From 83a17d6edef38cec15b54cbc71528aa085ae7f32 Mon Sep 17 00:00:00 2001
From: "Zhang, Bo {MDBR~South San Francisco}" <zhang.bo.bz1@gene.com>
Date: Mon, 18 Jul 2022 19:32:12 +0200
Subject: [PATCH 1/8] Template Review #140

---
 NAMESPACE                |   4 +
 R/aet03.R                |  10 +-
 R/aet04.R                | 202 +++++++++++++++++++++++++++++++++++++--
 man/aet04_2_main.Rd      |  87 +++++++++++++++++
 man/chevron_tlg-class.Rd |   7 ++
 5 files changed, 298 insertions(+), 12 deletions(-)
 create mode 100644 man/aet04_2_main.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 6c56e8ed12..cfe6691f84 100644
--- a/NAMESPACE
+++ b/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)
diff --git a/R/aet03.R b/R/aet03.R
index 8baf63b7fe..a768dcd7d6 100644
--- a/R/aet03.R
+++ b/R/aet03.R
@@ -37,7 +37,7 @@ 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,
@@ -107,7 +107,7 @@ aet03_1_lyt <- function(armvar = .study$actualarm,
     add_colcounts() %>%
     ifneeded_add_overall_col(lbl_overall) %>%
     summarize_occurrences_by_grade(
-      var = "AESEV",
+      var = "ASEV",
       grade_groups = list("- Any Intensity -" = severity_grade)
     ) %>%
     split_rows_by(
@@ -120,7 +120,7 @@ aet03_1_lyt <- function(armvar = .study$actualarm,
       split_label = lbl_aebodsys
     ) %>%
     summarize_occurrences_by_grade(
-      var = "AESEV",
+      var = "ASEV",
       grade_groups = list("- Any Intensity -" = severity_grade)
     ) %>%
     split_rows_by(
@@ -133,7 +133,7 @@ aet03_1_lyt <- function(armvar = .study$actualarm,
       split_label = lbl_aedecod
     ) %>%
     summarize_occurrences_by_grade(
-      var = "AESEV",
+      var = "ASEV",
       grade_groups = list("- Any Intensity -" = severity_grade)
     )
 }
@@ -153,7 +153,7 @@ 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()
 }
 
diff --git a/R/aet04.R b/R/aet04.R
index 9377533ae2..c230a7590a 100644
--- a/R/aet04.R
+++ b/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
     )
 }
 
@@ -178,7 +179,7 @@ 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()
 }
 
@@ -190,3 +191,190 @@ aet04_1_pre <- function(adam_db, ...) {
 #' @rdname chevron_tlg-class
 #' @export
 aet04_1 <- chevron_tlg(aet04_1_main, aet04_1_pre, adam_datasets = c("adsl", "adae"))
+
+
+
+
+#' #' `AET04` Table 2 (Supplementary) Adverse Events by Highest NCI CTACAE AE Grade with Analysis Toxicity Grade 3-5 combined Table 2.
+#' 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.
+#'
+#' @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$adsl
+  )
+
+  if (prune_0) tbl <- tbl %>% trim_rows()
+
+  tbl_sorted <- tbl %>%
+    sort_at_path(
+      path = c("AEBODSYS"),
+      scorefun = cont_n_allcols
+    ) %>%
+    sort_at_path(
+      path = c("AEBODSYS", "*", "AEDECOD"),
+      scorefun = cont_n_allcols
+    )
+
+  tbl_sorted
+}
+
+#' @describeIn aet04_2_main `aet04_2` Layout
+#'
+#' @inheritParams gen_args
+#'
+#' @param lbl_aebodsys (`character`) text label for `AEBODSYS`.
+#' @param lbl_aedecod (`character`) text label for `AEDECOD`.
+#' @param group_grades (`list`) putting in correspondence severity levels and labels.
+#'
+#' @export
+#'
+#' @examples
+#' aet04_2_lyt(armvar = "ACTARM")
+aet04_2_lyt <- function(armvar = .study$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_main `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_2`
+#'
+#' @seealso [aet04_2_main()]
+#' @rdname chevron_tlg-class
+#' @export
+aet04_2 <- chevron_tlg(aet04_2_main, aet04_2_pre, adam_datasets = c("adsl", "adae"))
+
diff --git a/man/aet04_2_main.Rd b/man/aet04_2_main.Rd
new file mode 100644
index 0000000000..68843f1431
--- /dev/null
+++ b/man/aet04_2_main.Rd
@@ -0,0 +1,87 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/aet04.R
+\name{aet04_2_main}
+\alias{aet04_2_main}
+\alias{aet04_2_lyt}
+\alias{aet04_2_pre}
+\title{#' \code{AET04} Table 2 (Supplementary) Adverse Events by Highest NCI CTACAE AE Grade with Analysis Toxicity Grade 3-5 combined Table 2.
+The \code{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.}
+\usage{
+aet04_2_main(
+  adam_db,
+  armvar = .study$actualarm,
+  group_grades = .study$group_grades,
+  lbl_overall = .study$lbl_overall,
+  prune_0 = TRUE,
+  deco = std_deco("AET04"),
+  .study = list(actualarm = "ACTARM", lbl_overall = NULL, group_grades = NULL)
+)
+
+aet04_2_lyt(
+  armvar = .study$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)
+)
+
+aet04_2_pre(adam_db, ...)
+}
+\arguments{
+\item{adam_db}{(\code{dm}) object containing the ADaM datasets}
+
+\item{armvar}{(\code{character}) variable used for column splitting}
+
+\item{group_grades}{(\code{list}) putting in correspondence severity levels and labels.}
+
+\item{lbl_overall}{(\code{character}) label used for overall column, if set to \code{NULL} the overall column is omitted}
+
+\item{prune_0}{(\code{logical}) remove 0 count rows}
+
+\item{deco}{(\code{character}) decoration with \code{title}, \code{subtitles} and \code{main_footer} content}
+
+\item{.study}{(\code{list})  with default values for the arguments of the function}
+
+\item{lbl_aebodsys}{(\code{character}) text label for \code{AEBODSYS}.}
+
+\item{lbl_aedecod}{(\code{character}) text label for \code{AEDECOD}.}
+
+\item{...}{not used.}
+}
+\description{
+#' \code{AET04} Table 2 (Supplementary) Adverse Events by Highest NCI CTACAE AE Grade with Analysis Toxicity Grade 3-5 combined Table 2.
+The \code{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.
+}
+\details{
+\itemize{
+\item Numbers represent absolute numbers of patients and fraction of \code{N}, or absolute number of event when specified.
+\item Remove zero-count rows unless overridden with \code{prune_0 = FALSE}.
+\item Split columns by arm, typically \code{ACTARM}.
+\item Does not include a total column by default.
+\item Sort Body System or Organ Class and Dictionary-Derived Term by highest overall frequencies. Analysis Toxicity
+Grade is sorted by severity.
+}
+}
+\section{Functions}{
+\itemize{
+\item \code{aet04_2_lyt}: \code{aet04_2} Layout
+
+\item \code{aet04_2_pre}: \code{aet04_2} Preprocessing
+}}
+
+\examples{
+library(dm)
+
+db <- syn_test_data() \%>\%
+  aet04_2_pre()
+
+aet04_2_main(db)
+
+aet04_2_lyt(armvar = "ACTARM")
+syn_test_data() \%>\%
+  aet04_2_pre()
+}
diff --git a/man/chevron_tlg-class.Rd b/man/chevron_tlg-class.Rd
index eb12d10c1d..6137fb144e 100644
--- a/man/chevron_tlg-class.Rd
+++ b/man/chevron_tlg-class.Rd
@@ -15,6 +15,7 @@
 \alias{aet02_3}
 \alias{aet03_1}
 \alias{aet04_1}
+\alias{aet04_2}
 \alias{cmt01a_1}
 \alias{cmt01a_2}
 \alias{cmt01a_3}
@@ -86,6 +87,8 @@ An object of class \code{chevron_tlg} of length 1.
 
 An object of class \code{chevron_tlg} of length 1.
 
+An object of class \code{chevron_tlg} of length 1.
+
 An object of class \code{chevron_tlg} of length 1.
 }
 \usage{
@@ -110,6 +113,8 @@ aet03_1
 
 aet04_1
 
+aet04_2
+
 cmt01a_1
 
 cmt01a_2
@@ -208,6 +213,8 @@ x <- chevron_tlg(aet01_1_main, aet01_1_pre, adam_datasets = c("adsl", "adae"))
 
 \code{\link[=aet04_1_main]{aet04_1_main()}}
 
+\code{\link[=aet04_2_main]{aet04_2_main()}}
+
 \code{\link[=cmt01a_1_main]{cmt01a_1_main()}}
 
 \code{\link[=cmt01a_2_main]{cmt01a_2_main()}}

From 25e6e5c147141894b03294c05b7d4c108f7b60cf Mon Sep 17 00:00:00 2001
From: "Zhang, Bo {MDBR~South San Francisco}" <zhang.bo.bz1@gene.com>
Date: Mon, 18 Jul 2022 19:45:07 +0200
Subject: [PATCH 2/8] #140 Changed the structure of template of AET03 to match
 standards

---
 R/aet03.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/R/aet03.R b/R/aet03.R
index a768dcd7d6..7d59fc7d6c 100644
--- a/R/aet03.R
+++ b/R/aet03.R
@@ -108,6 +108,7 @@ aet03_1_lyt <- function(armvar = .study$actualarm,
     ifneeded_add_overall_col(lbl_overall) %>%
     summarize_occurrences_by_grade(
       var = "ASEV",
+      .indent_mods = 11L,
       grade_groups = list("- Any Intensity -" = severity_grade)
     ) %>%
     split_rows_by(
@@ -121,6 +122,7 @@ aet03_1_lyt <- function(armvar = .study$actualarm,
     ) %>%
     summarize_occurrences_by_grade(
       var = "ASEV",
+      .indent_mods = 10L,
       grade_groups = list("- Any Intensity -" = severity_grade)
     ) %>%
     split_rows_by(
@@ -134,6 +136,7 @@ aet03_1_lyt <- function(armvar = .study$actualarm,
     ) %>%
     summarize_occurrences_by_grade(
       var = "ASEV",
+      .indent_mods = 8L,
       grade_groups = list("- Any Intensity -" = severity_grade)
     )
 }

From 8e23ddd48ed7e21a29d9d5dc977c6cbcd800a67e Mon Sep 17 00:00:00 2001
From: "Zhang, Bo {MDBR~South San Francisco}" <zhang.bo.bz1@gene.com>
Date: Tue, 19 Jul 2022 18:31:10 +0200
Subject: [PATCH 3/8] Updated some minor errors

---
 R/aet03.R |  2 +-
 R/aet04.R | 11 +++++------
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/R/aet03.R b/R/aet03.R
index 7d59fc7d6c..56518f60c8 100644
--- a/R/aet03.R
+++ b/R/aet03.R
@@ -156,7 +156,7 @@ aet03_1_pre <- function(adam_db, ...) {
 
   adam_db %>%
     dm_zoom_to("adae") %>%
-    filter(.data$ANL01FL == "Y", .data$ASEV != c('', NA)) %>%
+    filter(.data$ANL01FL == "Y", .data$ASEV != c("", NA)) %>%
     dm_update_zoomed()
 }
 
diff --git a/R/aet04.R b/R/aet04.R
index c230a7590a..8952fdd506 100644
--- a/R/aet04.R
+++ b/R/aet04.R
@@ -179,7 +179,7 @@ aet04_1_pre <- function(adam_db, ...) {
 
   adam_db %>%
     dm_zoom_to("adae") %>%
-    filter(.data$ANL01FL == "Y", .data$ATOXGR != c('', NA)) %>%
+    filter(.data$ANL01FL == "Y", .data$ATOXGR != c("", NA)) %>%
     dm_update_zoomed()
 }
 
@@ -195,9 +195,9 @@ aet04_1 <- chevron_tlg(aet04_1_main, aet04_1_pre, adam_datasets = c("adsl", "ada
 
 
 
-#' #' `AET04` Table 2 (Supplementary) Adverse Events by Highest NCI CTACAE AE Grade with Analysis Toxicity Grade 3-5 combined Table 2.
-#' 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.
+#' #' `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.
 #'
 #' @inheritParams gen_args
 #' @param group_grades (`list`) putting in correspondence severity levels and labels.
@@ -365,7 +365,7 @@ aet04_2_pre <- function(adam_db, ...) {
 
   adam_db %>%
     dm_zoom_to("adae") %>%
-    filter(.data$ANL01FL == "Y", .data$ATOXGR != c('', NA)) %>%
+    filter(.data$ANL01FL == "Y", .data$ATOXGR != c("", NA)) %>%
     dm_update_zoomed()
 }
 
@@ -377,4 +377,3 @@ aet04_2_pre <- function(adam_db, ...) {
 #' @rdname chevron_tlg-class
 #' @export
 aet04_2 <- chevron_tlg(aet04_2_main, aet04_2_pre, adam_datasets = c("adsl", "adae"))
-

From ba9a228f39927d5600deb1a5639b12f06c4d290a Mon Sep 17 00:00:00 2001
From: "Zhang, Bo {MDBR~South San Francisco}" <zhang.bo.bz1@gene.com>
Date: Tue, 19 Jul 2022 18:50:15 +0200
Subject: [PATCH 4/8] update

---
 man/aet04_2_main.Rd | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/man/aet04_2_main.Rd b/man/aet04_2_main.Rd
index 68843f1431..a35924c80b 100644
--- a/man/aet04_2_main.Rd
+++ b/man/aet04_2_main.Rd
@@ -4,9 +4,9 @@
 \alias{aet04_2_main}
 \alias{aet04_2_lyt}
 \alias{aet04_2_pre}
-\title{#' \code{AET04} Table 2 (Supplementary) Adverse Events by Highest NCI CTACAE AE Grade with Analysis Toxicity Grade 3-5 combined Table 2.
-The \code{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.}
+\title{#' \code{AET04} Table 2 (Supplementary) Adverse Events by Highest NCI CTACAE AE Grade with Analysis Toxicity Grade 3-5 combined.
+The \code{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.}
 \usage{
 aet04_2_main(
   adam_db,
@@ -52,9 +52,9 @@ aet04_2_pre(adam_db, ...)
 \item{...}{not used.}
 }
 \description{
-#' \code{AET04} Table 2 (Supplementary) Adverse Events by Highest NCI CTACAE AE Grade with Analysis Toxicity Grade 3-5 combined Table 2.
-The \code{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.
+#' \code{AET04} Table 2 (Supplementary) Adverse Events by Highest NCI CTACAE AE Grade with Analysis Toxicity Grade 3-5 combined.
+The \code{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.
 }
 \details{
 \itemize{

From 5bdc64878f12768023fd326b112d3c3a65c16422 Mon Sep 17 00:00:00 2001
From: benoit <benoit.falquet@roche.com>
Date: Wed, 20 Jul 2022 09:54:02 +0200
Subject: [PATCH 5/8] document

---
 man/aet04_2_main.Rd      |  2 +-
 man/chevron_tlg-class.Rd | 12 +++++++++++-
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/man/aet04_2_main.Rd b/man/aet04_2_main.Rd
index a35924c80b..88cdb68034 100644
--- a/man/aet04_2_main.Rd
+++ b/man/aet04_2_main.Rd
@@ -31,7 +31,7 @@ aet04_2_lyt(
 aet04_2_pre(adam_db, ...)
 }
 \arguments{
-\item{adam_db}{(\code{dm}) object containing the ADaM datasets}
+\item{adam_db}{(\code{dm}) object containing the \code{ADaM} datasets}
 
 \item{armvar}{(\code{character}) variable used for column splitting}
 
diff --git a/man/chevron_tlg-class.Rd b/man/chevron_tlg-class.Rd
index 0192a7903a..2a2f5d4300 100644
--- a/man/chevron_tlg-class.Rd
+++ b/man/chevron_tlg-class.Rd
@@ -1,11 +1,15 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/chevron_tlg-S4class.R
+% Please edit documentation in R/chevron_tlg-S4class.R, R/aet04.R
 \docType{class}
 \name{chevron_tlg-class}
 \alias{chevron_tlg-class}
 \alias{.chevron_tlg}
 \alias{chevron_tlg}
+\alias{aet04_2}
 \title{\code{chevron_tlg} class}
+\format{
+An object of class \code{chevron_tlg} of length 1.
+}
 \usage{
 chevron_tlg(
   main = function(adam_db, ...) adam_db,
@@ -13,6 +17,8 @@ chevron_tlg(
   postprocess = function(tlg, ...) tlg,
   adam_datasets = NA_character_
 )
+
+aet04_2
 }
 \arguments{
 \item{main}{(\code{function}) returning a \code{tlg}. Typically one of the \verb{_main} function of \code{chevron}.}
@@ -59,3 +65,7 @@ To ensure the correct execution of the workflow additional validation criteria a
 \examples{
 x <- chevron_tlg(aet01_1_main, aet01_1_pre, adam_datasets = c("adsl", "adae"))
 }
+\seealso{
+\code{\link[=aet04_2_main]{aet04_2_main()}}
+}
+\keyword{datasets}

From 90ce43bfd5b7d1317bf5efeead5639b3ddbd1289 Mon Sep 17 00:00:00 2001
From: benoit <benoit.falquet@roche.com>
Date: Wed, 20 Jul 2022 10:02:16 +0200
Subject: [PATCH 6/8] add in pkgdown

---
 R/aet04.R                           | 18 +++++++++---------
 _pkgdown.yaml                       |  1 +
 man/{aet04_2_main.Rd => aet04_2.Rd} | 20 ++++++++++++++------
 man/chevron_tlg-class.Rd            | 12 +-----------
 4 files changed, 25 insertions(+), 26 deletions(-)
 rename man/{aet04_2_main.Rd => aet04_2.Rd} (81%)

diff --git a/R/aet04.R b/R/aet04.R
index fb4ea71fb6..8af5450de2 100644
--- a/R/aet04.R
+++ b/R/aet04.R
@@ -193,10 +193,7 @@ aet04_1 <- chevron_tlg(aet04_1_main, aet04_1_pre, adam_datasets = c("adsl", "ada
 
 
 
-
-#' #' `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.
+#' @describeIn aet04_2 Main TLG function
 #'
 #' @inheritParams gen_args
 #' @param group_grades (`list`) putting in correspondence severity levels and labels.
@@ -272,7 +269,7 @@ aet04_2_main <- function(adam_db,
   tbl_sorted
 }
 
-#' @describeIn aet04_2_main `aet04_2` Layout
+#' @describeIn aet04_2 Layout
 #'
 #' @inheritParams gen_args
 #'
@@ -349,7 +346,7 @@ aet04_2_lyt <- function(armvar = .study$actualarm,
 
 
 
-#' @describeIn aet04_2_main `aet04_2` Preprocessing
+#' @describeIn aet04_2 Preprocessing
 #'
 #' @inheritParams gen_args
 #' @param ... not used.
@@ -370,9 +367,12 @@ aet04_2_pre <- function(adam_db, ...) {
 
 # `AET04_2` Pipeline ----
 
-#' `AET04_2`
+#' `AET04` Table 2 (Supplementary) Adverse Events by Highest NCI CTACAE AE Grade with Analysis Toxicity Grade 3-5
+#' combined.
 #'
-#' @seealso [aet04_2_main()]
-#' @rdname chevron_tlg-class
+#' 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"))
diff --git a/_pkgdown.yaml b/_pkgdown.yaml
index 22212c3b79..38a566db7f 100644
--- a/_pkgdown.yaml
+++ b/_pkgdown.yaml
@@ -44,6 +44,7 @@ reference:
       - aet02_3
       - aet03_1
       - aet04_1
+      - aet04_2
       - cmt01a_1
       - cmt01a_2
       - cmt01a_3
diff --git a/man/aet04_2_main.Rd b/man/aet04_2.Rd
similarity index 81%
rename from man/aet04_2_main.Rd
rename to man/aet04_2.Rd
index 88cdb68034..e8c9892ca1 100644
--- a/man/aet04_2_main.Rd
+++ b/man/aet04_2.Rd
@@ -1,12 +1,16 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/aet04.R
+\docType{data}
 \name{aet04_2_main}
 \alias{aet04_2_main}
 \alias{aet04_2_lyt}
 \alias{aet04_2_pre}
-\title{#' \code{AET04} Table 2 (Supplementary) Adverse Events by Highest NCI CTACAE AE Grade with Analysis Toxicity Grade 3-5 combined.
-The \code{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.}
+\alias{aet04_2}
+\title{\code{AET04} Table 2 (Supplementary) Adverse Events by Highest NCI CTACAE AE Grade with Analysis Toxicity Grade 3-5
+combined.}
+\format{
+An object of class \code{chevron_tlg} of length 1.
+}
 \usage{
 aet04_2_main(
   adam_db,
@@ -29,6 +33,8 @@ aet04_2_lyt(
 )
 
 aet04_2_pre(adam_db, ...)
+
+aet04_2
 }
 \arguments{
 \item{adam_db}{(\code{dm}) object containing the \code{ADaM} datasets}
@@ -52,7 +58,6 @@ aet04_2_pre(adam_db, ...)
 \item{...}{not used.}
 }
 \description{
-#' \code{AET04} Table 2 (Supplementary) Adverse Events by Highest NCI CTACAE AE Grade with Analysis Toxicity Grade 3-5 combined.
 The \code{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.
 }
@@ -68,9 +73,11 @@ Grade is sorted by severity.
 }
 \section{Functions}{
 \itemize{
-\item \code{aet04_2_lyt}: \code{aet04_2} Layout
+\item \code{aet04_2_main}: Main TLG function
+
+\item \code{aet04_2_lyt}: Layout
 
-\item \code{aet04_2_pre}: \code{aet04_2} Preprocessing
+\item \code{aet04_2_pre}: Preprocessing
 }}
 
 \examples{
@@ -85,3 +92,4 @@ aet04_2_lyt(armvar = "ACTARM")
 syn_test_data() \%>\%
   aet04_2_pre()
 }
+\keyword{datasets}
diff --git a/man/chevron_tlg-class.Rd b/man/chevron_tlg-class.Rd
index 2a2f5d4300..0192a7903a 100644
--- a/man/chevron_tlg-class.Rd
+++ b/man/chevron_tlg-class.Rd
@@ -1,15 +1,11 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/chevron_tlg-S4class.R, R/aet04.R
+% Please edit documentation in R/chevron_tlg-S4class.R
 \docType{class}
 \name{chevron_tlg-class}
 \alias{chevron_tlg-class}
 \alias{.chevron_tlg}
 \alias{chevron_tlg}
-\alias{aet04_2}
 \title{\code{chevron_tlg} class}
-\format{
-An object of class \code{chevron_tlg} of length 1.
-}
 \usage{
 chevron_tlg(
   main = function(adam_db, ...) adam_db,
@@ -17,8 +13,6 @@ chevron_tlg(
   postprocess = function(tlg, ...) tlg,
   adam_datasets = NA_character_
 )
-
-aet04_2
 }
 \arguments{
 \item{main}{(\code{function}) returning a \code{tlg}. Typically one of the \verb{_main} function of \code{chevron}.}
@@ -65,7 +59,3 @@ To ensure the correct execution of the workflow additional validation criteria a
 \examples{
 x <- chevron_tlg(aet01_1_main, aet01_1_pre, adam_datasets = c("adsl", "adae"))
 }
-\seealso{
-\code{\link[=aet04_2_main]{aet04_2_main()}}
-}
-\keyword{datasets}

From d4a39e15ee45a919bde2d0be70c2bfb820919d98 Mon Sep 17 00:00:00 2001
From: benoit <benoit.falquet@roche.com>
Date: Wed, 20 Jul 2022 10:09:45 +0200
Subject: [PATCH 7/8] spellcheck

---
 R/aet04.R      | 4 ++--
 man/aet04_2.Rd | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/aet04.R b/R/aet04.R
index 8af5450de2..aa288dfbcd 100644
--- a/R/aet04.R
+++ b/R/aet04.R
@@ -367,10 +367,10 @@ aet04_2_pre <- function(adam_db, ...) {
 
 # `AET04_2` Pipeline ----
 
-#' `AET04` Table 2 (Supplementary) Adverse Events by Highest NCI CTACAE AE Grade with Analysis Toxicity Grade 3-5
+#' `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,
+#' 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
diff --git a/man/aet04_2.Rd b/man/aet04_2.Rd
index e8c9892ca1..e67674f3e4 100644
--- a/man/aet04_2.Rd
+++ b/man/aet04_2.Rd
@@ -6,7 +6,7 @@
 \alias{aet04_2_lyt}
 \alias{aet04_2_pre}
 \alias{aet04_2}
-\title{\code{AET04} Table 2 (Supplementary) Adverse Events by Highest NCI CTACAE AE Grade with Analysis Toxicity Grade 3-5
+\title{\code{AET04} Table 2 (Supplementary) Adverse Events by Highest \code{NCI} \code{CTACAE} \code{AE} Grade with Analysis Toxicity Grade 3-5
 combined.}
 \format{
 An object of class \code{chevron_tlg} of length 1.
@@ -58,7 +58,7 @@ aet04_2
 \item{...}{not used.}
 }
 \description{
-The \code{AET04_2} table provides an overview of adverse event with the highest NCI CTCAE grade per individual,
+The \code{AET04_2} table provides an overview of adverse event with the highest \code{NCI} \code{CTCAE} grade per individual,
 with the Analysis Toxicity Grade 3-5 combined in one group.
 }
 \details{

From 2b459fb1f73775f7106376d9139dd4fdd6c64bd7 Mon Sep 17 00:00:00 2001
From: benoit <benoit.falquet@roche.com>
Date: Wed, 20 Jul 2022 10:33:00 +0200
Subject: [PATCH 8/8] document

---
 DESCRIPTION              |  2 +-
 man/aet01_1.Rd           | 26 +++++++++++++-------------
 man/aet01_2.Rd           | 28 ++++++++++++++--------------
 man/aet02_1.Rd           | 10 +++++-----
 man/aet02_2.Rd           | 10 +++++-----
 man/aet02_3.Rd           |  6 +++---
 man/aet03_1.Rd           |  8 ++++----
 man/aet04_1.Rd           |  8 ++++----
 man/aet04_2.Rd           |  8 ++++----
 man/chevron_tlg-class.Rd |  4 ++--
 man/cmt01a_1.Rd          |  8 ++++----
 man/cmt01a_2.Rd          |  6 +++---
 man/cmt01a_3.Rd          |  8 ++++----
 man/cmt02_pt_1.Rd        |  8 ++++----
 man/dmt01_1.Rd           |  8 ++++----
 man/dst01_1.Rd           |  8 ++++----
 man/dst01_2.Rd           |  8 ++++----
 man/dst01_3.Rd           |  8 ++++----
 man/dtht01_1.Rd          | 10 +++++-----
 man/egt01_1.Rd           |  8 ++++----
 man/egt02_1.Rd           |  8 ++++----
 man/egt02_2.Rd           |  8 ++++----
 man/ext01_1.Rd           |  8 ++++----
 man/ext01_2.Rd           |  8 ++++----
 man/lbt01_1.Rd           |  8 ++++----
 man/mht01_1.Rd           |  8 ++++----
 man/vst01_1.Rd           |  8 ++++----
 man/vst02_1.Rd           |  8 ++++----
 man/vst02_2.Rd           |  8 ++++----
 29 files changed, 131 insertions(+), 131 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 1b513510fd..39de10dee0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -43,7 +43,7 @@ Config/Needs/website: insightsengineering/nesttemplate
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.1
 Collate:
     'chevron_tlg-S4class.R'
     'aet01.R'
diff --git a/man/aet01_1.Rd b/man/aet01_1.Rd
index 00a9582b81..d4774a6866 100644
--- a/man/aet01_1.Rd
+++ b/man/aet01_1.Rd
@@ -20,8 +20,8 @@ aet01_1_main(
   deco = std_deco("AET01"),
   safety_var = .study$safety_var,
   lbl_safety_var = var_labels_for(adam_db$adae, safety_var),
-  .study = list(actualarm = "ACTARM", lbl_overall = NULL, safety_var = c("FATAL",
-    "SER", "SERWD", "SERDSM", "RELSER", "WD", "DSM", "REL", "RELWD", "RELDSM", "SEV")),
+  .study = list(actualarm = "ACTARM", lbl_overall = NULL, safety_var = c("FATAL", "SER",
+    "SERWD", "SERDSM", "RELSER", "WD", "DSM", "REL", "RELWD", "RELDSM", "SEV")),
   ...
 )
 
@@ -31,10 +31,10 @@ aet01_1_lyt(
   deco = std_deco("AET01"),
   safety_var = .study$safety_var,
   lbl_safety_var = .study$lbl_safety_var,
-  .study = list(actualarm = "ACTARM", lbl_overall = NULL, safety_var = c("FATAL",
-    "SER", "SERWD", "SERDSM", "RELSER", "WD", "DSM", "REL", "RELWD", "RELDSM", "CTC35",
-    "CTC45", "SEV"), lbl_safety_var = c("FATAL", "SER", "SERWD", "SERDSM", "RELSER",
-    "WD", "DSM", "REL", "RELWD", "RELDSM", "CTC35", "CTC45", "SEV"))
+  .study = list(actualarm = "ACTARM", lbl_overall = NULL, safety_var = c("FATAL", "SER",
+    "SERWD", "SERDSM", "RELSER", "WD", "DSM", "REL", "RELWD", "RELDSM", "CTC35", "CTC45",
+    "SEV"), lbl_safety_var = c("FATAL", "SER", "SERWD", "SERDSM", "RELSER", "WD", "DSM",
+    "REL", "RELWD", "RELDSM", "CTC35", "CTC45", "SEV"))
 )
 
 aet01_1_pre(adam_db, ...)
@@ -45,8 +45,8 @@ aet01_1_check(
   armvar = .study$actualarm,
   safety_var = .study$safety_var,
   lbl_safety_var = var_labels_for(adam_db$adae, safety_var),
-  .study = list(actualarm = "ACTARM", lbl_overall = NULL, safety_var = c("FATAL",
-    "SER", "SERWD", "SERDSM", "RELSER", "WD", "DSM", "REL", "RELWD", "RELDSM", "SEV")),
+  .study = list(actualarm = "ACTARM", lbl_overall = NULL, safety_var = c("FATAL", "SER",
+    "SERWD", "SERDSM", "RELSER", "WD", "DSM", "REL", "RELWD", "RELDSM", "SEV")),
   ...
 )
 
@@ -83,15 +83,15 @@ aet01_1
 }
 \section{Functions}{
 \itemize{
-\item \code{aet01_1_main}: Main TLG function
+\item \code{aet01_1_main()}: Main TLG function
 
-\item \code{aet01_1_lyt}: Layout
+\item \code{aet01_1_lyt()}: Layout
 
-\item \code{aet01_1_pre}: Preprocessing
+\item \code{aet01_1_pre()}: Preprocessing
 
-\item \code{aet01_1_check}: Checks
-}}
+\item \code{aet01_1_check()}: Checks
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/aet01_2.Rd b/man/aet01_2.Rd
index 76a40aef63..8d35072cad 100644
--- a/man/aet01_2.Rd
+++ b/man/aet01_2.Rd
@@ -23,8 +23,8 @@ aet01_2_main(
   lbl_safety_var = var_labels_for(adam_db$adae, safety_var),
   medconcept_var = .study$medconcept_var,
   lbl_medconcept_var = var_labels_for(adam_db$adae, medconcept_var),
-  .study = list(actualarm = "ACTARM", lbl_overall = NULL, safety_var = c("FATAL",
-    "SER", "SERWD", "SERDSM", "RELSER", "WD", "DSM", "REL", "RELWD", "RELDSM", "SEV"),
+  .study = list(actualarm = "ACTARM", lbl_overall = NULL, safety_var = c("FATAL", "SER",
+    "SERWD", "SERDSM", "RELSER", "WD", "DSM", "REL", "RELWD", "RELDSM", "SEV"),
     medconcept_var = c("SMQ01", "SMQ02", "CQ01"))
 )
 
@@ -36,11 +36,11 @@ aet01_2_lyt(
   lbl_safety_var = .study$lbl_safety_var,
   medconcept_var = .study$medconcept_var,
   lbl_medconcept_var = .study$lbl_medconcept_var,
-  .study = list(actualarm = "ACTARM", lbl_overall = NULL, safety_var = c("FATAL",
-    "SER", "SERWD", "SERDSM", "RELSER", "WD", "DSM", "REL", "RELWD", "RELDSM", "CTC35",
-    "CTC45", "SEV"), lbl_safety_var = c("FATAL", "SER", "SERWD", "SERDSM", "RELSER",
-    "WD", "DSM", "REL", "RELWD", "RELDSM", "CTC35", "CTC45", "SEV"), medconcept_var =
-    c("SMQ01", "SMQ02", "CQ01"), lbl_medconcept_var = c("SMQ01", "SMQ02", "CQ01"))
+  .study = list(actualarm = "ACTARM", lbl_overall = NULL, safety_var = c("FATAL", "SER",
+    "SERWD", "SERDSM", "RELSER", "WD", "DSM", "REL", "RELWD", "RELDSM", "CTC35", "CTC45",
+    "SEV"), lbl_safety_var = c("FATAL", "SER", "SERWD", "SERDSM", "RELSER", "WD", "DSM",
+    "REL", "RELWD", "RELDSM", "CTC35", "CTC45", "SEV"), medconcept_var = c("SMQ01",
+    "SMQ02", "CQ01"), lbl_medconcept_var = c("SMQ01", "SMQ02", "CQ01"))
 )
 
 aet01_2_pre(adam_db, ...)
@@ -53,8 +53,8 @@ aet01_2_check(
   lbl_safety_var = var_labels_for(adam_db$adae, safety_var),
   medconcept_var = .study$medconcept_var,
   lbl_medconcept_var = var_labels_for(adam_db$adae, medconcept_var),
-  .study = list(actualarm = "ACTARM", lbl_overall = NULL, safety_var = c("FATAL",
-    "SER", "SERWD", "SERDSM", "RELSER", "WD", "DSM", "REL", "RELWD", "RELDSM", "SEV"),
+  .study = list(actualarm = "ACTARM", lbl_overall = NULL, safety_var = c("FATAL", "SER",
+    "SERWD", "SERDSM", "RELSER", "WD", "DSM", "REL", "RELWD", "RELDSM", "SEV"),
     medconcept_var = c("SMQ01", "SMQ02", "CQ01")),
   ...
 )
@@ -97,15 +97,15 @@ of adverse events with medical concepts.
 }
 \section{Functions}{
 \itemize{
-\item \code{aet01_2_main}: Main TLG function
+\item \code{aet01_2_main()}: Main TLG function
 
-\item \code{aet01_2_lyt}: Layout
+\item \code{aet01_2_lyt()}: Layout
 
-\item \code{aet01_2_pre}: Preprocessing
+\item \code{aet01_2_pre()}: Preprocessing
 
-\item \code{aet01_2_check}: Checks
-}}
+\item \code{aet01_2_check()}: Checks
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/aet02_1.Rd b/man/aet02_1.Rd
index 0e0942b774..6f1d44ed19 100644
--- a/man/aet02_1.Rd
+++ b/man/aet02_1.Rd
@@ -79,15 +79,15 @@ events categorized by Body System and Dictionary-Derived Term.
 }
 \section{Functions}{
 \itemize{
-\item \code{aet02_1_main}: Main TLG function
+\item \code{aet02_1_main()}: Main TLG function
 
-\item \code{aet02_1_lyt}: Layout
+\item \code{aet02_1_lyt()}: Layout
 
-\item \code{aet02_1_pre}: Preprocessing
+\item \code{aet02_1_pre()}: Preprocessing
 
-\item \code{aet02_1_check}: Checks
-}}
+\item \code{aet02_1_check()}: Checks
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/aet02_2.Rd b/man/aet02_2.Rd
index 434aefb8d9..c29c40b594 100644
--- a/man/aet02_2.Rd
+++ b/man/aet02_2.Rd
@@ -91,15 +91,15 @@ frequencies.
 }
 \section{Functions}{
 \itemize{
-\item \code{aet02_2_main}: Main TLG function
+\item \code{aet02_2_main()}: Main TLG function
 
-\item \code{aet02_2_lyt}: Layout
+\item \code{aet02_2_lyt()}: Layout
 
-\item \code{aet02_2_pre}: Preprocessing
+\item \code{aet02_2_pre()}: Preprocessing
 
-\item \code{aet02_3_main}: Main TLG function
-}}
+\item \code{aet02_3_main()}: Main TLG function
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/aet02_3.Rd b/man/aet02_3.Rd
index 9d7de54a75..e3a3b2234f 100644
--- a/man/aet02_3.Rd
+++ b/man/aet02_3.Rd
@@ -44,11 +44,11 @@ adverse events categorized by Dictionary-Derived Term.
 }
 \section{Functions}{
 \itemize{
-\item \code{aet02_3_lyt}: Layout
+\item \code{aet02_3_lyt()}: Layout
 
-\item \code{aet02_3_pre}: Preprocessing
-}}
+\item \code{aet02_3_pre()}: Preprocessing
 
+}}
 \examples{
 aet02_3_lyt(
   armvar = "ACTARM",
diff --git a/man/aet03_1.Rd b/man/aet03_1.Rd
index 9c819e845b..55a653c541 100644
--- a/man/aet03_1.Rd
+++ b/man/aet03_1.Rd
@@ -72,13 +72,13 @@ Organ Class, Dictionary-Derived Term  and Greatest intensity.
 }
 \section{Functions}{
 \itemize{
-\item \code{aet03_1_main}: Main TLG function
+\item \code{aet03_1_main()}: Main TLG function
 
-\item \code{aet03_1_lyt}: Layout
+\item \code{aet03_1_lyt()}: Layout
 
-\item \code{aet03_1_pre}: Preprocessing
-}}
+\item \code{aet03_1_pre()}: Preprocessing
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/aet04_1.Rd b/man/aet04_1.Rd
index e57c13765b..12b3df77cf 100644
--- a/man/aet04_1.Rd
+++ b/man/aet04_1.Rd
@@ -72,13 +72,13 @@ Grade is sorted by severity.
 }
 \section{Functions}{
 \itemize{
-\item \code{aet04_1_main}: Main TLG function
+\item \code{aet04_1_main()}: Main TLG function
 
-\item \code{aet04_1_lyt}: Layout
+\item \code{aet04_1_lyt()}: Layout
 
-\item \code{aet04_1_pre}: Preprocessing
-}}
+\item \code{aet04_1_pre()}: Preprocessing
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/aet04_2.Rd b/man/aet04_2.Rd
index e67674f3e4..ee3b482464 100644
--- a/man/aet04_2.Rd
+++ b/man/aet04_2.Rd
@@ -73,13 +73,13 @@ Grade is sorted by severity.
 }
 \section{Functions}{
 \itemize{
-\item \code{aet04_2_main}: Main TLG function
+\item \code{aet04_2_main()}: Main TLG function
 
-\item \code{aet04_2_lyt}: Layout
+\item \code{aet04_2_lyt()}: Layout
 
-\item \code{aet04_2_pre}: Preprocessing
-}}
+\item \code{aet04_2_pre()}: Preprocessing
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/chevron_tlg-class.Rd b/man/chevron_tlg-class.Rd
index 0192a7903a..93b3dba82e 100644
--- a/man/chevron_tlg-class.Rd
+++ b/man/chevron_tlg-class.Rd
@@ -31,9 +31,9 @@ optionally a \code{postprocess} function.
 }
 \section{Functions}{
 \itemize{
-\item \code{chevron_tlg}: Default Constructor
-}}
+\item \code{chevron_tlg()}: Default Constructor
 
+}}
 \section{Slots}{
 
 \describe{
diff --git a/man/cmt01a_1.Rd b/man/cmt01a_1.Rd
index 3c061c9b41..419154c34c 100644
--- a/man/cmt01a_1.Rd
+++ b/man/cmt01a_1.Rd
@@ -80,13 +80,13 @@ the specific medication.
 }
 \section{Functions}{
 \itemize{
-\item \code{cmt01a_1_main}: Main TLG function
+\item \code{cmt01a_1_main()}: Main TLG function
 
-\item \code{cmt01a_1_lyt}: Layout
+\item \code{cmt01a_1_lyt()}: Layout
 
-\item \code{cmt01a_1_pre}: Preprocessing
-}}
+\item \code{cmt01a_1_pre()}: Preprocessing
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/cmt01a_2.Rd b/man/cmt01a_2.Rd
index 33e89081e6..3213628411 100644
--- a/man/cmt01a_2.Rd
+++ b/man/cmt01a_2.Rd
@@ -68,11 +68,11 @@ the specific medication.
 }
 \section{Functions}{
 \itemize{
-\item \code{cmt01a_2_main}: Main TLG function
+\item \code{cmt01a_2_main()}: Main TLG function
 
-\item \code{cmt01a_2_pre}: Preprocessing
-}}
+\item \code{cmt01a_2_pre()}: Preprocessing
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/cmt01a_3.Rd b/man/cmt01a_3.Rd
index 0b49ccbe64..4d37b3170f 100644
--- a/man/cmt01a_3.Rd
+++ b/man/cmt01a_3.Rd
@@ -81,13 +81,13 @@ the specific medication.
 }
 \section{Functions}{
 \itemize{
-\item \code{cmt01a_3_main}: Main TLG function
+\item \code{cmt01a_3_main()}: Main TLG function
 
-\item \code{cmt01a_3_lyt}: Layout
+\item \code{cmt01a_3_lyt()}: Layout
 
-\item \code{cmt01a_3_pre}: Preprocessing
-}}
+\item \code{cmt01a_3_pre()}: Preprocessing
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/cmt02_pt_1.Rd b/man/cmt02_pt_1.Rd
index 5ec1b3d193..aa62a6c465 100644
--- a/man/cmt02_pt_1.Rd
+++ b/man/cmt02_pt_1.Rd
@@ -59,13 +59,13 @@ number of subjects and the total number of treatments by medication name sorted
 }
 \section{Functions}{
 \itemize{
-\item \code{cmt02_pt_1_main}: Main TLG function
+\item \code{cmt02_pt_1_main()}: Main TLG function
 
-\item \code{cmt02_pt_1_lyt}: Layout
+\item \code{cmt02_pt_1_lyt()}: Layout
 
-\item \code{cmt02_pt_1_pre}: Preprocessing
-}}
+\item \code{cmt02_pt_1_pre()}: Preprocessing
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/dmt01_1.Rd b/man/dmt01_1.Rd
index 7df720684f..c497254850 100644
--- a/man/dmt01_1.Rd
+++ b/man/dmt01_1.Rd
@@ -72,13 +72,13 @@ by default based on the number of patients in the corresponding \code{n} row.
 }
 \section{Functions}{
 \itemize{
-\item \code{dmt01_1_main}: Main TLG function
+\item \code{dmt01_1_main()}: Main TLG function
 
-\item \code{dmt01_1_lyt}: Layout
+\item \code{dmt01_1_lyt()}: Layout
 
-\item \code{dmt01_1_pre}: Preprocessing
-}}
+\item \code{dmt01_1_pre()}: Preprocessing
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/dst01_1.Rd b/man/dst01_1.Rd
index fccddcf1d5..a75134b391 100644
--- a/man/dst01_1.Rd
+++ b/man/dst01_1.Rd
@@ -94,13 +94,13 @@ which allows the tables to be constructed and pruned separately before binding.
 }
 \section{Functions}{
 \itemize{
-\item \code{dst01_1_main}: Main TLG function
+\item \code{dst01_1_main()}: Main TLG function
 
-\item \code{dst01_1_lyt}: Layout
+\item \code{dst01_1_lyt()}: Layout
 
-\item \code{dst01_1_pre}: Preprocessing
-}}
+\item \code{dst01_1_pre()}: Preprocessing
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/dst01_2.Rd b/man/dst01_2.Rd
index 73d8a8f430..28f54d1a19 100644
--- a/man/dst01_2.Rd
+++ b/man/dst01_2.Rd
@@ -104,13 +104,13 @@ which allows the tables to be constructed and pruned separately before binding.
 }
 \section{Functions}{
 \itemize{
-\item \code{dst01_2_main}: Main TLG function
+\item \code{dst01_2_main()}: Main TLG function
 
-\item \code{dst01_2_lyt}: Layout
+\item \code{dst01_2_lyt()}: Layout
 
-\item \code{dst01_2_pre}: Preprocessing
-}}
+\item \code{dst01_2_pre()}: Preprocessing
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/dst01_3.Rd b/man/dst01_3.Rd
index 14f08d1dc9..b551c98138 100644
--- a/man/dst01_3.Rd
+++ b/man/dst01_3.Rd
@@ -101,13 +101,13 @@ the study, the reason provided is categorized as "Safety" or "Non-Safety" issue.
 }
 \section{Functions}{
 \itemize{
-\item \code{dst01_3_main}: Main TLG function
+\item \code{dst01_3_main()}: Main TLG function
 
-\item \code{dst01_3_lyt}: Layout
+\item \code{dst01_3_lyt()}: Layout
 
-\item \code{dst01_3_pre}: Preprocessing
-}}
+\item \code{dst01_3_pre()}: Preprocessing
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/dtht01_1.Rd b/man/dtht01_1.Rd
index 7483b4c8c4..1ea8e03f8d 100644
--- a/man/dtht01_1.Rd
+++ b/man/dtht01_1.Rd
@@ -74,15 +74,15 @@ A description of the causes of death optionally with the breakdown of the
 }
 \section{Functions}{
 \itemize{
-\item \code{dtht01_1_main}: Main TLG function
+\item \code{dtht01_1_main()}: Main TLG function
 
-\item \code{dtht01_1_lyt}: Layout
+\item \code{dtht01_1_lyt()}: Layout
 
-\item \code{dtht01_1_opt_lyt}: Optional Layout
+\item \code{dtht01_1_opt_lyt()}: Optional Layout
 
-\item \code{dtht01_1_pre}: Preprocessing
-}}
+\item \code{dtht01_1_pre()}: Preprocessing
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/egt01_1.Rd b/man/egt01_1.Rd
index 40f78df1e3..5c240d4758 100644
--- a/man/egt01_1.Rd
+++ b/man/egt01_1.Rd
@@ -81,13 +81,13 @@ by \code{AVISIT}. Re-level to customize order
 }
 \section{Functions}{
 \itemize{
-\item \code{egt01_1_main}: Main TLG function
+\item \code{egt01_1_main()}: Main TLG function
 
-\item \code{egt01_1_lyt}: Layout
+\item \code{egt01_1_lyt()}: Layout
 
-\item \code{egt01_1_pre}: Preprocessing
-}}
+\item \code{egt01_1_pre()}: Preprocessing
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/egt02_1.Rd b/man/egt02_1.Rd
index a9c6e6f07f..4e53943a27 100644
--- a/man/egt02_1.Rd
+++ b/man/egt02_1.Rd
@@ -68,13 +68,13 @@ Baseline Table.
 }
 \section{Functions}{
 \itemize{
-\item \code{egt02_1_main}: Main TLG function
+\item \code{egt02_1_main()}: Main TLG function
 
-\item \code{egt02_1_lyt}: Layout
+\item \code{egt02_1_lyt()}: Layout
 
-\item \code{egt02_1_pre}: Preprocessing
-}}
+\item \code{egt02_1_pre()}: Preprocessing
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/egt02_2.Rd b/man/egt02_2.Rd
index c103df1843..68687e08c0 100644
--- a/man/egt02_2.Rd
+++ b/man/egt02_2.Rd
@@ -68,13 +68,13 @@ Abnormality at Baseline.
 }
 \section{Functions}{
 \itemize{
-\item \code{egt02_2_main}: Main TLG function
+\item \code{egt02_2_main()}: Main TLG function
 
-\item \code{egt02_2_lyt}: Layout
+\item \code{egt02_2_lyt()}: Layout
 
-\item \code{egt02_2_pre}: Preprocessing
-}}
+\item \code{egt02_2_pre()}: Preprocessing
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/ext01_1.Rd b/man/ext01_1.Rd
index bc377ac197..580fdc1b9f 100644
--- a/man/ext01_1.Rd
+++ b/man/ext01_1.Rd
@@ -79,13 +79,13 @@ patients in the corresponding analysis population given by \code{N}.
 }
 \section{Functions}{
 \itemize{
-\item \code{ext01_1_main}: Main TLG function
+\item \code{ext01_1_main()}: Main TLG function
 
-\item \code{ext01_1_lyt}: Layout
+\item \code{ext01_1_lyt()}: Layout
 
-\item \code{ext01_1_pre}: Preprocessing
-}}
+\item \code{ext01_1_pre()}: Preprocessing
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/ext01_2.Rd b/man/ext01_2.Rd
index a08007dfae..284cbd0e6c 100644
--- a/man/ext01_2.Rd
+++ b/man/ext01_2.Rd
@@ -81,13 +81,13 @@ patients in the corresponding analysis population given by \code{N}.
 }
 \section{Functions}{
 \itemize{
-\item \code{ext01_2_main}: Main TLG function
+\item \code{ext01_2_main()}: Main TLG function
 
-\item \code{ext01_2_lyt}: Layout
+\item \code{ext01_2_lyt()}: Layout
 
-\item \code{ext01_2_pre}: Preprocessing
-}}
+\item \code{ext01_2_pre()}: Preprocessing
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/lbt01_1.Rd b/man/lbt01_1.Rd
index 92a72b6aa3..6cde9a4b5d 100644
--- a/man/lbt01_1.Rd
+++ b/man/lbt01_1.Rd
@@ -80,13 +80,13 @@ by \code{AVISIT}. Re-level to customize order
 }
 \section{Functions}{
 \itemize{
-\item \code{lbt01_1_main}: Main TLG function
+\item \code{lbt01_1_main()}: Main TLG function
 
-\item \code{lbt01_1_lyt}: Layout
+\item \code{lbt01_1_lyt()}: Layout
 
-\item \code{lbt01_1_pre}: Preprocessing
-}}
+\item \code{lbt01_1_pre()}: Preprocessing
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/mht01_1.Rd b/man/mht01_1.Rd
index 2a9a976e39..c2d55a2942 100644
--- a/man/mht01_1.Rd
+++ b/man/mht01_1.Rd
@@ -70,13 +70,13 @@ patients with the specific condition.
 }
 \section{Functions}{
 \itemize{
-\item \code{mht01_1_main}: Main TLG function
+\item \code{mht01_1_main()}: Main TLG function
 
-\item \code{mht01_1_lyt}: Layout
+\item \code{mht01_1_lyt()}: Layout
 
-\item \code{mht01_1_pre}: Preprocessing
-}}
+\item \code{mht01_1_pre()}: Preprocessing
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/vst01_1.Rd b/man/vst01_1.Rd
index 0e16256080..f93150754a 100644
--- a/man/vst01_1.Rd
+++ b/man/vst01_1.Rd
@@ -82,13 +82,13 @@ by \code{AVISIT}. Re-level to customize order
 }
 \section{Functions}{
 \itemize{
-\item \code{vst01_1_main}: Main TLG function
+\item \code{vst01_1_main()}: Main TLG function
 
-\item \code{vst01_1_lyt}: Layout
+\item \code{vst01_1_lyt()}: Layout
 
-\item \code{vst01_1_pre}: Preprocessing
-}}
+\item \code{vst01_1_pre()}: Preprocessing
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/vst02_1.Rd b/man/vst02_1.Rd
index 013ccc4b0d..a2499a5b80 100644
--- a/man/vst02_1.Rd
+++ b/man/vst02_1.Rd
@@ -68,13 +68,13 @@ Abnormality at Baseline Table.
 }
 \section{Functions}{
 \itemize{
-\item \code{vst02_1_main}: Main TLG function
+\item \code{vst02_1_main()}: Main TLG function
 
-\item \code{vst02_1_lyt}: Layout
+\item \code{vst02_1_lyt()}: Layout
 
-\item \code{vst02_1_pre}: Preprocessing
-}}
+\item \code{vst02_1_pre()}: Preprocessing
 
+}}
 \examples{
 library(dm)
 
diff --git a/man/vst02_2.Rd b/man/vst02_2.Rd
index 46fe6936ae..a4b09a2f77 100644
--- a/man/vst02_2.Rd
+++ b/man/vst02_2.Rd
@@ -69,13 +69,13 @@ Without Abnormality at Baseline.
 }
 \section{Functions}{
 \itemize{
-\item \code{vst02_2_main}: Main TLG function
+\item \code{vst02_2_main()}: Main TLG function
 
-\item \code{vst02_2_lyt}: Layout
+\item \code{vst02_2_lyt()}: Layout
 
-\item \code{vst02_2_pre}: Preprocessing
-}}
+\item \code{vst02_2_pre()}: Preprocessing
 
+}}
 \examples{
 library(dm)