Added updateColumnValues FUN to change names of cohorts or other variables in summarised result

R/updateColumnValues.R

@@ -0,0 +1,27 @@
+#' Update values in a summarised result
+#'
+#' @description
+#' Updates the character values of specific column(s) in a summarised result object
+#' (e.g., changing cohort names to a more polished version for Shiny app labels)
+#' according to a given name mapping.
+#'
+#' @param summarised_result The summarised result with values to update.
+#' @param names_map A named vector containing the mapping between old and new names.
+#' @param variable The column name(s) containing the values to be updated in the
+#' summarised result object.
+#'
+#' @returns The summarised result itself with updated values.
+#'
+updateColumnValues <- function(
+    summarised_result,
+    names_map,
+    variable
+) {
+
+  summarised_result[[variable]] <- dplyr::recode(
+    summarised_result[[variable]],
+    !!!names_map
+  )
+
+  return(summarised_result)
+}

tests/testthat/test-cdmNames.R

@@ -1,5 +1,5 @@
 test_that("assertCdmNames works", {
-  # Assert a group of acryonims
+  # Assert a group of acronyms
   labels <- c(
     "BCR",
     "IQVIA LPD Belgium",
@@ -9,9 +9,9 @@ test_that("assertCdmNames works", {
   )
   assertCdmNames(labels = labels) |>
     expect_invisible()
-  # Error acronim do not match
+  # Error acronym do not match
   labels <- c(
-    "BCRX", # Mispelled acronym
+    "BCRX", # Misspelled acronym
     "IQVIA LPD Belgium",
     "NLHR@UiO:PERINATAL",
     "IQVIA US - AmbEMR",
@@ -22,7 +22,7 @@ test_that("assertCdmNames works", {
 })
 
 test_that("assertCdmNames against expected acronyms", {
-  # Assert a group of acryonims
+  # Assert a group of acronyms
   labels <- c(
     "BCR",
     "IQVIA LPD Belgium",
@@ -42,7 +42,7 @@ test_that("assertCdmNames against expected acronyms", {
     expect_error()
   # Incorrect acronym
   labels <- c(
-    "BCRX", # Mispelled acronym
+    "BCRX", # Misspelled acronym
     "IQVIA LPD Belgium",
     "NLHR@UiO:PERINATAL",
     "IQVIA US - AmbEMR",
@@ -78,9 +78,9 @@ test_that("arrangeCdmNames returns required acronyms in order", {
       "IQVIA US - AmbEMR",
       "IQVIA US - PMTX+"
     ))
-  # Error acronim do not match
+  # Error acronym do not match
   labels <- c(
-    "BCRX", # Mispelled acronym
+    "BCRX", # Misspelled acronym
     "IQVIA LPD Belgium",
     "NLHR@UiO:PERINATAL",
     "IQVIA US - AmbEMR",

tests/testthat/test-updateColumnValues.R

@@ -0,0 +1,48 @@
+test_that("updateColumnValues updates summarised result correctly", {
+
+  # Create mock summarised result
+  x <- dplyr::tibble(
+    "result_id" = 1L,
+    "cdm_name" = "cprd",
+    "group_name" = "cohort_name",
+    "group_level" = c(
+      "acetaminophen",
+      "acetaminophen",
+      "diclofenac",
+      "ibuprofen"
+      ),
+    "strata_name" = "sex &&& age_group",
+    "strata_level" = c(
+      "male &&& <40",
+      "male &&& >=40",
+      "male &&& >=40",
+      "male &&& >=40"
+      ),
+    "variable_name" = "number_subjects",
+    "variable_level" = NA_character_,
+    "estimate_name" = "count",
+    "estimate_type" = "integer",
+    "estimate_value" = c("5", "15", "8", "12"),
+    "additional_name" = "overall",
+    "additional_level" = "overall"
+  ) |>
+    omopgenerics::newSummarisedResult()
+
+  # Define mapping to custom new names
+  names_map <- c(
+    "acetaminophen" = "Acetamoniphen cohort",
+    "diclofenac" ="Diclofenac cohort (outdated)",
+    "ibuprofen" = "Ibuprofen cohort"
+  )
+
+  # Test function
+  x <- updateColumnValues(
+    summarised_result = x,
+    names_map = names_map,
+    variable = "group_level"
+  )
+
+  check_names <- all(x$group_level %in% unname(names_map))
+  expect_true(check_names)
+
+})