add prototype (#747)

new ael03 template

thank you for the review

---------

Signed-off-by: b_falquet <[email protected]>

DESCRIPTION

@@ -85,6 +85,7 @@ Collate:
     'chevron_tlg-S4class.R'
     'ael01_nollt.R'
     'ael02.R'
+    'ael03.R'
     'aet01.R'
     'aet01_aesi.R'
     'aet02.R'

NAMESPACE

@@ -19,6 +19,9 @@ export(ael01_nollt_pre)
 export(ael02)
 export(ael02_main)
 export(ael02_pre)
+export(ael03)
+export(ael03_main)
+export(ael03_pre)
 export(aet01)
 export(aet01_aesi)
 export(aet01_aesi_main)

NEWS.md

@@ -1,6 +1,6 @@
 # chevron 0.2.6.9004
 
-* Add `AEL02` template.
+* Add `AEL02`, `AEL03` templates.
 * Modify the post processing of `MHT01` to allow multiple `row_split_var`.
 
 # chevron 0.2.6

R/ael01_nollt.R

@@ -20,7 +20,8 @@ ael01_nollt_main <- modify_default_args(
   std_listing,
   dataset = "adae",
   key_cols = c("AEBODSYS", "AEDECOD"),
-  disp_cols = "AETERM"
+  disp_cols = "AETERM",
+  split_into_pages_by_var = NULL
 )
 
 #' @describeIn ael01_nollt Preprocessing

R/ael02.R

@@ -8,11 +8,12 @@
 #'
 ael02_main <- modify_default_args(std_listing,
   dataset = "adae",
-  key_cols = c("ID", "ASR", "ACTARM"),
+  key_cols = c("ID", "ASR"),
   disp_cols = c(
     "AEDECOD", "TRTSDTM", "ASTDY", "ADURN", "AESER",
     "ASEV", "AREL", "AEOUT", "AECONTRT", "AEACN"
-  )
+  ),
+  split_into_pages_by_var = "ACTARM"
 )
 
 #' @describeIn ael02 Preprocessing

R/ael03.R

@@ -0,0 +1,80 @@
+# ael03_main ----
+
+#' @describeIn ael03 Main TLG function
+#'
+#' @inheritParams gen_args
+#' @returns the main function returns an `rlistings` or a `list` object.
+#' @export
+#'
+ael03_main <- modify_default_args(
+  std_listing,
+  dataset = "adae",
+  key_cols = c("ID", "ASR"),
+  disp_cols = c(
+    "AEDECOD", "TRTSDTM", "ASTDY", "ADURN", "ASEV",
+    "AREL", "AEOUT", "AECONTRT", "AEACN", "SERREAS"
+  ),
+  split_into_pages_by_var = "ACTARM"
+)
+
+#' @describeIn ael03 Preprocessing
+#'
+#' @inheritParams ael03_main
+#' @inheritParams gen_args
+#'
+#' @export
+#'
+ael03_pre <- function(adam_db,
+                      dataset = "adae",
+                      arm_var = "ACTARM",
+                      ...) {
+  adam_db[[dataset]] <- adam_db[[dataset]] %>%
+    filter(.data$ANL01FL == "Y") %>%
+    filter(.data$AESER == "Y") %>%
+    mutate(
+      across(
+        all_of(c(arm_var, "AEDECOD", "ASEV", "AEOUT", "AEACN")),
+        ~ reformat(.x, missing_rule)
+      )
+    ) %>%
+    mutate(
+      !!arm_var := with_label(.data[[arm_var]], "Treatment"),
+      ID = create_id_listings(.data$SITEID, .data$SUBJID),
+      AEDECOD = with_label(reformat(.data$AEDECOD, nocoding), "Adverse\nEvent MedDRA\nPreferred Term"),
+      ASR = with_label(paste(.data$AGE, .data$SEX, .data$RACE, sep = "/"), "Age/Sex/Race"),
+      # Datetime of First Exposure to Treatment
+      TRTSDTM = with_label(.data$TRTSDTM, "Date of\nFirst Study\nDrug\nAdministration"),
+      ASTDY = with_label(.data$ASTDY, "Study\nDay of\nOnset"),
+      ADURN = with_label(.data$AENDY - .data$ASTDY + 1, "AE\nDuration\nin Days"),
+      AESER = with_label(.data$AESER, "Serious"),
+      ASEV = with_label(.data$ASEV, "Most\nExtreme\nIntensity"),
+      AREL = with_label(reformat(.data$AREL, yes_no_rule), "Caused by\nStudy\nDrug"), # Analysis Causality
+      AEOUT = with_label(reformat(.data$AEOUT, outcome_rule), "Outcome\n(1)"),
+      AECONTRT = with_label(reformat(.data$AECONTRT, yes_no_rule), "Treatment\nfor AE"),
+      AEACN = with_label(reformat(.data$AEACN, dose_change_rule), "Action\nTaken\n(2)"),
+      # New derived column
+      SERREAS = with_label(case_when(
+        AESDTH == "Y" ~ "1",
+        AESLIFE == "Y" ~ "2",
+        AESHOSP == "Y" ~ "3",
+        AESDISAB == "Y" ~ "4",
+        AESCONG == "Y" ~ "5",
+        AESMIE == "Y" ~ "6",
+        TRUE ~ " "
+      ), "Reason\nClassified\nas Serious\n(3)"),
+    )
+
+  adam_db
+}
+
+#' `AEL03` Listing 1 (Default) Listing of Serious Adverse Events.
+#'
+#' @include chevron_tlg-S4class.R
+#' @export
+#'
+#' @examples
+#' res <- run(ael03, syn_data)
+ael03 <- chevron_l(
+  main = ael03_main,
+  preprocess = ael03_pre
+)

R/gen_args.R

@@ -22,6 +22,7 @@
 #'   Key columns allow you to group repeat occurrences.
 #' @param disp_cols (`character`) names of non-key columns which should be displayed when the listing is rendered.
 #' @param row_split_var (`character`) additional row split variables.
+#' @param split_into_pages_by_var (`character` or `NULL`) the name of the variable to split the listing by.
 #' @param page_var (`string`) variable name prior to which the row split is by page.
 #' @param unique_rows (`flag`) whether to keep only unique rows in listing.
 #' @param ... not used.
@@ -32,5 +33,5 @@
 gen_args <- function(adam_db, main, preprocess, postprocess, dataset,
                      type, arm_var, lbl_overall, prune_0, req_tables, deco, group,
                      tlg, visitvar, visit_value, paramcd_value,
-                     key_cols, disp_cols, row_split_var, page_var, unique_rows, ...) {
+                     key_cols, disp_cols, row_split_var, split_into_pages_by_var, page_var, unique_rows, ...) {
 }

R/utils.R

@@ -67,6 +67,7 @@ std_listing <- function(adam_db,
                         dataset,
                         key_cols,
                         disp_cols,
+                        split_into_pages_by_var,
                         ...) {
   assert_all_tablenames(adam_db, dataset)
   assert_valid_variable(adam_db[[dataset]], c(key_cols, disp_cols), label = paste0("adam_db$", dataset))
@@ -76,6 +77,7 @@ std_listing <- function(adam_db,
     df = adam_db[[dataset]],
     key_cols = key_cols,
     disp_cols = disp_cols,
+    split_into_pages_by_var = split_into_pages_by_var,
     ...,
     default_formatting = listing_format_chevron(),
     unique_rows = TRUE

_pkgdown.yaml

@@ -52,6 +52,7 @@ reference:
     contents:
       - ael01_nollt
       - ael02
+      - ael03
       - aet01
       - aet01_aesi
       - aet02