Merge pull request #214 from OHDSI/mah_concept

Fix concept argument
OHDSI · Oct 21, 2024 · b575776 · b575776
2 parents 5749f1a + 5b1c161
commit b575776
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Showing 3 changed files with 48 additions and 1 deletion.
diff --git a/R/summariseConceptCounts.R b/R/summariseConceptCounts.R
@@ -26,6 +26,7 @@
 #' results
 #'
 #' PatientProfiles::mockDisconnect(cdm)
+#'
 #' }
 summariseConceptCounts <- function(cdm,
                                    conceptId,
@@ -176,12 +177,19 @@ getCodeUse <- function(x,
   }
 
   if(!"number subjects" %in% c(countBy)){records <- records |> dplyr::select(-"person_id")}
+  if(concept){
+    group <- list("standard_concept_id")
+  }else{
+    group <- list()
+    records <- records |>
+      dplyr::mutate("standard_concept_name" = !!names(x))
+    }
 
   cc <- records |>
     # dplyr::collect() |> # https://github.com/darwin-eu-dev/PatientProfiles/issues/706
     PatientProfiles::summariseResult(strata = strata,
                                      variable = "standard_concept_name",
-                                     group = "standard_concept_id",
+                                     group = group,
                                      includeOverallGroup = TRUE,
                                      includeOverallStrata = TRUE,
                                      counts = TRUE,

diff --git a/man/summariseConceptCounts.Rd b/man/summariseConceptCounts.Rd
diff --git a/tests/testthat/test-summariseConceptCounts.R b/tests/testthat/test-summariseConceptCounts.R
@@ -168,6 +168,43 @@ test_that("summarise code use - eunomia", {
                 dplyr::tally() %>%
                 dplyr::pull("n"))
 
+  results1 <- summariseConceptCounts(cdm = cdm,
+                                     conceptId = cs,
+                                     interval = "years",
+                                     concept = FALSE,
+                                     sex = TRUE,
+                                     ageGroup = list(c(0,17),
+                                                     c(18,65),
+                                                     c(66, 100)))
+
+  expect_true(results1$additional_level |> unique() |> length() == 1)
+  expect_equal(
+    results1 |>
+      dplyr::filter(variable_name == "Number records") |>
+      dplyr::arrange(dplyr::across(dplyr::everything())),
+    results |>
+      dplyr::filter(variable_name == "Number records", additional_name == "overall") |>
+      dplyr::arrange(dplyr::across(dplyr::everything()))
+  )
+  expect_true(results1 |>
+    dplyr::filter(variable_name  == "Number subjects",
+                  group_level == "acetiminophen",
+                  variable_level == "1909-01-01 to 1909-12-31",
+                  strata_level == "0 to 17")  |>
+    dplyr::pull("estimate_value") |>
+    as.numeric() ==
+    cdm$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"))
+  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",
                               interval = "years",
@@ -178,6 +215,7 @@ test_that("summarise code use - eunomia", {
   expect_true(nrow(results %>%
                      dplyr::filter(variable_name == "Number records")) == 0)
 
+
   results <- summariseConceptCounts(list("acetiminophen" = acetiminophen),
                               cdm = cdm, countBy = "record",
                               interval = "years",