$age_group, .data$variable_level, .data$variable_name) |>
+        dplyr::group_by(.data$age_group, .data$additional_level, .data$variable_name) |>
         dplyr::summarise(estimate_value = sum(.data$estimate_value, na.rm = TRUE), .groups = "drop") |>
-        dplyr::mutate(sex = "overall")
+        dplyr::mutate(sex = "overall",
+                      additional_name = dplyr::if_else(additional_level == "overall", "overall", "time_interval"))
     )
   }
   return(result)
diff --git a/R/summariseRecordCount.R b/R/summariseRecordCount.R
index 2c19171..8c82fb4 100644
--- a/R/summariseRecordCount.R
+++ b/R/summariseRecordCount.R
@@ -37,6 +37,7 @@ summariseRecordCount <- function(cdm,
   # Initial checks ----
   omopgenerics::validateCdmArgument(cdm)
   omopgenerics::assertCharacter(omopTableName)
+  original_interval <- interval
   x <- validateIntervals(interval)
   interval <- x$interval
   unitInterval <- x$unitInterval
@@ -54,6 +55,7 @@ summariseRecordCount <- function(cdm,
                                                       cdm = cdm,
                                                       interval = interval,
                                                       unitInterval = unitInterval,
+                                                      original_interval,
                                                       ageGroup = ageGroup,
                                                       sex = sex)
                        }
@@ -65,7 +67,7 @@ summariseRecordCount <- function(cdm,
 
 #' @noRd
 summariseRecordCountInternal <- function(omopTableName, cdm, interval, unitInterval,
-                                         ageGroup, sex) {
+                                         original_interval, ageGroup, sex) {
 
   prefix <- omopgenerics::tmpPrefix()
   omopTable <- cdm[[omopTableName]] |> dplyr::ungroup()
@@ -107,7 +109,7 @@ summariseRecordCountInternal <- function(omopTableName, cdm, interval, unitInter
   }
 
   # Create summarised result ----
-  result <- createSummarisedResultRecordCount(result, strata, omopTable, omopTableName, interval, unitInterval)
+  result <- createSummarisedResultRecordCount(result, strata, omopTable, omopTableName, original_interval)
   omopgenerics::dropTable(cdm = cdm, name = dplyr::starts_with(prefix))
 
   return(result)
@@ -230,12 +232,11 @@ splitIncidenceBetweenIntervals <- function(cdm, omopTable, date, prefix){
     dplyr::select(-c("interval_start_date", "interval_end_date", "incidence_date"))
 }
 
-createSummarisedResultRecordCount <- function(result, strata, omopTable, omopTableName, interval, unitInterval){
+createSummarisedResultRecordCount <- function(result, strata, omopTable, omopTableName, original_interval){
 
   result <- result |>
     dplyr::mutate(n = 1) |>
     dplyr::select(-"person_id") |>
-    # dplyr::collect() |> # https://github.com/darwin-eu-dev/PatientProfiles/issues/706
     PatientProfiles::summariseResult(
       variables = "n",
       strata = strata,
@@ -246,18 +247,15 @@ createSummarisedResultRecordCount <- function(result, strata, omopTable, omopTab
     suppressMessages() |>
     dplyr::mutate("variable_name" = stringr::str_to_sentence(.data$variable_name)) |>
     dplyr::mutate(
-      "result_id" = as.integer(1),
-      "cdm_name" = omopgenerics::cdmName(omopgenerics::cdmReference(omopTable)),
       "group_name"  = "omop_table",
-      "group_level" = omopTableName,
-      "additional_name" = "overall",
-      "additional_level" = "overall"
+      "group_level" = omopTableName
     )
 
-  if(interval != "overall"){
+  if(original_interval != "overall"){
     result <- result |>
       visOmopResults::splitStrata() |>
-      dplyr::mutate(variable_level = .data$interval_group) |>
+      dplyr::mutate(additional_level = .data$interval_group) |>
+      dplyr::mutate(additional_name = dplyr::if_else(additional_level == "overall", "overall", "time_interval")) |>
       visOmopResults::uniteStrata(unique(unlist(strata))[unique(unlist(strata)) != "interval_group"]) |>
       dplyr::select(-"interval_group")
   }
@@ -268,7 +266,8 @@ createSummarisedResultRecordCount <- function(result, strata, omopTable, omopTab
         "result_id" = 1L,
         "result_type" = "summarise_record_count",
         "package_name" = "OmopSketch",
-        "package_version" = as.character(utils::packageVersion("OmopSketch"))
+        "package_version" = as.character(utils::packageVersion("OmopSketch")),
+        "interval" = .env$original_interval
       )
     )
 }
diff --git a/R/utilities.R b/R/utilities.R
index aa23797..007e858 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -1,18 +1,23 @@
 startDate <- function(name) {
   tables$start_date[tables$table_name == name]
 }
+
 endDate <- function(name) {
   tables$end_date[tables$table_name == name]
 }
+
 standardConcept <- function(name) {
   tables$standard_concept[tables$table_name == name]
 }
+
 sourceConcept <- function(name) {
   tables$source_concept[tables$table_name == name]
 }
+
 typeConcept <- function(name) {
   tables$type_concept[tables$table_name == name]
 }
+
 tableId <- function(name) {
   tables$id[tables$table_name == name]
 }
@@ -21,7 +26,7 @@ warnFacetColour <- function(result, cols) {
   colsToWarn <- result |>
     dplyr::select(
       "cdm_name", "group_name", "group_level", "strata_name", "strata_level",
-      "variable_name", "variable_level", "additional_name", "additional_level"
+      "variable_name", "variable_level"
     ) |>
     dplyr::distinct() |>
     visOmopResults::splitAll() |>
@@ -36,12 +41,14 @@ warnFacetColour <- function(result, cols) {
   }
   invisible(NULL)
 }
+
 collapseStr <- function(x, sep) {
   x <- x[x != ""]
   if (length(x) == 1) return(x)
   len <- length(x)
   paste0(paste0(x[-len], collapse = ", "), " ", sep, " ", x[len])
 }
+
 asCharacterFacet <- function(facet) {
   if (rlang::is_formula(facet)) {
     facet <- as.character(facet)
diff --git a/tests/testthat/test-summariseConceptCounts.R b/tests/testthat/test-summariseConceptCounts.R
index 7752849..6486e28 100644
--- a/tests/testthat/test-summariseConceptCounts.R
+++ b/tests/testthat/test-summariseConceptCounts.R
@@ -1,6 +1,6 @@
 test_that("summarise code use - eunomia", {
   skip_on_cran()
-  cdm <- cdmEunomia()
+ cdm <- cdmEunomia()
   acetiminophen <- c(1125315,  1127433, 40229134,
                      40231925, 40162522, 19133768,  1127078)
   poliovirus_vaccine <- c(40213160)
diff --git a/tests/testthat/test-summariseInObservation.R b/tests/testthat/test-summariseInObservation.R
index 6ffeb97..d2c7d10 100644
--- a/tests/testthat/test-summariseInObservation.R
+++ b/tests/testthat/test-summariseInObservation.R
@@ -12,7 +12,7 @@ test_that("check summariseInObservation works", {
 
   # Check inputs ----
   x <- summariseInObservation(cdm$observation_period, interval = "years") |>
-    dplyr::filter(variable_level == "1909-01-01 to 1909-12-31", estimate_name == "count") |>
+    dplyr::filter(additional_level == "1909-01-01 to 1909-12-31", estimate_name == "count") |>
     dplyr::pull("estimate_value") |>
     as.numeric()
   y <- cdm$observation_period %>%
@@ -24,8 +24,13 @@ test_that("check summariseInObservation works", {
     dplyr::pull("n") |> as.numeric()
   expect_equal(x,y)
 
+  x <- summariseInObservation(cdm$observation_period, interval = "years")
+  expect_equal(x |> dplyr::filter(additional_level != "overall") |> dplyr::pull("additional_name") |> unique(), "time_interval")
+  x <- summariseInObservation(cdm$observation_period, interval = "overall")
+  expect_equal(x |> dplyr::filter(additional_level == "overall") |> dplyr::pull("additional_name") |> unique(), "overall")
+
   x <- summariseInObservation(cdm$observation_period, interval = "years") |>
-    dplyr::filter(variable_level == c("1936-01-01 to 1936-12-31"), estimate_name == "count") |>
+    dplyr::filter(additional_level == c("1936-01-01 to 1936-12-31"), estimate_name == "count") |>
     dplyr::pull("estimate_value") |>
     as.numeric()
   y <- cdm$observation_period %>%
@@ -39,7 +44,7 @@ test_that("check summariseInObservation works", {
   expect_equal(x,y)
 
   x <- summariseInObservation(cdm$observation_period, interval = "years") |>
-    dplyr::filter(variable_level == c("1998-01-01 to 1998-12-31"), estimate_name == "count") |>
+    dplyr::filter(additional_level == c("1998-01-01 to 1998-12-31"), estimate_name == "count") |>
     dplyr::pull("estimate_value") |>
     as.numeric()
   y <- cdm$observation_period %>%
@@ -54,7 +59,7 @@ test_that("check summariseInObservation works", {
 
   # Check inputs ----
   x <- summariseInObservation(cdm$observation_period, interval = "months") |>
-    dplyr::filter(variable_level == "1942-03-01 to 1942-03-31", estimate_name == "count") |>
+    dplyr::filter(additional_level == "1942-03-01 to 1942-03-31", estimate_name == "count") |>
     dplyr::pull("estimate_value") |>
     as.numeric()
   y <- cdm$observation_period %>%
@@ -67,7 +72,7 @@ test_that("check summariseInObservation works", {
 
 
   x <- summariseInObservation(cdm$observation_period, interval = "months") |>
-    dplyr::filter(variable_level == "2015-09-01 to 2015-09-30", estimate_name == "count") |>
+    dplyr::filter(additional_level == "2015-09-01 to 2015-09-30", estimate_name == "count") |>
     dplyr::pull("estimate_value") |>
     as.numeric()
   y <- cdm$observation_period %>%
@@ -79,7 +84,7 @@ test_that("check summariseInObservation works", {
   expect_equal(x,y)
 
   x <- summariseInObservation(cdm$observation_period, interval = "months") |>
-    dplyr::filter(variable_level == "1982-03-01 to 1982-03-31", estimate_name == "count") |>
+    dplyr::filter(additional_level == "1982-03-01 to 1982-03-31", estimate_name == "count") |>
     dplyr::pull("estimate_value") |>
     as.numeric()
   y <- cdm$observation_period %>%
@@ -98,11 +103,16 @@ test_that("check sex argument works", {
   cdm <- cdmEunomia()
 
   # Check overall
+  x <- summariseInObservation(cdm$observation_period, interval = "years", sex = TRUE)
+  expect_equal(x |> dplyr::filter(additional_level != "overall") |> dplyr::pull("additional_name") |> unique(), "time_interval")
+  x <- summariseInObservation(cdm$observation_period, interval = "overall")
+  expect_equal(x |> dplyr::filter(additional_level == "overall") |> dplyr::pull("additional_name") |> unique(), "overall")
+
   x <- summariseInObservation(cdm$observation_period, interval = "years", sex = TRUE) |>
-    dplyr::filter(strata_level %in% c("Male","Female"), variable_level == "1908-01-01 to 1908-12-31", estimate_name == "count") |>
+    dplyr::filter(strata_level %in% c("Male","Female"), additional_level == "1908-01-01 to 1908-12-31", estimate_name == "count") |>
     dplyr::pull(estimate_value) |> as.numeric() |> sum()
   y <- summariseInObservation(cdm$observation_period, interval = "years", sex = TRUE) |>
-    dplyr::filter(strata_level %in% c("overall"), variable_level == "1908-01-01 to 1908-12-31", estimate_name == "count") |>
+    dplyr::filter(strata_level %in% c("overall"), additional_level == "1908-01-01 to 1908-12-31", estimate_name == "count") |>
     dplyr::pull(estimate_value) |> as.numeric()
   expect_equal(x,y)
 
@@ -116,7 +126,7 @@ test_that("check sex argument works", {
 
   # Check a random group
   x <- summariseInObservation(cdm$observation_period, interval = "years", sex = TRUE) |>
-    dplyr::filter(strata_level == "Male", variable_level == "1915-01-01 to 1915-12-31", estimate_name == "count") |>
+    dplyr::filter(strata_level == "Male", additional_level == "1915-01-01 to 1915-12-31", estimate_name == "count") |>
     dplyr::pull(estimate_value) |> as.numeric()
   y <- cdm$observation_period |>
     dplyr::inner_join(cdm[["person"]] |> dplyr::select("person_id"), by = "person_id") %>%
@@ -129,7 +139,7 @@ test_that("check sex argument works", {
   expect_equal(x,y)
 
   x <- summariseInObservation(cdm$observation_period, interval = "years", sex = TRUE) |>
-    dplyr::filter(strata_level == "Male", variable_level == "1915-01-01 to 1915-12-31", estimate_name == "percentage") |>
+    dplyr::filter(strata_level == "Male", additional_level == "1915-01-01 to 1915-12-31", estimate_name == "percentage") |>
     dplyr::pull(estimate_value) |> as.numeric()
   y <- (cdm$observation_period |>
           dplyr::inner_join(cdm[["person"]] |> dplyr::select("person_id"), by = "person_id") %>%
@@ -152,7 +162,7 @@ test_that("check ageGroup argument works", {
   expect_no_error(summariseInObservation(cdm$observation_period, ageGroup = list(c(0,20), c(21, Inf))))
 
   x <- summariseInObservation(cdm$observation_period, interval = "years", ageGroup = list("<=20" = c(0,20), ">20" = c(21,Inf))) |>
-    dplyr::filter(variable_level == "1928-01-01 to 1928-12-31", estimate_name == "count", strata_level == "<=20") |>
+    dplyr::filter(additional_level == "1928-01-01 to 1928-12-31", estimate_name == "count", strata_level == "<=20") |>
     dplyr::pull(estimate_value) |> as.numeric()
   y <- cdm$observation_period |>
     dplyr::inner_join(cdm[["person"]] |> dplyr::select("person_id"), by = "person_id") %>%
@@ -167,7 +177,7 @@ test_that("check ageGroup argument works", {
   expect_equal(x,y)
 
   x <- summariseInObservation(cdm$observation_period, interval = "years", sex = TRUE) |>
-    dplyr::filter(strata_level == "Male", variable_level == "1918-01-01 to 1918-12-31", estimate_name == "percentage") |>
+    dplyr::filter(strata_level == "Male", additional_level == "1918-01-01 to 1918-12-31", estimate_name == "percentage") |>
     dplyr::pull(estimate_value) |> as.numeric()
   y <- (cdm$observation_period |>
           dplyr::inner_join(cdm[["person"]] |> dplyr::select("person_id"), by = "person_id") %>%
@@ -189,7 +199,7 @@ test_that("check output argument works", {
 
   # check value
   x <- summariseInObservation(cdm$observation_period, interval = "years", output = c("records","person-days"), ageGroup = NULL, sex = FALSE) |>
-    dplyr::filter(variable_name == "Number person-days", variable_level == "1970-01-01 to 1970-12-31", estimate_type == "integer") |>
+    dplyr::filter(variable_name == "Number person-days", additional_level == "1970-01-01 to 1970-12-31", estimate_type == "integer") |>
     dplyr::pull("estimate_value") |> as.numeric()
   y <- cdm$observation_period |>
     dplyr::inner_join(cdm[["person"]] |> dplyr::select("person_id"), by = "person_id") %>%
@@ -208,7 +218,7 @@ test_that("check output argument works", {
     dplyr::mutate(days = !!CDMConnector::datediff("observation_period_start_date","observation_period_end_date", interval = "day")+1) |>
     dplyr::summarise(n = sum(days, na.rm = TRUE)) |> dplyr::pull("n")
   x <- summariseInObservation(cdm$observation_period, interval = "years", output = c("records","person-days"), ageGroup = NULL, sex = FALSE) |>
-    dplyr::filter(variable_name == "Number person-days", variable_level == "1964-01-01 to 1964-12-31", estimate_type == "percentage") |>
+    dplyr::filter(variable_name == "Number person-days", additional_level == "1964-01-01 to 1964-12-31", estimate_type == "percentage") |>
     dplyr::pull("estimate_value") |> as.numeric()
   y <- cdm$observation_period |>
     dplyr::inner_join(cdm[["person"]] |> dplyr::select("person_id"), by = "person_id") %>%
@@ -223,19 +233,19 @@ test_that("check output argument works", {
 
   # Check sex stratified
   x <- summariseInObservation(cdm$observation_period, interval = "years", output = "person-days", sex = TRUE) |>
-    dplyr::filter(variable_name == "Number person-days", variable_level == "1964-01-01 to 1964-12-31", estimate_type == "integer") |>
+    dplyr::filter(variable_name == "Number person-days", additional_level == "1964-01-01 to 1964-12-31", estimate_type == "integer") |>
     dplyr::filter(strata_level == "overall") |> dplyr::pull("estimate_value") |> as.numeric()
   y <- summariseInObservation(cdm$observation_period, interval = "years", output = "person-days", sex = TRUE) |>
-    dplyr::filter(variable_name == "Number person-days", variable_level == "1964-01-01 to 1964-12-31", estimate_type == "integer") |>
+    dplyr::filter(variable_name == "Number person-days", additional_level == "1964-01-01 to 1964-12-31", estimate_type == "integer") |>
     dplyr::filter(strata_level != "overall") |> dplyr::pull("estimate_value") |> as.numeric() |> sum()
   expect_equal(x,y)
 
   # Check age stratified
   x <- summariseInObservation(cdm$observation_period, interval = "years", output = "person-days", ageGroup = list("<=20" = c(0,20), ">20" = c(21,Inf))) |>
-    dplyr::filter(variable_name == "Number person-days", variable_level == "2000-01-01 to 2000-12-31", estimate_type == "integer") |>
+    dplyr::filter(variable_name == "Number person-days", additional_level == "2000-01-01 to 2000-12-31", estimate_type == "integer") |>
     dplyr::filter(strata_level == "overall") |> dplyr::pull("estimate_value") |> as.numeric()
   y <- summariseInObservation(cdm$observation_period, interval = "years", output = "person-days", sex = TRUE) |>
-    dplyr::filter(variable_name == "Number person-days", variable_level == "2000-01-01 to 2000-12-31", estimate_type == "integer") |>
+    dplyr::filter(variable_name == "Number person-days", additional_level == "2000-01-01 to 2000-12-31", estimate_type == "integer") |>
     dplyr::filter(strata_level != "overall") |> dplyr::pull("estimate_value") |> as.numeric() |> sum()
   expect_equal(x,y)
 
diff --git a/tests/testthat/test-summariseRecordCount.R b/tests/testthat/test-summariseRecordCount.R
index 7ab6b7e..2c0e7eb 100644
--- a/tests/testthat/test-summariseRecordCount.R
+++ b/tests/testthat/test-summariseRecordCount.R
@@ -22,11 +22,10 @@ test_that("summariseRecordCount() works", {
                                                       "device_exposure","observation")))
   expect_equal(all, dplyr::bind_rows(co,de,o))
 
-
   # Check inputs ----
   expect_true(
     (summariseRecordCount(cdm, "observation_period", interval = "years") |>
-       dplyr::filter(variable_level == "1963-01-01 to 1963-12-31") |>
+       dplyr::filter(additional_level == "1963-01-01 to 1963-12-31") |>
        dplyr::pull("estimate_value") |>
        as.numeric()) ==
       (cdm$observation_period |>
@@ -40,7 +39,7 @@ test_that("summariseRecordCount() works", {
 
   expect_true(
   summariseRecordCount(cdm, "condition_occurrence", interval = "months") |>
-    dplyr::filter(variable_level == "1961-02-01 to 1961-02-28") |>
+    dplyr::filter(additional_level == "1961-02-01 to 1961-02-28") |>
     dplyr::pull("estimate_value") |>
     as.numeric() ==
   (cdm$condition_occurrence |>
@@ -55,7 +54,7 @@ test_that("summariseRecordCount() works", {
 
   expect_true(
     (summariseRecordCount(cdm, "condition_occurrence", interval = "months") |>
-      dplyr::filter(variable_level %in% c("1984-01-01 to 1984-01-31", "1984-02-01 to 1984-02-29", "1984-03-01 to 1984-03-31")) |>
+      dplyr::filter(additional_level %in% c("1984-01-01 to 1984-01-31", "1984-02-01 to 1984-02-29", "1984-03-01 to 1984-03-31")) |>
       dplyr::summarise("estimate_value" = sum(as.numeric(estimate_value), na.rm = TRUE)) |>
       dplyr::pull("estimate_value") |>
       as.numeric()) ==
@@ -71,7 +70,7 @@ test_that("summariseRecordCount() works", {
 
   expect_true(
     (summariseRecordCount(cdm, "drug_exposure", interval = "years") |>
-       dplyr::filter(variable_level %in% c("1981-01-01 to 1981-12-31", "1982-01-01 to 1982-12-31", "1983-01-01 to 1983-12-31",
+       dplyr::filter(additional_level %in% c("1981-01-01 to 1981-12-31", "1982-01-01 to 1982-12-31", "1983-01-01 to 1983-12-31",
                                            "1984-01-01 to 1984-12-31", "1985-01-01 to 1985-12-31", "1986-01-01 to 1986-12-31",
                                            "1987-01-01 to 1987-12-31", "1988-01-01 to 1988-12-31")) |>
        dplyr::summarise("estimate_value" = sum(as.numeric(.data$estimate_value), na.rm = TRUE)) |>
@@ -124,16 +123,16 @@ test_that("summariseRecordCount() ageGroup argument works", {
   expect_no_error(t <- summariseRecordCount(cdm, "condition_occurrence",
                                              ageGroup = list(">=65" = c(65, Inf), "<65" = c(0,64))))
   x <- t |>
-    dplyr::select("strata_level", "variable_level", "estimate_value") |>
+    dplyr::select("strata_level", "additional_level", "estimate_value") |>
     dplyr::filter(strata_level != "overall") |>
-    dplyr::group_by(variable_level) |>
+    dplyr::group_by(additional_level) |>
     dplyr::summarise(estimate_value = sum(as.numeric(estimate_value))) |>
-    dplyr::arrange(variable_level) |>
+    dplyr::arrange(additional_level) |>
     dplyr::pull("estimate_value")
   y <- t |>
-    dplyr::select("strata_level", "variable_level", "estimate_value") |>
+    dplyr::select("strata_level", "additional_level", "estimate_value") |>
     dplyr::filter(strata_level == "overall") |>
-    dplyr::arrange(variable_level) |>
+    dplyr::arrange(additional_level) |>
     dplyr::mutate(estimate_value = as.numeric(estimate_value)) |>
     dplyr::pull("estimate_value")
   expect_equal(x,y)
@@ -141,16 +140,16 @@ test_that("summariseRecordCount() ageGroup argument works", {
   expect_no_error(t <- summariseRecordCount(cdm, "condition_occurrence",
                                              ageGroup = list("<=20" = c(0,20), "21 to 40" = c(21,40), "41 to 60" = c(41,60), ">60" = c(61, Inf))))
   x <- t |>
-    dplyr::select("strata_level", "variable_level", "estimate_value") |>
+    dplyr::select("strata_level", "additional_level", "estimate_value") |>
     dplyr::filter(strata_level != "overall") |>
-    dplyr::group_by(variable_level) |>
+    dplyr::group_by(additional_level) |>
     dplyr::summarise(estimate_value = sum(as.numeric(estimate_value))) |>
-    dplyr::arrange(variable_level) |>
+    dplyr::arrange(additional_level) |>
     dplyr::pull("estimate_value")
   y <- t |>
-    dplyr::select("strata_level", "variable_level", "estimate_value") |>
+    dplyr::select("strata_level", "additional_level", "estimate_value") |>
     dplyr::filter(strata_level == "overall") |>
-    dplyr::arrange(variable_level) |>
+    dplyr::arrange(additional_level) |>
     dplyr::mutate(estimate_value = as.numeric(estimate_value)) |>
     dplyr::pull("estimate_value")
   expect_equal(x,y)
@@ -158,8 +157,8 @@ test_that("summariseRecordCount() ageGroup argument works", {
   expect_no_error(t <- summariseRecordCount(cdm, "condition_occurrence", interval = "years",
                                             ageGroup = list("<=20" = c(0,20), "21 to 40" = c(21,40), "41 to 60" = c(41,60), ">60" = c(61, Inf))))
   x <- t |>
-    dplyr::select("strata_level", "variable_level", "estimate_value") |>
-    dplyr::filter(strata_level == "<=20" & variable_level == "1920-01-01 to 1920-12-31") |>
+    dplyr::select("strata_level", "additional_level", "estimate_value") |>
+    dplyr::filter(strata_level == "<=20" & additional_level == "1920-01-01 to 1920-12-31") |>
     dplyr::summarise(n = sum(as.numeric(estimate_value))) |>
     dplyr::pull("n")
   y <- cdm$condition_occurrence |>
@@ -175,8 +174,8 @@ test_that("summariseRecordCount() ageGroup argument works", {
   expect_no_error(t <- summariseRecordCount(cdm, "condition_occurrence", interval = "years",
                                             ageGroup = list("<=20" = c(0,20), "21 to 40" = c(21,40), "41 to 60" = c(41,60))))
   x <- t |>
-    dplyr::select("strata_level", "variable_level", "estimate_value") |>
-    dplyr::filter(strata_level == "<=20" & variable_level == "1920-01-01 to 1920-12-31") |>
+    dplyr::select("strata_level", "additional_level", "estimate_value") |>
+    dplyr::filter(strata_level == "<=20" & additional_level == "1920-01-01 to 1920-12-31") |>
     dplyr::summarise(n = sum(as.numeric(estimate_value))) |>
     dplyr::pull("n") |> as.numeric()
   y <- cdm$condition_occurrence |>
@@ -199,40 +198,40 @@ test_that("summariseRecordCount() sex argument works", {
   # Check that works ----
   expect_no_error(t <- summariseRecordCount(cdm, "condition_occurrence", sex = TRUE))
   x <- t |>
-    dplyr::select("strata_level", "variable_level", "estimate_value") |>
+    dplyr::select("strata_level", "additional_level", "estimate_value") |>
     dplyr::filter(strata_level != "overall") |>
-    dplyr::group_by(variable_level) |>
+    dplyr::group_by(additional_level) |>
     dplyr::summarise(estimate_value = sum(as.numeric(estimate_value))) |>
-    dplyr::arrange(variable_level) |>
+    dplyr::arrange(additional_level) |>
     dplyr::pull("estimate_value")
   y <- t |>
-    dplyr::select("strata_level", "variable_level", "estimate_value") |>
+    dplyr::select("strata_level", "additional_level", "estimate_value") |>
     dplyr::filter(strata_level == "overall") |>
-    dplyr::arrange(variable_level) |>
+    dplyr::arrange(additional_level) |>
     dplyr::mutate(estimate_value = as.numeric(estimate_value)) |>
     dplyr::pull("estimate_value")
   expect_equal(x,y)
 
   expect_warning(t <- summariseRecordCount(cdm, "observation_period", sex = TRUE))
   x <- t |>
-    dplyr::select("strata_level", "variable_level", "estimate_value") |>
+    dplyr::select("strata_level", "additional_level", "estimate_value") |>
     dplyr::filter(strata_level != "overall") |>
-    dplyr::group_by(variable_level) |>
+    dplyr::group_by(additional_level) |>
     dplyr::summarise(estimate_value = sum(as.numeric(estimate_value))) |>
-    dplyr::arrange(variable_level) |>
+    dplyr::arrange(additional_level) |>
     dplyr::pull("estimate_value")
   y <- t |>
-    dplyr::select("strata_level", "variable_level", "estimate_value") |>
+    dplyr::select("strata_level", "additional_level", "estimate_value") |>
     dplyr::filter(strata_level == "overall") |>
-    dplyr::arrange(variable_level) |>
+    dplyr::arrange(additional_level) |>
     dplyr::mutate(estimate_value = as.numeric(estimate_value)) |>
     dplyr::pull("estimate_value")
   expect_equal(x,y)
 
   expect_no_error(t <- summariseRecordCount(cdm, "condition_occurrence", sex = TRUE, interval = "years"))
   x <- t |>
-    dplyr::select("strata_level", "variable_level", "estimate_value") |>
-    dplyr::filter(strata_level == "Male", variable_level == "1937-01-01 to 1937-12-31") |> dplyr::pull(estimate_value)
+    dplyr::select("strata_level", "additional_level", "estimate_value") |>
+    dplyr::filter(strata_level == "Male", additional_level == "1937-01-01 to 1937-12-31") |> dplyr::pull(estimate_value)
 
   y <- cdm$condition_occurrence |>
     dplyr::inner_join(cdm[["person"]] |> dplyr::select("person_id"), by = "person_id") |>
@@ -261,7 +260,7 @@ test_that("summariseRecordCount() works with mockOmopSketch", {
 
   expect_true(co |> dplyr::filter(grepl("Male",strata_level)) |>
                 dplyr::tally() |> dplyr::pull() == 0)
-  expect_true(all(co |> dplyr::filter(grepl("&&&",strata_level), variable_level != "overall") |>
+  expect_true(all(co |> dplyr::filter(grepl("&&&",strata_level), additional_level != "overall") |>
                 dplyr::pull("estimate_value") |> sort() ==
                   conditionpp |> dplyr::pull("n") |> as.character() |> sort()))
 

From 98030e89e2968adc831760c7c761cbfcaab22b0d Mon Sep 17 00:00:00 2001
From: Marta Alcalde-Herraiz <marta.alcalde@estudiantat.upc.edu>
Date: Tue, 5 Nov 2024 11:53:58 +0000
Subject: [PATCH 2/2] Update ConceptCounts

---
 DESCRIPTION                                  |  8 +-
 R/plotConceptCounts.R                        | 35 +++++----
 R/plotRecordCount.R                          |  4 +-
 R/summariseConceptCounts.R                   |  6 +-
 R/summariseInObservation.R                   |  2 +-
 R/summariseRecordCount.R                     |  2 +-
 man/OmopSketch-package.Rd                    |  1 +
 man/plotConceptCounts.Rd                     |  2 +-
 tests/testthat/test-summariseConceptCounts.R | 78 ++++++++++----------
 9 files changed, 79 insertions(+), 59 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 2380e90..9699fbc 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: OmopSketch
 Title: Characterise Tables of an OMOP Common Data Model Instance
-Version: 0.1.2
+Version: 0.1.1
 Authors@R: c(
     person( 
         "Marta", "Alcalde-Herraiz", 
@@ -15,6 +15,10 @@ Authors@R: c(
         "Elin", "Rowlands", email = "elin.rowlands@ndorms.ox.ac.uk", 
         role = c("aut"), comment = c(ORCID = "0009-0005-5166-0417")
     ),
+    person(
+        "Cecilia", "Campanile", email = "cecilia.campanile@ndorms.ox.ac.uk", 
+        role = c("aut"), comment = c(ORCID = "0009-0007-6629-4661")
+    ),
     person(
         "Edward", "Burn", email = "edward.burn@ndorms.ox.ac.uk", 
         role = c("aut"), comment = c(ORCID = "0000-0002-9286-1128")
@@ -71,4 +75,4 @@ URL: https://OHDSI.github.io/OmopSketch/
 BugReports: https://github.com/OHDSI/OmopSketch/issues
 VignetteBuilder: knitr
 Remotes: 
-    darwin-eu-dev/omopgenerics@mah_vl
+    darwin-eu-dev/omopgenerics
diff --git a/R/plotConceptCounts.R b/R/plotConceptCounts.R
index f92326c..ae0b2b0 100644
--- a/R/plotConceptCounts.R
+++ b/R/plotConceptCounts.R
@@ -23,7 +23,7 @@
 #'
 #' result |>
 #'   filter(variable_name == "Number subjects") |>
-#'   plotConceptCounts(facet = "codelist_name", colour = "codelist_name")
+#'   plotConceptCounts(facet = "codelist_name", colour = "standard_concept_name")
 #'
 #' PatientProfiles::mockDisconnect(cdm)
 #' }
@@ -35,9 +35,7 @@ plotConceptCounts <- function(result,
 
   # subset to results of interest
   result <- result |>
-    visOmopResults::filterSettings(.data$result_type == "summarise_concept_counts") |>
-    dplyr::mutate(variable_level = gsub(" to.*","",.data$variable_level)) |>
-    dplyr::mutate(variable_level = gsub("-01$","",.data$variable_level))
+    visOmopResults::filterSettings(.data$result_type == "summarise_concept_counts")
 
   if (nrow(result) == 0) {
     cli::cli_abort(c("!" = "No records found with result_type == summarise_concept_counts"))
@@ -52,12 +50,14 @@ plotConceptCounts <- function(result,
     ))
   }
 
+  result1 <- result |> visOmopResults::splitAdditional()
   # Detect if there are several time intervals
-  if(length(unique(result$variable_level)) > 1 ){
+  if("time_interval" %in% colnames(result1)){
     # Line plot where each concept is a different line
-    p <- result |>
-      dplyr::filter(.data$variable_level != "overall") |>
-      visOmopResults::scatterPlot(x = "variable_level",
+    p <- result1 |>
+      dplyr::filter(.data$time_interval != "overall") |>
+      visOmopResults::uniteAdditional(cols = c("time_interval", "standard_concept_name", "standard_concept_id", "source_concept_name", "source_concept_id", "domain_id")) |>
+      visOmopResults::scatterPlot(x = "time_interval",
                                   y = "count",
                                   line   = TRUE,
                                   point  = TRUE,
@@ -66,11 +66,20 @@ plotConceptCounts <- function(result,
                                   facet  = facet,
                                   colour = colour)
   }else{
-    p <- result |>
-      visOmopResults::barPlot(x = "standard_concept_name",
-                              y = "count",
-                              facet = facet,
-                              colour = colour)  +
+    if("standard_concept_name" %in% colnames(result1)){
+      p <- result |>
+        visOmopResults::barPlot(x = "standard_concept_name",
+                                y = "count",
+                                facet = facet,
+                                colour = colour)
+    }else{
+      p <- result |>
+        visOmopResults::barPlot(x = "codelist_name",
+                                y = "count",
+                                facet = facet,
+                                colour = colour)
+    }
+    p <- p +
       ggplot2::labs(
         x = "Concept name"
       )
diff --git a/R/plotRecordCount.R b/R/plotRecordCount.R
index f8b902e..221cb4b 100644
--- a/R/plotRecordCount.R
+++ b/R/plotRecordCount.R
@@ -57,13 +57,13 @@ plotRecordCount <- function(result,
       )
   }else{
     p <- result |>
-      visOmopResults::barPlot(x = "additional_level",
+      visOmopResults::barPlot(x = "variable_name",
                               y = "count",
                               facet = facet,
                               colour = colour)  +
       ggplot2::labs(
         y = "Count",
-        x = "Number records"
+        x = ""
       )
   }
   p
diff --git a/R/summariseConceptCounts.R b/R/summariseConceptCounts.R
index 20a1cee..e6ea43a 100644
--- a/R/summariseConceptCounts.R
+++ b/R/summariseConceptCounts.R
@@ -186,7 +186,6 @@ getCodeUse <- function(x,
     }
 
   cc <- records |>
-    # dplyr::collect() |> # https://github.com/darwin-eu-dev/PatientProfiles/issues/706
     PatientProfiles::summariseResult(strata = strata,
                                      variable = "standard_concept_name",
                                      group = group,
@@ -211,7 +210,10 @@ getCodeUse <- function(x,
   if(interval != "overall"){
     cc <- cc |>
       visOmopResults::splitStrata() |>
-      dplyr::mutate(variable_level = .data$interval_group) |>
+      dplyr::mutate("additional_level" = dplyr::if_else(.data$interval_group == "overall", .data$additional_level, paste0(.data$interval_group, " &&& ", .data$additional_level))) |>
+      dplyr::mutate("additional_name" = dplyr::if_else(.data$interval_group == "overall", .data$additional_name, paste0("time_interval &&& ", .data$additional_name))) |>
+      dplyr::mutate("additional_level" = gsub(" &&& overall$", "", .data$additional_level)) |>
+      dplyr::mutate("additional_name" = gsub(" &&& overall$", "", .data$additional_name)) |>
       visOmopResults::uniteStrata(unique(unlist(strata))[unique(unlist(strata)) != "interval_group"]) |>
       dplyr::select(-"interval_group")
   }
diff --git a/R/summariseInObservation.R b/R/summariseInObservation.R
index e52d6b8..bc0e2a5 100644
--- a/R/summariseInObservation.R
+++ b/R/summariseInObservation.R
@@ -338,7 +338,7 @@ addSexOverall <- function(result, sex){
         dplyr::group_by(.data$age_group, .data$additional_level, .data$variable_name) |>
         dplyr::summarise(estimate_value = sum(.data$estimate_value, na.rm = TRUE), .groups = "drop") |>
         dplyr::mutate(sex = "overall",
-                      additional_name = dplyr::if_else(additional_level == "overall", "overall", "time_interval"))
+                      additional_name = dplyr::if_else(.data$additional_level == "overall", "overall", "time_interval"))
     )
   }
   return(result)
diff --git a/R/summariseRecordCount.R b/R/summariseRecordCount.R
index 8c82fb4..c5cb0f2 100644
--- a/R/summariseRecordCount.R
+++ b/R/summariseRecordCount.R
@@ -255,7 +255,7 @@ createSummarisedResultRecordCount <- function(result, strata, omopTable, omopTab
     result <- result |>
       visOmopResults::splitStrata() |>
       dplyr::mutate(additional_level = .data$interval_group) |>
-      dplyr::mutate(additional_name = dplyr::if_else(additional_level == "overall", "overall", "time_interval")) |>
+      dplyr::mutate(additional_name = dplyr::if_else(.data$additional_level == "overall", "overall", "time_interval")) |>
       visOmopResults::uniteStrata(unique(unlist(strata))[unique(unlist(strata)) != "interval_group"]) |>
       dplyr::select(-"interval_group")
   }
diff --git a/man/OmopSketch-package.Rd b/man/OmopSketch-package.Rd
index 0bc315f..459a2b9 100644
--- a/man/OmopSketch-package.Rd
+++ b/man/OmopSketch-package.Rd
@@ -25,6 +25,7 @@ Authors:
 \itemize{
   \item Kim Lopez-Guell \email{kim.lopez@spc.ox.ac.uk} (\href{https://orcid.org/0000-0002-8462-8668}{ORCID})
   \item Elin Rowlands \email{elin.rowlands@ndorms.ox.ac.uk} (\href{https://orcid.org/0009-0005-5166-0417}{ORCID})
+  \item Cecilia Campanile \email{cecilia.campanile@ndorms.ox.ac.uk}
   \item Edward Burn \email{edward.burn@ndorms.ox.ac.uk} (\href{https://orcid.org/0000-0002-9286-1128}{ORCID})
   \item Martí Català \email{marti.catalasabate@ndorms.ox.ac.uk} (\href{https://orcid.org/0000-0003-3308-9905}{ORCID})
 }
diff --git a/man/plotConceptCounts.Rd b/man/plotConceptCounts.Rd
index 63492a7..2492a3d 100644
--- a/man/plotConceptCounts.Rd
+++ b/man/plotConceptCounts.Rd
@@ -37,7 +37,7 @@ result <- cdm |>
 
 result |>
   filter(variable_name == "Number subjects") |>
-  plotConceptCounts(facet = "codelist_name", colour = "codelist_name")
+  plotConceptCounts(facet = "codelist_name", colour = "standard_concept_name")
 
 PatientProfiles::mockDisconnect(cdm)
 }
diff --git a/tests/testthat/test-summariseConceptCounts.R b/tests/testthat/test-summariseConceptCounts.R
index 6486e28..6e63e46 100644
--- a/tests/testthat/test-summariseConceptCounts.R
+++ b/tests/testthat/test-summariseConceptCounts.R
@@ -1,6 +1,6 @@
 test_that("summarise code use - eunomia", {
   skip_on_cran()
- cdm <- cdmEunomia()
+  cdm <- cdmEunomia()
   acetiminophen <- c(1125315,  1127433, 40229134,
                      40231925, 40162522, 19133768,  1127078)
   poliovirus_vaccine <- c(40213160)
@@ -10,6 +10,8 @@ test_that("summarise code use - eunomia", {
   results <- summariseConceptCounts(cdm = cdm,
                                     conceptId = cs,
                                     interval = "years",
+                                    countBy = c("record", "person"),
+                                    concept = TRUE,
                                     sex = TRUE,
                                     ageGroup = list(c(0,17),
                                                     c(18,65),
@@ -23,12 +25,15 @@ test_that("summarise code use - eunomia", {
   # min cell counts:
   expect_equal(
       omopgenerics::suppress(results, 5) |>
+        visOmopResults::splitAdditional() |>
         dplyr::filter(
-          variable_name == "overall",
-          strata_level == "1909-01-01 to 1909-12-31",
+          strata_level == "overall",
+          variable_name == "Number records",
+          standard_concept_id == "overall",
+          time_interval == "1909-01-01 to 1909-12-31",
           group_level == "acetiminophen") |>
         dplyr::pull("estimate_value"),
-      as.character()
+      as.character(NA)
   )
 
   # check is a summarised result
@@ -38,13 +43,12 @@ test_that("summarise code use - eunomia", {
 
   # overall record count
   expect_true(results %>%
-                dplyr::filter(group_name == "codelist_name" &
-                                strata_name == "overall" &
-                                strata_level == "overall" &
-                                variable_level == "overall" &
-                                group_level == "acetiminophen" &
-                                variable_name == "Number records",
-                              additional_name == "overall") %>%
+                dplyr::filter(group_name == "codelist_name",
+                                strata_name == "overall",
+                                strata_level == "overall",
+                                additional_level == "overall",
+                                group_level == "acetiminophen",
+                                variable_name == "Number records") %>%
                 dplyr::pull("estimate_value") |>
                 as.numeric() ==
                 cdm$drug_exposure %>%
@@ -58,7 +62,6 @@ test_that("summarise code use - eunomia", {
                 dplyr::filter(group_name == "codelist_name" &
                                 strata_name == "overall" &
                                 strata_level == "overall" &
-                                variable_level == "overall" &
                                 group_level == "acetiminophen" &
                                 variable_name == "Number subjects",
                               additional_name == "overall") %>%
@@ -74,12 +77,13 @@ test_that("summarise code use - eunomia", {
   # by year
   # overall record count
   expect_true(results %>%
+                visOmopResults::splitAdditional() |>
                 dplyr::filter(group_name == "codelist_name" &
                                 strata_name == "overall" &
-                                variable_level == "2008-01-01 to 2008-12-31" &
+                                time_interval == "2008-01-01 to 2008-12-31" &
                                 group_level == "acetiminophen" &
                                 variable_name == "Number records",
-                              additional_name == "overall") %>%
+                              standard_concept_name == "overall") %>%
                 dplyr::pull("estimate_value") |>
                 as.numeric()  ==
                 cdm$drug_exposure %>%
@@ -90,12 +94,13 @@ test_that("summarise code use - eunomia", {
 
   # overall person count
   expect_true(results %>%
+                visOmopResults::splitAdditional() |>
                 dplyr::filter(group_name == "codelist_name" &
                                 strata_name == "overall" &
-                                variable_level == "2008-01-01 to 2008-12-31" &
+                                time_interval == "2008-01-01 to 2008-12-31" &
                                 group_level == "acetiminophen" &
                                 variable_name == "Number subjects",
-                              additional_name == "overall") %>%
+                              standard_concept_name == "overall") %>%
                 dplyr::pull("estimate_value") |>
                 as.numeric() ==
                 cdm$drug_exposure %>%
@@ -112,7 +117,6 @@ test_that("summarise code use - eunomia", {
                 dplyr::filter(group_name == "codelist_name" &
                                 strata_name == "sex" &
                                 strata_level == "Male" &
-                                variable_level == "overall" &
                                 group_level == "acetiminophen" &
                                 variable_name == "Number records" &
                               additional_name == "overall") %>%
@@ -129,7 +133,6 @@ test_that("summarise code use - eunomia", {
                 dplyr::filter(group_name == "codelist_name" &
                                 strata_name == "age_group &&& sex" &
                                 strata_level == "18 to 65 &&& Male" &
-                                variable_level == "overall" &
                                 group_level == "acetiminophen" &
                                 variable_name == "Number records",
                               additional_name == "overall") %>%
@@ -150,7 +153,6 @@ test_that("summarise code use - eunomia", {
                 dplyr::filter(group_name == "codelist_name" &
                                 strata_name == "age_group &&& sex" &
                                 strata_level == "18 to 65 &&& Male" &
-                                variable_level == "overall" &
                                 group_level == "acetiminophen" &
                                 variable_name == "Number subjects",
                               additional_name == "overall") %>%
@@ -177,33 +179,35 @@ test_that("summarise code use - eunomia", {
                                                      c(18,65),
                                                      c(66, 100)))
 
-  expect_true(results1$additional_level |> unique() |> length() == 1)
   expect_equal(
     results1 |>
+      visOmopResults::splitAdditional() |>
       dplyr::filter(variable_name == "Number records") |>
       dplyr::arrange(dplyr::across(dplyr::everything())),
     results |>
-      dplyr::filter(variable_name == "Number records", additional_name == "overall") |>
+      visOmopResults::splitAdditional() |>
+      dplyr::filter(variable_name == "Number records", standard_concept_name == "overall") |>
+      dplyr::select(-c(starts_with("standard_"), starts_with("source_"), "domain_id")) |>
       dplyr::arrange(dplyr::across(dplyr::everything()))
   )
   expect_true(results1 |>
-    dplyr::filter(variable_name  == "Number subjects",
-                  group_level == "acetiminophen",
-                  variable_level == "1909-01-01 to 1909-12-31",
-                  strata_level == "0 to 17")  |>
-    dplyr::pull("estimate_value") |>
-    as.numeric() ==
-    cdm$drug_exposure %>%
-    dplyr::filter(drug_concept_id %in% acetiminophen) %>%
-    PatientProfiles::addAge(indexDate = "drug_exposure_start_date") %>%
-    PatientProfiles::addSex() %>%
-    dplyr::filter(age >= "0", age <= "17", clock::get_year(drug_exposure_start_date) == 1909) |>
-    dplyr::select("person_id") %>%
-    dplyr::distinct() %>%
-    dplyr::tally() %>%
-    dplyr::pull("n"))
+                visOmopResults::splitAdditional() |>
+                dplyr::filter(variable_name  == "Number subjects",
+                              group_level == "acetiminophen",
+                              time_interval == "1909-01-01 to 1909-12-31",
+                              strata_level == "0 to 17")  |>
+                dplyr::pull("estimate_value") |>
+                as.numeric() ==
+                cdm$drug_exposure %>%
+                dplyr::filter(drug_concept_id %in% acetiminophen) %>%
+                PatientProfiles::addAge(indexDate = "drug_exposure_start_date") %>%
+                PatientProfiles::addSex() %>%
+                dplyr::filter(age >= "0", age <= "17", clock::get_year(drug_exposure_start_date) == 1909) |>
+                dplyr::select("person_id") %>%
+                dplyr::distinct() %>%
+                dplyr::tally() %>%
+                dplyr::pull("n"))
   expect_true(results1$group_level |> unique() |> length() == 2)
-  expect_true(results1$additional_name |> unique() |> length() == 1)
 
   results <- summariseConceptCounts(list("acetiminophen" = acetiminophen),
                               cdm = cdm, countBy = "person",