From 44b47c1ee07f4da82ae2a82c01a269daf6cd3ba6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Tue, 3 Dec 2024 15:41:44 +0100
Subject: [PATCH 01/10] Introduce decorators for `tm_t_events_by_grade`

---
 R/tm_t_events_by_grade.R | 41 +++++++++++++++++++++++++++++++---------
 1 file changed, 32 insertions(+), 9 deletions(-)

diff --git a/R/tm_t_events_by_grade.R b/R/tm_t_events_by_grade.R
index f0b01a543..fda747195 100644
--- a/R/tm_t_events_by_grade.R
+++ b/R/tm_t_events_by_grade.R
@@ -7,9 +7,18 @@
 #' @param grade (`character`)\cr name of the severity level variable.
 #' @param label_grade (`string`)\cr label of the `grade` variable from `dataname`. The label will be extracted from the
 #' module.
+#' @param decorators `r roxygen_decorators_param("tm_t_events_by_grade")`
 #'
 #' @inherit template_arguments return
 #'
+#' @section Decorating `tm_t_events_by_grade`:
+#'
+#' This module generates the following objects, which can be modified in place using decorators:
+#' - `table` (`TableTree` as created from `rtables::build_table`)
+#'
+#' For additional details and examples of decorators, refer to the vignette
+#' `vignette("decorate-modules-output", package = "teal")` or the [`teal_transform_module()`] documentation.
+#'
 #' @seealso [tm_t_events_by_grade()]
 #'
 #' @keywords internal
@@ -303,7 +312,7 @@ template_events_by_grade <- function(dataname,
     prune_list <- add_expr(
       prune_list,
       substitute(
-        expr = pruned_result <- pruned_result %>% rtables::prune_table(keep_content_rows(row_condition))
+        expr = table <- pruned_result %>% rtables::prune_table(keep_content_rows(row_condition))
       )
     )
   }
@@ -345,7 +354,7 @@ template_events_by_grade <- function(dataname,
       sort_list,
       substitute(
         expr = {
-          pruned_and_sorted_result <- pruned_result %>%
+          table <- pruned_result %>%
             sort_at_path(path = hlt, scorefun = scorefun, decreasing = TRUE) %>%
             sort_at_path(path = c(hlt, "*", llt), scorefun = scorefun, decreasing = TRUE)
         },
@@ -359,7 +368,7 @@ template_events_by_grade <- function(dataname,
 
     sort_list <- add_expr(
       sort_list,
-      quote(pruned_and_sorted_result)
+      quote(table)
     )
   }
   y$sort <- bracket_expr(sort_list)
@@ -865,7 +874,8 @@ tm_t_events_by_grade <- function(label,
                                  drop_arm_levels = TRUE,
                                  pre_output = NULL,
                                  post_output = NULL,
-                                 basic_table_args = teal.widgets::basic_table_args()) {
+                                 basic_table_args = teal.widgets::basic_table_args(),
+                                 decorators = NULL) {
   message("Initializing tm_t_events_by_grade")
   checkmate::assert_string(label)
   checkmate::assert_string(dataname)
@@ -883,6 +893,8 @@ tm_t_events_by_grade <- function(label,
   checkmate::assert_class(pre_output, classes = "shiny.tag", null.ok = TRUE)
   checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE)
   checkmate::assert_class(basic_table_args, "basic_table_args")
+  decorators <- normalize_decorators(decorators)
+  assert_decorators(decorators, "table", null.ok = TRUE)
 
   args <- as.list(environment())
 
@@ -907,7 +919,8 @@ tm_t_events_by_grade <- function(label,
         total_label = total_label,
         grading_groups = grading_groups,
         na_level = na_level,
-        basic_table_args = basic_table_args
+        basic_table_args = basic_table_args,
+        decorators = decorators
       )
     ),
     datanames = teal.transform::get_extract_datanames(data_extract_list)
@@ -962,6 +975,7 @@ ui_t_events_by_grade <- function(id, ...) {
         "Display grade groupings in nested columns",
         value = a$col_by_grade
       ),
+      ui_decorate_teal_data(ns("decorator"), decorators = select_decorators(a$decorators, "table")),
       teal.widgets::panel_group(
         teal.widgets::panel_item(
           "Additional table settings",
@@ -1017,7 +1031,8 @@ srv_t_events_by_grade <- function(id,
                                   drop_arm_levels,
                                   total_label,
                                   na_level,
-                                  basic_table_args) {
+                                  basic_table_args,
+                                  decorators) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
   checkmate::assert_class(data, "reactive")
@@ -1202,9 +1217,17 @@ srv_t_events_by_grade <- function(id,
       teal.code::eval_code(merged$anl_q(), as.expression(unlist(my_calls)))
     })
 
+
+    decorated_table_q <- srv_decorate_teal_data(
+      id = "decorator",
+      data = table_q,
+      decorators = select_decorators(decorators, "table"),
+      expr = table
+    )
     # Outputs to render.
     table_r <- reactive({
-      table_q()[["pruned_and_sorted_result"]]
+      browser()
+      decorated_table_q()[["table"]]
     })
 
     teal.widgets::table_with_settings_srv(
@@ -1215,7 +1238,7 @@ srv_t_events_by_grade <- function(id,
     # Render R code.
     teal.widgets::verbatim_popup_srv(
       id = "rcode",
-      verbatim_content = reactive(teal.code::get_code(table_q())),
+      verbatim_content = reactive(teal.code::get_code(req(decorated_table_q()))),
       title = label
     )
 
@@ -1234,7 +1257,7 @@ srv_t_events_by_grade <- function(id,
           card$append_text("Comment", "header3")
           card$append_text(comment)
         }
-        card$append_src(teal.code::get_code(table_q()))
+        card$append_src(teal.code::get_code(req(decorated_table_q())))
         card
       }
       teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)

From ef1dd5dea80c2d37e7763668b330ddbcedc23621 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Tue, 3 Dec 2024 15:48:39 +0100
Subject: [PATCH 02/10] Remove browse

---
 R/tm_t_events_by_grade.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/R/tm_t_events_by_grade.R b/R/tm_t_events_by_grade.R
index fda747195..f1230f95e 100644
--- a/R/tm_t_events_by_grade.R
+++ b/R/tm_t_events_by_grade.R
@@ -1226,7 +1226,6 @@ srv_t_events_by_grade <- function(id,
     )
     # Outputs to render.
     table_r <- reactive({
-      browser()
       decorated_table_q()[["table"]]
     })
 

From bceadbb636bda545e8f5bc8844382eaae99987df Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Wed, 4 Dec 2024 10:17:07 +0100
Subject: [PATCH 03/10] Rename results by table specially
 `template_events_col_by_grade`

---
 R/tm_t_events_by_grade.R | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/R/tm_t_events_by_grade.R b/R/tm_t_events_by_grade.R
index f1230f95e..e487340b5 100644
--- a/R/tm_t_events_by_grade.R
+++ b/R/tm_t_events_by_grade.R
@@ -258,7 +258,7 @@ template_events_by_grade <- function(dataname,
 
   # Full table.
   y$table <- substitute(
-    expr = result <- rtables::build_table(lyt = lyt, df = anl, alt_counts_df = parent),
+    expr = table <- rtables::build_table(lyt = lyt, df = anl, alt_counts_df = parent),
     env = list(parent = as.name(parentname))
   )
 
@@ -267,7 +267,7 @@ template_events_by_grade <- function(dataname,
   prune_list <- add_expr(
     prune_list,
     quote(
-      pruned_result <- result
+      pruned_table <- table
     )
   )
 
@@ -276,7 +276,7 @@ template_events_by_grade <- function(dataname,
     prune_list <- add_expr(
       prune_list,
       substitute(
-        expr = col_indices <- 1:(ncol(result) - add_total),
+        expr = col_indices <- 1:(ncol(table) - add_total),
         env = list(add_total = add_total)
       )
     )
@@ -312,7 +312,7 @@ template_events_by_grade <- function(dataname,
     prune_list <- add_expr(
       prune_list,
       substitute(
-        expr = table <- pruned_result %>% rtables::prune_table(keep_content_rows(row_condition))
+        expr = table <- pruned_table %>% rtables::prune_table(keep_content_rows(row_condition))
       )
     )
   }
@@ -339,9 +339,9 @@ template_events_by_grade <- function(dataname,
       sort_list,
       substitute(
         expr = {
-          pruned_and_sorted_result <- pruned_result %>%
+          pruned_and_sorted_table <- pruned_table %>%
             sort_at_path(path = term_var, scorefun = scorefun, decreasing = TRUE)
-          pruned_and_sorted_result
+          pruned_and_sorted_table
         },
         env = list(
           term_var = term_var,
@@ -354,7 +354,7 @@ template_events_by_grade <- function(dataname,
       sort_list,
       substitute(
         expr = {
-          table <- pruned_result %>%
+          table <- pruned_table %>%
             sort_at_path(path = hlt, scorefun = scorefun, decreasing = TRUE) %>%
             sort_at_path(path = c(hlt, "*", llt), scorefun = scorefun, decreasing = TRUE)
         },
@@ -647,7 +647,7 @@ template_events_col_by_grade <- function(dataname,
   )
 
   # Full table.
-  y$table <- quote(result <- rtables::build_table(lyt = lyt, df = anl, col_counts = col_counts))
+  y$table <- quote(table <- rtables::build_table(lyt = lyt, df = anl, col_counts = col_counts))
 
   # Start sorting table.
   sort_list <- list()
@@ -666,7 +666,7 @@ template_events_col_by_grade <- function(dataname,
   sort_list <- add_expr(
     sort_list,
     substitute(
-      expr = col_indices <- seq(start_index, ncol(result), by = length(grading_groups)),
+      expr = col_indices <- seq(start_index, ncol(table), by = length(grading_groups)),
       env = list(grading_groups = grading_groups)
     )
   )
@@ -688,7 +688,7 @@ template_events_col_by_grade <- function(dataname,
       sort_list,
       substitute(
         expr = {
-          sorted_result <- result %>%
+          sorted_table <- table %>%
             sort_at_path(path = c(llt), scorefun = scorefun_term, decreasing = TRUE)
         },
         env = list(llt = llt)
@@ -699,7 +699,7 @@ template_events_col_by_grade <- function(dataname,
       sort_list,
       substitute(
         expr = {
-          sorted_result <- result %>%
+          sorted_table <- table %>%
             sort_at_path(path = c(hlt), scorefun = scorefun_soc, decreasing = TRUE) %>%
             sort_at_path(path = c(hlt, "*", llt), scorefun = scorefun_term, decreasing = TRUE)
         },
@@ -748,7 +748,7 @@ template_events_col_by_grade <- function(dataname,
   prune_pipe <- add_expr(
     prune_pipe,
     quote(
-      pruned_and_sorted_result <- sorted_result %>% rtables::trim_rows(criteria = criteria_fun)
+      pruned_and_sorted_table <- sorted_table %>% rtables::trim_rows(criteria = criteria_fun)
     )
   )
 
@@ -780,7 +780,7 @@ template_events_col_by_grade <- function(dataname,
   )
   prune_list <- add_expr(
     prune_list,
-    quote(pruned_and_sorted_result)
+    quote(pruned_and_sorted_table)
   )
 
   y$prune <- bracket_expr(prune_list)

From f68f68bcec8d142553ca760254564c8d8c115657 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Wed, 4 Dec 2024 12:01:18 +0100
Subject: [PATCH 04/10] Document module

---
 man/template_events_by_grade.Rd | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/man/template_events_by_grade.Rd b/man/template_events_by_grade.Rd
index bb7b8a8bc..80bdf8ac3 100644
--- a/man/template_events_by_grade.Rd
+++ b/man/template_events_by_grade.Rd
@@ -72,6 +72,12 @@ user input for this parameter is ignored.}
 with settings for the module table. The argument is merged with option \code{teal.basic_table_args} and with default
 module arguments (hard coded in the module body).
 For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.}
+
+\item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}  (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or \code{NULL}) optional, if not \code{NULL}, decorator for tables or plots included in the module. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects.
+
+Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}.
+
+See section "Decorating \code{tm_t_events_by_grade}" below for more details.}
 }
 \value{
 a \code{list} of expressions to generate a table or plot object.
@@ -79,6 +85,18 @@ a \code{list} of expressions to generate a table or plot object.
 \description{
 Creates a valid expression to generate a table to summarize events by grade.
 }
+\section{Decorating \code{tm_t_events_by_grade}}{
+
+
+This module generates the following objects, which can be modified in place using decorators:
+\itemize{
+\item \code{table} (\code{TableTree} as created from \code{rtables::build_table})
+}
+
+For additional details and examples of decorators, refer to the vignette
+\code{vignette("decorate-modules-output", package = "teal")} or the \code{\link[=teal_transform_module]{teal_transform_module()}} documentation.
+}
+
 \seealso{
 \code{\link[=tm_t_events_by_grade]{tm_t_events_by_grade()}}
 }

From fd3f7ac7da30a692644467ff03ef95cf000a69eb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Wed, 4 Dec 2024 12:34:53 +0100
Subject: [PATCH 05/10] Fix documentation issues

---
 R/tm_t_events_by_grade.R        | 18 +++++++++---------
 man/template_events_by_grade.Rd | 18 ------------------
 man/tm_t_events_by_grade.Rd     | 21 ++++++++++++++++++++-
 3 files changed, 29 insertions(+), 28 deletions(-)

diff --git a/R/tm_t_events_by_grade.R b/R/tm_t_events_by_grade.R
index e487340b5..fcce86dd0 100644
--- a/R/tm_t_events_by_grade.R
+++ b/R/tm_t_events_by_grade.R
@@ -7,18 +7,9 @@
 #' @param grade (`character`)\cr name of the severity level variable.
 #' @param label_grade (`string`)\cr label of the `grade` variable from `dataname`. The label will be extracted from the
 #' module.
-#' @param decorators `r roxygen_decorators_param("tm_t_events_by_grade")`
 #'
 #' @inherit template_arguments return
 #'
-#' @section Decorating `tm_t_events_by_grade`:
-#'
-#' This module generates the following objects, which can be modified in place using decorators:
-#' - `table` (`TableTree` as created from `rtables::build_table`)
-#'
-#' For additional details and examples of decorators, refer to the vignette
-#' `vignette("decorate-modules-output", package = "teal")` or the [`teal_transform_module()`] documentation.
-#'
 #' @seealso [tm_t_events_by_grade()]
 #'
 #' @keywords internal
@@ -797,9 +788,18 @@ template_events_col_by_grade <- function(dataname,
 #' @inheritParams template_events_col_by_grade
 #' @param col_by_grade (`logical`)\cr whether to display the grading groups in nested columns.
 #' @param grading_groups (`list`)\cr named list of grading groups used when `col_by_grade = TRUE`.
+#' @param decorators `r roxygen_decorators_param("tm_t_events_by_grade")`
 #'
 #' @inherit module_arguments return seealso
 #'
+#' @section Decorating `tm_t_events_by_grade`:
+#'
+#' This module generates the following objects, which can be modified in place using decorators:
+#' - `table` (`TableTree` as created from `rtables::build_table`)
+#'
+#' For additional details and examples of decorators, refer to the vignette
+#' `vignette("decorate-modules-output", package = "teal")` or the [`teal_transform_module()`] documentation.
+#'
 #' @export
 #'
 #' @examplesShinylive
diff --git a/man/template_events_by_grade.Rd b/man/template_events_by_grade.Rd
index 80bdf8ac3..bb7b8a8bc 100644
--- a/man/template_events_by_grade.Rd
+++ b/man/template_events_by_grade.Rd
@@ -72,12 +72,6 @@ user input for this parameter is ignored.}
 with settings for the module table. The argument is merged with option \code{teal.basic_table_args} and with default
 module arguments (hard coded in the module body).
 For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.}
-
-\item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}  (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or \code{NULL}) optional, if not \code{NULL}, decorator for tables or plots included in the module. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects.
-
-Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}.
-
-See section "Decorating \code{tm_t_events_by_grade}" below for more details.}
 }
 \value{
 a \code{list} of expressions to generate a table or plot object.
@@ -85,18 +79,6 @@ a \code{list} of expressions to generate a table or plot object.
 \description{
 Creates a valid expression to generate a table to summarize events by grade.
 }
-\section{Decorating \code{tm_t_events_by_grade}}{
-
-
-This module generates the following objects, which can be modified in place using decorators:
-\itemize{
-\item \code{table} (\code{TableTree} as created from \code{rtables::build_table})
-}
-
-For additional details and examples of decorators, refer to the vignette
-\code{vignette("decorate-modules-output", package = "teal")} or the \code{\link[=teal_transform_module]{teal_transform_module()}} documentation.
-}
-
 \seealso{
 \code{\link[=tm_t_events_by_grade]{tm_t_events_by_grade()}}
 }
diff --git a/man/tm_t_events_by_grade.Rd b/man/tm_t_events_by_grade.Rd
index 158dcdced..e2ff4a1bd 100644
--- a/man/tm_t_events_by_grade.Rd
+++ b/man/tm_t_events_by_grade.Rd
@@ -24,7 +24,8 @@ tm_t_events_by_grade(
   drop_arm_levels = TRUE,
   pre_output = NULL,
   post_output = NULL,
-  basic_table_args = teal.widgets::basic_table_args()
+  basic_table_args = teal.widgets::basic_table_args(),
+  decorators = NULL
 )
 }
 \arguments{
@@ -80,6 +81,12 @@ For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are use
 with settings for the module table. The argument is merged with option \code{teal.basic_table_args} and with default
 module arguments (hard coded in the module body).
 For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.}
+
+\item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}  (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or \code{NULL}) optional, if not \code{NULL}, decorator for tables or plots included in the module. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects.
+
+Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}.
+
+See section "Decorating \code{tm_t_events_by_grade}" below for more details.}
 }
 \value{
 a \code{teal_module} object.
@@ -87,6 +94,18 @@ a \code{teal_module} object.
 \description{
 This module produces a table to summarize events by grade.
 }
+\section{Decorating \code{tm_t_events_by_grade}}{
+
+
+This module generates the following objects, which can be modified in place using decorators:
+\itemize{
+\item \code{table} (\code{TableTree} as created from \code{rtables::build_table})
+}
+
+For additional details and examples of decorators, refer to the vignette
+\code{vignette("decorate-modules-output", package = "teal")} or the \code{\link[=teal_transform_module]{teal_transform_module()}} documentation.
+}
+
 \examples{
 library(dplyr)
 data <- teal_data()

From 0f9ff50df533953b0ad1fd91615df0d4551ef40b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Thu, 5 Dec 2024 12:16:24 +0100
Subject: [PATCH 06/10] Revert table to result and add a reactive rename at the
 end the final object to table

---
 R/tm_t_events_by_grade.R | 38 ++++++++++++++++++++++++--------------
 1 file changed, 24 insertions(+), 14 deletions(-)

diff --git a/R/tm_t_events_by_grade.R b/R/tm_t_events_by_grade.R
index fcce86dd0..357ba81be 100644
--- a/R/tm_t_events_by_grade.R
+++ b/R/tm_t_events_by_grade.R
@@ -249,7 +249,7 @@ template_events_by_grade <- function(dataname,
 
   # Full table.
   y$table <- substitute(
-    expr = table <- rtables::build_table(lyt = lyt, df = anl, alt_counts_df = parent),
+    expr = result <- rtables::build_table(lyt = lyt, df = anl, alt_counts_df = parent),
     env = list(parent = as.name(parentname))
   )
 
@@ -258,7 +258,7 @@ template_events_by_grade <- function(dataname,
   prune_list <- add_expr(
     prune_list,
     quote(
-      pruned_table <- table
+      pruned_result <- result
     )
   )
 
@@ -267,7 +267,7 @@ template_events_by_grade <- function(dataname,
     prune_list <- add_expr(
       prune_list,
       substitute(
-        expr = col_indices <- 1:(ncol(table) - add_total),
+        expr = col_indices <- 1:(ncol(result) - add_total),
         env = list(add_total = add_total)
       )
     )
@@ -303,7 +303,7 @@ template_events_by_grade <- function(dataname,
     prune_list <- add_expr(
       prune_list,
       substitute(
-        expr = table <- pruned_table %>% rtables::prune_table(keep_content_rows(row_condition))
+        expr = result <- pruned_result %>% rtables::prune_table(keep_content_rows(row_condition))
       )
     )
   }
@@ -330,9 +330,9 @@ template_events_by_grade <- function(dataname,
       sort_list,
       substitute(
         expr = {
-          pruned_and_sorted_table <- pruned_table %>%
+          pruned_and_sorted_result <- pruned_result %>%
             sort_at_path(path = term_var, scorefun = scorefun, decreasing = TRUE)
-          pruned_and_sorted_table
+          pruned_and_sorted_result
         },
         env = list(
           term_var = term_var,
@@ -345,7 +345,7 @@ template_events_by_grade <- function(dataname,
       sort_list,
       substitute(
         expr = {
-          table <- pruned_table %>%
+          result <- pruned_result %>%
             sort_at_path(path = hlt, scorefun = scorefun, decreasing = TRUE) %>%
             sort_at_path(path = c(hlt, "*", llt), scorefun = scorefun, decreasing = TRUE)
         },
@@ -359,7 +359,7 @@ template_events_by_grade <- function(dataname,
 
     sort_list <- add_expr(
       sort_list,
-      quote(table)
+      quote(result)
     )
   }
   y$sort <- bracket_expr(sort_list)
@@ -539,7 +539,7 @@ template_events_col_by_grade <- function(dataname,
     layout_list <- add_expr(
       layout_list,
       substitute(
-        expr = rtables::split_cols_by(var = arm_var, split_fun = add_overall_level(total_label, first = FALSE)),
+        expr = result <- rtables::split_cols_by(var = arm_var, split_fun = add_overall_level(total_label, first = FALSE)),
         env = list(
           arm_var = arm_var,
           total_label = total_label
@@ -638,7 +638,7 @@ template_events_col_by_grade <- function(dataname,
   )
 
   # Full table.
-  y$table <- quote(table <- rtables::build_table(lyt = lyt, df = anl, col_counts = col_counts))
+  y$table <- quote(result <- rtables::build_table(lyt = lyt, df = anl, col_counts = col_counts))
 
   # Start sorting table.
   sort_list <- list()
@@ -657,7 +657,7 @@ template_events_col_by_grade <- function(dataname,
   sort_list <- add_expr(
     sort_list,
     substitute(
-      expr = col_indices <- seq(start_index, ncol(table), by = length(grading_groups)),
+      expr = col_indices <- seq(start_index, ncol(result), by = length(grading_groups)),
       env = list(grading_groups = grading_groups)
     )
   )
@@ -679,7 +679,7 @@ template_events_col_by_grade <- function(dataname,
       sort_list,
       substitute(
         expr = {
-          sorted_table <- table %>%
+          sorted_result <- result %>%
             sort_at_path(path = c(llt), scorefun = scorefun_term, decreasing = TRUE)
         },
         env = list(llt = llt)
@@ -690,7 +690,7 @@ template_events_col_by_grade <- function(dataname,
       sort_list,
       substitute(
         expr = {
-          sorted_table <- table %>%
+          sorted_result <- result %>%
             sort_at_path(path = c(hlt), scorefun = scorefun_soc, decreasing = TRUE) %>%
             sort_at_path(path = c(hlt, "*", llt), scorefun = scorefun_term, decreasing = TRUE)
         },
@@ -1218,9 +1218,19 @@ srv_t_events_by_grade <- function(id,
     })
 
 
+    table_renamed_q <- reactive({
+      req(table_q())
+      if (length(table_q()[["prunned_and_sorted_result"]])) {
+        out <- within(table_q(), {table <- pruned_and_sorted_result})
+      } else {
+        out <- within(table_q(), {table <- pruned_result})
+      }
+      out
+    })
+
     decorated_table_q <- srv_decorate_teal_data(
       id = "decorator",
-      data = table_q,
+      data = table_renamed_q,
       decorators = select_decorators(decorators, "table"),
       expr = table
     )

From df9e050cab2ade048ea90e081d6f95c002c98f2b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Thu, 5 Dec 2024 12:27:02 +0100
Subject: [PATCH 07/10] I had erroneously changed this

---
 R/tm_t_events_by_grade.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/tm_t_events_by_grade.R b/R/tm_t_events_by_grade.R
index 357ba81be..7fb0772f2 100644
--- a/R/tm_t_events_by_grade.R
+++ b/R/tm_t_events_by_grade.R
@@ -345,7 +345,7 @@ template_events_by_grade <- function(dataname,
       sort_list,
       substitute(
         expr = {
-          result <- pruned_result %>%
+          pruned_and_sorted_result <- pruned_result %>%
             sort_at_path(path = hlt, scorefun = scorefun, decreasing = TRUE) %>%
             sort_at_path(path = c(hlt, "*", llt), scorefun = scorefun, decreasing = TRUE)
         },

From d5324c868633294ab668bb6e545b3b14cfa725f1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Thu, 5 Dec 2024 14:43:28 +0100
Subject: [PATCH 08/10] Avoid printing the tables twice

---
 R/tm_t_events_by_grade.R | 20 ++++----------------
 1 file changed, 4 insertions(+), 16 deletions(-)

diff --git a/R/tm_t_events_by_grade.R b/R/tm_t_events_by_grade.R
index 7fb0772f2..02fc9ff86 100644
--- a/R/tm_t_events_by_grade.R
+++ b/R/tm_t_events_by_grade.R
@@ -303,7 +303,7 @@ template_events_by_grade <- function(dataname,
     prune_list <- add_expr(
       prune_list,
       substitute(
-        expr = result <- pruned_result %>% rtables::prune_table(keep_content_rows(row_condition))
+        expr = pruned_result <- pruned_result %>% rtables::prune_table(keep_content_rows(row_condition))
       )
     )
   }
@@ -332,7 +332,6 @@ template_events_by_grade <- function(dataname,
         expr = {
           pruned_and_sorted_result <- pruned_result %>%
             sort_at_path(path = term_var, scorefun = scorefun, decreasing = TRUE)
-          pruned_and_sorted_result
         },
         env = list(
           term_var = term_var,
@@ -356,11 +355,6 @@ template_events_by_grade <- function(dataname,
         )
       )
     )
-
-    sort_list <- add_expr(
-      sort_list,
-      quote(result)
-    )
   }
   y$sort <- bracket_expr(sort_list)
 
@@ -539,7 +533,7 @@ template_events_col_by_grade <- function(dataname,
     layout_list <- add_expr(
       layout_list,
       substitute(
-        expr = result <- rtables::split_cols_by(var = arm_var, split_fun = add_overall_level(total_label, first = FALSE)),
+        expr = rtables::split_cols_by(var = arm_var, split_fun = add_overall_level(total_label, first = FALSE)),
         env = list(
           arm_var = arm_var,
           total_label = total_label
@@ -739,7 +733,7 @@ template_events_col_by_grade <- function(dataname,
   prune_pipe <- add_expr(
     prune_pipe,
     quote(
-      pruned_and_sorted_table <- sorted_table %>% rtables::trim_rows(criteria = criteria_fun)
+      pruned_and_sorted_result <- sorted_result %>% rtables::trim_rows(criteria = criteria_fun)
     )
   )
 
@@ -769,11 +763,6 @@ template_events_col_by_grade <- function(dataname,
     prune_list,
     prune_pipe
   )
-  prune_list <- add_expr(
-    prune_list,
-    quote(pruned_and_sorted_table)
-  )
-
   y$prune <- bracket_expr(prune_list)
 
   y
@@ -1219,8 +1208,7 @@ srv_t_events_by_grade <- function(id,
 
 
     table_renamed_q <- reactive({
-      req(table_q())
-      if (length(table_q()[["prunned_and_sorted_result"]])) {
+      if (length(table_q()[["pruned_and_sorted_result"]])) {
         out <- within(table_q(), {table <- pruned_and_sorted_result})
       } else {
         out <- within(table_q(), {table <- pruned_result})

From 2afa1e9dac352cd88b95538b798d07ef32346f97 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?=
 <185338939+llrs-roche@users.noreply.github.com>
Date: Wed, 11 Dec 2024 09:40:59 +0100
Subject: [PATCH 09/10] Apply suggestions from code review
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: André Veríssimo <211358+averissimo@users.noreply.github.com>
Signed-off-by: Lluís Revilla <185338939+llrs-roche@users.noreply.github.com>
---
 R/tm_t_events_by_grade.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/R/tm_t_events_by_grade.R b/R/tm_t_events_by_grade.R
index 02fc9ff86..5ea465397 100644
--- a/R/tm_t_events_by_grade.R
+++ b/R/tm_t_events_by_grade.R
@@ -777,11 +777,10 @@ template_events_col_by_grade <- function(dataname,
 #' @inheritParams template_events_col_by_grade
 #' @param col_by_grade (`logical`)\cr whether to display the grading groups in nested columns.
 #' @param grading_groups (`list`)\cr named list of grading groups used when `col_by_grade = TRUE`.
-#' @param decorators `r roxygen_decorators_param("tm_t_events_by_grade")`
 #'
 #' @inherit module_arguments return seealso
 #'
-#' @section Decorating `tm_t_events_by_grade`:
+#' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `table` (`TableTree` as created from `rtables::build_table`)

From e3435a3eca3f7f7198fbdc75a0bd78082da183a0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Wed, 11 Dec 2024 09:45:21 +0100
Subject: [PATCH 10/10] Simplify renaming

---
 R/tm_t_events_by_grade.R | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/R/tm_t_events_by_grade.R b/R/tm_t_events_by_grade.R
index 02fc9ff86..91fcaacd0 100644
--- a/R/tm_t_events_by_grade.R
+++ b/R/tm_t_events_by_grade.R
@@ -1208,12 +1208,7 @@ srv_t_events_by_grade <- function(id,
 
 
     table_renamed_q <- reactive({
-      if (length(table_q()[["pruned_and_sorted_result"]])) {
-        out <- within(table_q(), {table <- pruned_and_sorted_result})
-      } else {
-        out <- within(table_q(), {table <- pruned_result})
-      }
-      out
+      within(table_q(), {table <- pruned_and_sorted_result})
     })
 
     decorated_table_q <- srv_decorate_teal_data(