128 aet02 template

R/aet02.R

@@ -34,13 +34,6 @@
 #' aet02_1(adam_db = list(adsl = db$adsl, adae = db$adae)) %>% head()
 #'
 #' aet02_1(db, lbl_overall = "All Patients") %>% head()
-#'
-#' db_m <- db %>%
-#'   dm_zoom_to(adae) %>%
-#'   mutate(AEBODSYS = formatters::with_label(AEBODSYS, "Medra System Organ Class")) %>%
-#'   dm_update_zoomed()
-#'
-#' aet02_1(db_m) %>% head()
 aet02_1 <- function(adam_db,
                     armvar = .study$actualarm,
                     lbl_overall = .study$lbl_overall,
@@ -55,8 +48,6 @@ aet02_1 <- function(adam_db,
   lyt <- aet02_1_lyt(
     armvar = armvar,
     lbl_overall = lbl_overall,
-    lbl_aebodsys = var_labels_for(dbsel$adae, "AEBODSYS"),
-    lbl_aedecod = var_labels_for(dbsel$adae, "AEDECOD"),
     deco = deco
   )
 
@@ -69,7 +60,7 @@ aet02_1 <- function(adam_db,
   tbl_sorted <- tbl %>%
     sort_at_path(
       path = c("AEBODSYS"),
-      scorefun = cont_n_onecol(ncol(tbl))
+      scorefun = cont_n_allcols
     ) %>%
     sort_at_path(
       path = c("AEBODSYS", "*", "AEDECOD"),
@@ -95,8 +86,8 @@ aet02_1 <- function(adam_db,
 #' )
 aet02_1_lyt <- function(armvar = .study$actualarm,
                         lbl_overall = .study$lbl_overall,
-                        lbl_aebodsys = "Body System or Organ Class",
-                        lbl_aedecod = "Dictionary-Derived Term",
+                        lbl_aebodsys = "MedDRA System Organ Class",
+                        lbl_aedecod = "MedDRA Preferred Term",
                         deco = std_deco("AET02"),
                         .study = list(
                           actualarm = "ACTARM",
@@ -154,7 +145,8 @@ aet02_1_pre <- function(adam_db) {
   adam_db %>%
     dm_zoom_to("adae") %>%
     filter(.data$ANL01FL == "Y") %>%
-    dm_update_zoomed()
+    dm_update_zoomed() %>%
+    dm_explicit_na(na_level = "No Coding available")
 }
 
 # Version2 ----
@@ -188,13 +180,6 @@ aet02_1_pre <- function(adam_db) {
 #'
 #' # Additional Examples
 #' aet02_2(db, lbl_overall = "All Patients") %>% head()
-#'
-#' db_m <- db %>%
-#'   dm_zoom_to(adae) %>%
-#'   mutate(AEBODSYS = formatters::with_label(AEBODSYS, "MedDRA System Organ Class")) %>%
-#'   dm_update_zoomed()
-#'
-#' aet02_2(db_m) %>% head()
 aet02_2 <- function(adam_db,
                     armvar = .study$actualarm,
                     lbl_overall = .study$lbl_overall,
@@ -205,18 +190,14 @@ aet02_2 <- function(adam_db,
                       lbl_overall = NULL
                     )) {
   dbsel <- get_db_data(adam_db, "adsl", "adae")
-  adae <- dbsel$adae
 
   lyt <- aet02_2_lyt(
     armvar = armvar,
     lbl_overall = lbl_overall,
-    lbl_aebodsys = var_labels_for(adae, "AEBODSYS"),
-    lbl_aehlt = var_labels_for(adae, "AEHLT"),
-    lbl_aedecod = var_labels_for(adae, "AEDECOD"),
     deco = deco
   )
 
-  tbl <- build_table(lyt, adae, alt_counts_df = dbsel$adsl)
+  tbl <- build_table(lyt, dbsel$adae, alt_counts_df = dbsel$adsl)
 
   if (prune_0) {
     tbl <- prune_table(tbl)
@@ -260,9 +241,9 @@ aet02_2 <- function(adam_db,
 #' )
 aet02_2_lyt <- function(armvar = .study$actualarm,
                         lbl_overall = .study$lbl_overall,
-                        lbl_aebodsys = "AEBODSYS",
-                        lbl_aehlt = "AEHLT",
-                        lbl_aedecod = "AEDECOD",
+                        lbl_aebodsys = "MedDRA System Organ Class",
+                        lbl_aehlt = "MedDRA High-Level Term",
+                        lbl_aedecod = "MedDRA Preferred Term",
                         deco = std_deco("AET02"),
                         .study = list(
                           actualarm = "ACTARM",
@@ -336,7 +317,8 @@ aet02_2_pre <- function(adam_db) {
   adam_db %>%
     dm_zoom_to("adae") %>%
     filter(.data$ANL01FL == "Y") %>%
-    dm_update_zoomed()
+    dm_update_zoomed() %>%
+    dm_explicit_na(na_level = "No Coding available")
 }
 
 # Version 3 ----
@@ -380,7 +362,6 @@ aet02_3 <- function(adam_db,
   lyt <- aet02_3_lyt(
     armvar = armvar,
     lbl_overall = lbl_overall,
-    lbl_aedecod = var_labels_for(adam_db$adae, "AEDECOD"),
     deco = deco
   )
 
@@ -416,7 +397,7 @@ aet02_3 <- function(adam_db,
 #' )
 aet02_3_lyt <- function(armvar = .study$actualarm,
                         lbl_overall = .study$lbl_overall,
-                        lbl_aedecod = "AEDECOD",
+                        lbl_aedecod = "MedDRA Preferred Term",
                         deco = std_deco("AET02"),
                         .study = list(
                           actualarm = "ACTARM",
@@ -431,7 +412,7 @@ aet02_3_lyt <- function(armvar = .study$actualarm,
       .stats = c("unique", "nonunique"),
       .labels = c(
         unique = "Total number of patients with at least one adverse event",
-        nonunique = "Overall total number of events"
+        nonunique = "Total number of events"
       )
     ) %>%
     count_occurrences(vars = "AEDECOD", .indent_mods = -2L) %>%
@@ -453,5 +434,6 @@ aet02_3_pre <- function(adam_db) {
   adam_db %>%
     dm_zoom_to("adae") %>%
     filter(.data$ANL01FL == "Y") %>%
-    dm_update_zoomed()
+    dm_update_zoomed() %>%
+    dm_explicit_na(na_level = "No Coding available")
 }

R/dtht01.R

@@ -13,6 +13,7 @@
 #'  * Numbers represent absolute numbers of subjects and fraction of `N`, or absolute numbers when specified.
 #'  * Remove zero-count rows unless overridden with `prune_0 = FALSE`.
 #'  * Does not include a total column by default.
+#'  * For the breakdown of `OTHER`, the percentages are based on `N`.
 #'
 #' @export
 #'
@@ -27,9 +28,9 @@
 #'   dtht01_1_pre()
 #'
 #' dtht01_1(adam_db = db)
-#' dtht01_1(adam_db = db, other_category = FALSE)
+#' dtht01_1(adam_db = db, other_category = TRUE)
 #' dtht01_1(adam_db = db, time_since_last_dose = TRUE)
-#' dtht01_1(adam_db = db, time_since_last_dose = TRUE, other_category = FALSE)
+#' dtht01_1(adam_db = db, time_since_last_dose = TRUE, other_category = TRUE)
 dtht01_1 <- function(adam_db,
                      armvar = .study$actualarm,
                      time_since_last_dose = FALSE,
@@ -114,7 +115,11 @@ dtht01_1_lyt <- function(armvar = .study$actualarm,
       .labels =  c(count_fraction = "Total number of deaths"),
       .formats = c(count_fraction = "xx (xx.x%)")
     ) %>%
-    summarize_vars(vars = c("DTHCAT"), var_labels = c("Primary cause of death"))
+    summarize_vars(
+      vars = c("DTHCAT"),
+      var_labels = c("Primary cause of death"),
+      denom = "N_col"
+    )
 
   if (other_category) {
     tab <-
@@ -128,7 +133,8 @@ dtht01_1_lyt <- function(armvar = .study$actualarm,
         "DTHCAUS",
         nested = TRUE,
         .stats = "count_fraction",
-        .indent_mods = c("count_fraction" = 4L)
+        .indent_mods = c("count_fraction" = 4L),
+        denom = "N_col"
       )
   }
   tab
@@ -159,15 +165,38 @@ dtht01_1_opt_lyt <- function(armvar = .study$actualarm,
     summarize_vars(
       vars = "LDDTHGR1",
       var_labels = "Days from last drug administration",
-      show_labels = "visible"
+      show_labels = "visible",
+      denom = "N_col"
     ) %>%
     split_rows_by(
       "LDDTHGR1",
       split_fun = remove_split_levels("<Missing>"),
       split_label = "Primary cause by days from last study drug administration",
       label_pos = "visible"
     ) %>%
-    summarize_vars("DTHCAT")
+    summarize_vars("DTHCAT", denom = "N_col")
+}
+
+#' @describeIn dtht01_1 `dtht01_1` Preprocessing
+#'
+#' @inheritParams gen_args
+#'
+#' @export
+#'
+#' @examples
+#' syn_test_data() %>%
+#'   dtht01_1_pre()
+dtht01_1_pre <- function(adam_db) {
+  checkmate::assert_class(adam_db, "dm")
+
+  death_fact <- levels(adam_db$adsl$DTHCAT)
+  death_fact <- setdiff(death_fact, "OTHER")
+  death_fact <- c(death_fact, "OTHER")
+
+  adam_db %>%
+    dm_zoom_to("adsl") %>%
+    mutate(DTHCAT = fct_relevel(.data$DTHCAT, death_fact)) %>%
+    dm_update_zoomed()
 }
 
 #' @describeIn dtht01_1 `dtht01_1` Preprocessing