cml02a_gl listing

DESCRIPTION

@@ -92,6 +92,7 @@ Collate:
     'cfbt01.R'
     'checks.R'
     'chevron_tlg-S4methods.R'
+    'cml02a_gl.R'
     'cmt01a.R'
     'cmt02_pt.R'
     'coxt01.R'

NAMESPACE

@@ -65,6 +65,9 @@ export(chevron_g)
 export(chevron_l)
 export(chevron_simple)
 export(chevron_t)
+export(cml02a_gl)
+export(cml02a_gl_main)
+export(cml02a_gl_pre)
 export(cmt01_label)
 export(cmt01a)
 export(cmt01a_main)

NEWS.md

@@ -1,6 +1,6 @@
 # chevron 0.2.6.9019
 
-* Add `AEL02`, `AEL03` templates.
+* Add `AEL02`, `AEL03`, `CML02A_gl` templates.
 * Modify the post processing of `MHT01` to allow multiple `row_split_var`.
 * Improve the `report_null` method to facilitate the creation of null reports
 * Export the `std_postprocessing` function to simplify post processing logic.

R/ael01_nollt.R

@@ -21,7 +21,8 @@ ael01_nollt_main <- modify_default_args(
   dataset = "adae",
   key_cols = c("AEBODSYS", "AEDECOD"),
   disp_cols = "AETERM",
-  split_into_pages_by_var = NULL
+  split_into_pages_by_var = NULL,
+  unique_rows = TRUE
 )
 
 #' @describeIn ael01_nollt Preprocessing

R/cml02a_gl.R

@@ -0,0 +1,51 @@
+# cml02a_gl_main ----
+
+#' @describeIn cml02a_gl Main TLG function
+#'
+#' @inheritParams gen_args
+#' @returns the main function returns an `rlistings` or a `list` object.
+#' @export
+#'
+cml02a_gl_main <- modify_default_args(std_listing,
+  dataset = "adcm",
+  key_cols = c("ATC2", "CMDECOD"),
+  disp_cols = c("ATC2", "CMDECOD", "CMTRT"),
+  split_into_pages_by_var = NULL,
+  unique_rows = TRUE
+)
+
+#' @describeIn cml02a_gl Preprocessing
+#'
+#' @inheritParams cml02a_gl_main
+#' @inheritParams gen_args
+#' @returns the preprocessing function returns a `list` of `data.frame`.
+#'
+#' @export
+#'
+cml02a_gl_pre <- function(adam_db,
+                          dataset = "adcm",
+                          disp_cols = c("ATC2", "CMDECOD", "CMTRT"),
+                          ...) {
+  adam_db[[dataset]] <- adam_db[[dataset]] %>%
+    mutate(across(all_of(disp_cols), ~ reformat(.x, nocoding))) %>%
+    mutate(
+      ATC2 = with_label(.data$ATC2, "ATC Class Level 2"),
+      CMDECOD = with_label(.data$CMDECOD, "WHODrug Preferred Name"),
+      CMTRT = with_label(.data$CMTRT, "Investigator-Specified Treatment Term")
+    )
+
+  adam_db
+}
+
+#' `CML02A_GL` Listing 1 (Default) Concomitant Medication Class Level 2, Preferred Name, and Investigator-Specified
+#' Terms.
+#'
+#' @include chevron_tlg-S4class.R
+#' @export
+#'
+#' @examples
+#' run(cml02a_gl, syn_data)
+cml02a_gl <- chevron_l(
+  main = cml02a_gl_main,
+  preprocess = cml02a_gl_pre
+)

R/utils.R

@@ -46,6 +46,7 @@ std_listing <- function(adam_db,
                         key_cols,
                         disp_cols,
                         split_into_pages_by_var,
+                        unique_rows = FALSE,
                         ...) {
   assert_all_tablenames(adam_db, dataset)
   assert_valid_variable(adam_db[[dataset]], c(key_cols, disp_cols), label = paste0("adam_db$", dataset))
@@ -58,7 +59,7 @@ std_listing <- function(adam_db,
     split_into_pages_by_var = split_into_pages_by_var,
     ...,
     default_formatting = listing_format_chevron(),
-    unique_rows = TRUE
+    unique_rows = unique_rows
   )
 }
 

_pkgdown.yaml

@@ -64,6 +64,7 @@ reference:
       - aet05_all
       - aet10
       - cfbt01
+      - cml02a_gl
       - cmt01a
       - cmt02_pt
       - coxt01

tests/testthat/_snaps/cml02a_gl.md

@@ -0,0 +1,67 @@
+# cml02a_gl works with adcm dataset
+
+    Code
+      cat(export_as_txt(res, lpp = 100, cpp = 110))
+    Output
+      ATC Class Level 2   WHODrug Preferred Name   Investigator-Specified Treatment Term
+      ——————————————————————————————————————————————————————————————————————————————————
+      ATCCLAS2 A          medname A_1/3            A_1/3                                
+                          medname A_2/3            A_2/3                                
+                          medname A_3/3            A_3/3                                
+      ATCCLAS2 A p2       medname A_3/3            A_3/3                                
+      ATCCLAS2 B          medname B_1/4            B_1/4                                
+                          medname B_2/4            B_2/4                                
+                          medname B_3/4            B_3/4                                
+                          medname B_4/4            B_4/4                                
+      ATCCLAS2 B p2       medname B_1/4            B_1/4                                
+                          medname B_2/4            B_2/4                                
+      ATCCLAS2 B p3       medname B_1/4            B_1/4                                
+                          medname B_2/4            B_2/4                                
+      ATCCLAS2 C          medname C_1/2            C_1/2                                
+                          medname C_2/2            C_2/2                                
+      ATCCLAS2 C p2       medname C_1/2            C_1/2                                
+                          medname C_2/2            C_2/2                                
+      ATCCLAS2 C p3       medname C_2/2            C_2/2                                
+
+# cml02a_gl works with missing data
+
+    Code
+      cat(export_as_txt(res, lpp = 100, cpp = 110))
+    Output
+       ATC Class Level 2    WHODrug Preferred Name   Investigator-Specified Treatment Term
+      ————————————————————————————————————————————————————————————————————————————————————
+      No Coding Available   medname A_1/3            A_1/3                                
+                            medname A_2/3            A_2/3                                
+                            medname A_3/3            A_3/3                                
+                            medname B_1/4            B_1/4                                
+                            medname B_2/4            B_2/4                                
+                            medname B_3/4            B_3/4                                
+                            medname B_4/4            B_4/4                                
+                            medname C_1/2            C_1/2                                
+                            medname C_2/2            C_2/2                                
+
+# cml02a_gl functions work as expected
+
+    Code
+      cat(export_as_txt(res, lpp = 100, cpp = 110))
+    Output
+      ATC Class Level 2   WHODrug Preferred Name   Investigator-Specified Treatment Term
+      ——————————————————————————————————————————————————————————————————————————————————
+      ATCCLAS2 A          medname A_1/3            A_1/3                                
+                          medname A_2/3            A_2/3                                
+                          medname A_3/3            A_3/3                                
+      ATCCLAS2 A p2       medname A_3/3            A_3/3                                
+      ATCCLAS2 B          medname B_1/4            B_1/4                                
+                          medname B_2/4            B_2/4                                
+                          medname B_3/4            B_3/4                                
+                          medname B_4/4            B_4/4                                
+      ATCCLAS2 B p2       medname B_1/4            B_1/4                                
+                          medname B_2/4            B_2/4                                
+      ATCCLAS2 B p3       medname B_1/4            B_1/4                                
+                          medname B_2/4            B_2/4                                
+      ATCCLAS2 C          medname C_1/2            C_1/2                                
+                          medname C_2/2            C_2/2                                
+      ATCCLAS2 C p2       medname C_1/2            C_1/2                                
+                          medname C_2/2            C_2/2                                
+      ATCCLAS2 C p3       medname C_2/2            C_2/2                                
+

tests/testthat/test-cml02a_gl.R

@@ -0,0 +1,23 @@
+# cml02a_gl ----
+
+test_that("cml02a_gl works with adcm dataset", {
+  expect_silent(res <- run(cml02a_gl, syn_data))
+  expect_snapshot(cat(export_as_txt(res, lpp = 100, cpp = 110)))
+})
+
+test_that("cml02a_gl works with missing data", {
+  proc_data <- syn_data
+  proc_data$adcm$ATC2 <- NA_character_
+  expect_silent(res <- run(cml02a_gl, proc_data))
+  expect_snapshot(cat(export_as_txt(res, lpp = 100, cpp = 110)))
+})
+
+# cml02a_gl functions ----
+
+test_that("cml02a_gl functions work as expected", {
+  expect_silent(
+    res <- cml02a_gl_pre(syn_data) %>%
+      cml02a_gl_main()
+  )
+  expect_snapshot(cat(export_as_txt(res, lpp = 100, cpp = 110)))
+})