Template Review #140

NAMESPACE

@@ -28,6 +28,10 @@ export(aet04_1)
 export(aet04_1_lyt)
 export(aet04_1_main)
 export(aet04_1_pre)
+export(aet04_2)
+export(aet04_2_lyt)
+export(aet04_2_main)
+export(aet04_2_pre)
 export(assert_all_tablenames)
 export(assert_colnames)
 export(assert_one_tablenames)

R/aet03.R

@@ -34,7 +34,7 @@ aet03_1_main <- function(adam_db,
                          )) {
   # specific to AET03: avoid error if some severity levels are not present
   # TODO: rename all gradation to grade or grading (depending on context)
-  severity_grade <- levels(adam_db$adae[["AESEV"]])
+  severity_grade <- levels(adam_db$adae[["ASEV"]])
 
   lyt <- aet03_1_lyt(
     armvar = armvar,
@@ -104,7 +104,8 @@ aet03_1_lyt <- function(armvar = .study$actualarm,
     add_colcounts() %>%
     ifneeded_add_overall_col(lbl_overall) %>%
     summarize_occurrences_by_grade(
-      var = "AESEV",
+      var = "ASEV",
+      .indent_mods = 11L,
       grade_groups = list("- Any Intensity -" = severity_grade)
     ) %>%
     split_rows_by(
@@ -117,7 +118,8 @@ aet03_1_lyt <- function(armvar = .study$actualarm,
       split_label = lbl_aebodsys
     ) %>%
     summarize_occurrences_by_grade(
-      var = "AESEV",
+      var = "ASEV",
+      .indent_mods = 10L,
       grade_groups = list("- Any Intensity -" = severity_grade)
     ) %>%
     split_rows_by(
@@ -130,7 +132,8 @@ aet03_1_lyt <- function(armvar = .study$actualarm,
       split_label = lbl_aedecod
     ) %>%
     summarize_occurrences_by_grade(
-      var = "AESEV",
+      var = "ASEV",
+      .indent_mods = 8L,
       grade_groups = list("- Any Intensity -" = severity_grade)
     )
 }
@@ -149,7 +152,7 @@ aet03_1_pre <- function(adam_db, ...) {
 
   adam_db %>%
     dm_zoom_to("adae") %>%
-    filter(.data$ANL01FL == "Y") %>%
+    filter(.data$ANL01FL == "Y", .data$ASEV != c("", NA)) %>%
     dm_update_zoomed()
 }
 

R/aet04.R

@@ -125,7 +125,8 @@ aet04_1_lyt <- function(armvar = .study$actualarm,
     add_colcounts() %>%
     ifneeded_add_overall_col(lbl_overall) %>%
     summarize_occurrences_by_grade(
-      var = "AETOXGR",
+      .indent_mods = 11L,
+      var = "ATOXGR",
       grade_groups = group_grades
     ) %>%
     split_rows_by(
@@ -138,9 +139,9 @@ aet04_1_lyt <- function(armvar = .study$actualarm,
       split_label = lbl_aebodsys
     ) %>%
     summarize_occurrences_by_grade(
-      var = "AETOXGR",
+      var = "ATOXGR",
       grade_groups = group_grades,
-      .indent_mods = 0L
+      .indent_mods = 10L
     ) %>%
     split_rows_by(
       "AEDECOD",
@@ -154,12 +155,12 @@ aet04_1_lyt <- function(armvar = .study$actualarm,
     summarize_num_patients(
       var = "USUBJID",
       .stats = "unique",
-      .labels = "Any Grade"
+      .labels = "                  Any Grade"
     ) %>%
     count_occurrences_by_grade(
-      var = "AETOXGR",
+      var = "ATOXGR",
       grade_groups = group_grades[-1],
-      .indent_mods = -1L
+      .indent_mods = 8L
     )
 }
 
@@ -177,7 +178,7 @@ aet04_1_pre <- function(adam_db, ...) {
 
   adam_db %>%
     dm_zoom_to("adae") %>%
-    filter(.data$ANL01FL == "Y") %>%
+    filter(.data$ANL01FL == "Y", .data$ATOXGR != c("", NA)) %>%
     dm_update_zoomed()
 }
 
@@ -189,3 +190,189 @@ aet04_1_pre <- function(adam_db, ...) {
 #' @include chevron_tlg-S4class.R
 #' @export
 aet04_1 <- chevron_tlg(aet04_1_main, aet04_1_pre, adam_datasets = c("adsl", "adae"))
+
+
+
+#' @describeIn aet04_2 Main TLG function
+#'
+#' @inheritParams gen_args
+#' @param group_grades (`list`) putting in correspondence severity levels and labels.
+#'
+#' @details
+#'  * Numbers represent absolute numbers of patients and fraction of `N`, or absolute number of event when specified.
+#'  * Remove zero-count rows unless overridden with `prune_0 = FALSE`.
+#'  * Split columns by arm, typically `ACTARM`.
+#'  * Does not include a total column by default.
+#'  * Sort Body System or Organ Class and Dictionary-Derived Term by highest overall frequencies. Analysis Toxicity
+#'  Grade is sorted by severity.
+#'
+#' @export
+#'
+#' @examples
+#' library(dm)
+#'
+#' db <- syn_test_data() %>%
+#'   aet04_2_pre()
+#'
+#' aet04_2_main(db)
+#'
+aet04_2_main <- function(adam_db,
+                         armvar = .study$actualarm,
+                         group_grades = .study$group_grades,
+                         lbl_overall = .study$lbl_overall,
+                         prune_0 = TRUE,
+                         deco = std_deco("AET04"),
+                         .study = list(
+                           actualarm = "ACTARM",
+                           lbl_overall = NULL,
+                           group_grades = NULL
+                         )) {
+  lbl_aebodsys <- var_labels_for(adam_db$adae, "AEBODSYS")
+  lbl_aedecod <- var_labels_for(adam_db$adae, "AEDECOD")
+
+  # TODO: check that there are not grades in the data that are not defined in the `group_grades` map
+  if (is.null(group_grades)) {
+    group_grades <- list(
+      "Any Grade" = c("1", "2", "3", "4", "5"),
+      "Grade 1-2" = c("1", "2"),
+      "Grade 3-5" = c("3", "4", "5")
+    )
+  }
+
+  lyt <- aet04_2_lyt(
+    armvar = armvar,
+    lbl_overall = lbl_overall,
+    lbl_aebodsys = lbl_aebodsys,
+    lbl_aedecod = lbl_aedecod,
+    group_grades = group_grades,
+    deco = deco
+  )
+
+  tbl <- build_table(
+    lyt,
+    df = adam_db$adae,
+    alt_counts_df = adam_db$adsl
+  )
+
+  if (prune_0) tbl <- tbl %>% trim_rows()
+
+  tbl_sorted <- tbl %>%
+    sort_at_path(
+      path = c("AEBODSYS"),
+      scorefun = cont_n_allcols
+    ) %>%
+    sort_at_path(
+      path = c("AEBODSYS", "*", "AEDECOD"),
+      scorefun = cont_n_allcols
+    )
+
+  tbl_sorted
+}
+
+#' @describeIn aet04_2 Layout
+#'
+#' @inheritParams gen_args
+#'
+#' @param lbl_aebodsys (`character`) text label for `AEBODSYS`.
+#' @param lbl_aedecod (`character`) text label for `AEDECOD`.
+#' @param group_grades (`list`) putting in correspondence severity levels and labels.
+#'
+#' @export
+#'
+#' @examples
+#' aet04_2_lyt(armvar = "ACTARM")
+aet04_2_lyt <- function(armvar = .study$actualarm,
+                        lbl_aebodsys = "AEBODSYS",
+                        lbl_aedecod = "AEDECOD",
+                        group_grades = .study$group_grades,
+                        lbl_overall = .study$lbl_overall,
+                        deco = std_deco("AET04"),
+                        .study = list(
+                          actualarm = "ACTARM",
+                          lbl_overall = NULL,
+                          group_grades = NULL
+                        )) {
+  if (is.null(group_grades)) {
+    group_grades <- list(
+      "Any Grade" = c("1", "2", "3", "4", "5"),
+      "Grade 1-2" = c("1", "2"),
+      "Grade 3-5" = c("3", "4", "5")
+    )
+  }
+
+  basic_table_deco(deco) %>%
+    split_cols_by(var = armvar) %>%
+    add_colcounts() %>%
+    ifneeded_add_overall_col(lbl_overall) %>%
+    summarize_occurrences_by_grade(
+      .indent_mods = 11L,
+      var = "ATOXGR",
+      grade_groups = group_grades
+    ) %>%
+    split_rows_by(
+      "AEBODSYS",
+      child_labels = "visible",
+      nested = FALSE,
+      indent_mod = -1L,
+      split_fun = drop_split_levels,
+      label_pos = "topleft",
+      split_label = lbl_aebodsys
+    ) %>%
+    summarize_occurrences_by_grade(
+      var = "ATOXGR",
+      grade_groups = group_grades,
+      .indent_mods = 10L
+    ) %>%
+    split_rows_by(
+      "AEDECOD",
+      child_labels = "visible",
+      nested = TRUE,
+      indent_mod = -1L,
+      split_fun = drop_split_levels,
+      label_pos = "topleft",
+      split_label = lbl_aedecod
+    ) %>%
+    summarize_num_patients(
+      var = "USUBJID",
+      .stats = "unique",
+      .labels = "                  Any Grade"
+    ) %>%
+    count_occurrences_by_grade(
+      var = "ATOXGR",
+      grade_groups = group_grades[-1],
+      .indent_mods = 8L
+    )
+}
+
+
+
+#' @describeIn aet04_2 Preprocessing
+#'
+#' @inheritParams gen_args
+#' @param ... not used.
+#'
+#' @export
+#'
+#' @examples
+#' syn_test_data() %>%
+#'   aet04_2_pre()
+aet04_2_pre <- function(adam_db, ...) {
+  checkmate::assert_class(adam_db, "dm")
+
+  adam_db %>%
+    dm_zoom_to("adae") %>%
+    filter(.data$ANL01FL == "Y", .data$ATOXGR != c("", NA)) %>%
+    dm_update_zoomed()
+}
+
+# `AET04_2` Pipeline ----
+
+#' `AET04` Table 2 (Supplementary) Adverse Events by Highest `NCI` `CTACAE` `AE` Grade with Analysis Toxicity Grade 3-5
+#' combined.
+#'
+#' The `AET04_2` table provides an overview of adverse event with the highest `NCI` `CTCAE` grade per individual,
+#' with the Analysis Toxicity Grade 3-5 combined in one group.
+#'
+#' @include chevron_tlg-S4class.R
+#' @export
+aet04_2 <- chevron_tlg(aet04_2_main, aet04_2_pre, adam_datasets = c("adsl", "adae"))

_pkgdown.yaml

@@ -44,6 +44,7 @@ reference:
       - aet02_3
       - aet03_1
       - aet04_1
+      - aet04_2
       - cmt01a_1
       - cmt01a_2
       - cmt01a_3