From d30234b228a126f95ce068f04236cb6068e56812 Mon Sep 17 00:00:00 2001
From: Emily de la Rua <emily.de_la_rua@contractors.roche.com>
Date: Thu, 1 Feb 2024 18:00:56 -0500
Subject: [PATCH 1/3] Clean up documentation for tm_g_pp_therapy

---
 R/argument_convention.R   | 16 +++++++++++
 R/tm_g_pp_therapy.R       | 60 ++++++++++++++++-----------------------
 man/module_arguments.Rd   | 16 +++++++++++
 man/template_arguments.Rd | 12 ++++++++
 man/template_g_km.Rd      |  2 +-
 man/template_therapy.Rd   | 14 ++++++---
 man/tm_g_pp_therapy.Rd    | 51 +++++++++++++++++----------------
 7 files changed, 107 insertions(+), 64 deletions(-)

diff --git a/R/argument_convention.R b/R/argument_convention.R
index a5e1ea69ca..868d558519 100644
--- a/R/argument_convention.R
+++ b/R/argument_convention.R
@@ -12,6 +12,7 @@
 #' @param add_total (`logical`)\cr whether to include column with total number of patients.
 #' @param anl_name (`character`)\cr analysis data used in teal module.
 #' @param arm_var (`character`)\cr variable names that can be used as `arm_var`.
+#' @param atirel (`character`)\cr name of time relation of medication variable.
 #' @param aval `r lifecycle::badge("deprecated")` Please use the `aval_var` argument instead.
 #' @param avalu `r lifecycle::badge("deprecated")` Please use the `avalu_var` argument instead.
 #' @param avalu_var (`character`)\cr name of the analysis value unit variable.
@@ -23,6 +24,9 @@
 #'
 #'   For more details, see the vignette: `vignette("custom-basic-table-arguments", package = "teal.widgets")`.
 #' @param by_vars (`character`)\cr variable names used to split the summary by rows.
+#' @param cmdecod (`character`)\cr name of standardized medication name variable.
+#' @param cmindc (`character`)\cr name of indication variable.
+#' @param cmstdy (`character`)\cr name of study relative day of start of medication variable.
 #' @param cnsr_var (`character`)\cr name of the censoring variable.
 #' @param combine_comp_arms (`logical`)\cr triggers the combination of comparison arms.
 #' @param compare_arm (`logical`)\cr triggers the comparison between study arms.
@@ -37,6 +41,7 @@
 #' @param drop_arm_levels (`logical`)\cr drop the unused `arm_var` levels.
 #'   When `TRUE`, `arm_var` levels are set to those used in the `dataname` dataset. When `FALSE`,
 #'   `arm_var` levels are set to those used in the `parantname` dataset.
+#' @param font_size (`numeric`)\cr font size value.
 #' @param ggplot2_args optional, (`ggplot2_args`)\cr object created by [teal.widgets::ggplot2_args()] with settings
 #'   for the module plot. The argument is merged with option `teal.ggplot2_args` and with default module arguments
 #'   (hard coded in the module body).
@@ -50,6 +55,7 @@
 #' @param interact_y (`character`)\cr a selected item from the interact_var column which will be used to select the
 #'   specific `ANCOVA` results. If the interaction is not needed, the default option is `FALSE`.
 #' @param llt (`character`)\cr name of the variable with low level term for events.
+#' @param patient_id (`character`)\cr patient ID.
 #' @param na_level (`string`)\cr used to replace all `NA` or empty values
 #'   in character or factor variables in the data. Defaults to `"<Missing>"`. To set a
 #'   default `na_level` to apply in all modules, run `set_default_na_str("new_default")`.
@@ -110,6 +116,8 @@ NULL
 #'   It defines the grouping variable(s) in the results table.
 #'   If there are two elements selected for `arm_var`,
 #'   second variable will be nested under the first variable.
+#' @param atirel ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#'   available choices and preselected option for the `ATIREL` variable from `dataname`.
 #' @param aval_var (`choices_selected` or `data_extract_spec`)\cr object with all available choices and preselected
 #'   option for the analysis variable.
 #' @param avisit (`choices_selected` or `data_extract_spec`)\cr value of analysis visit `AVISIT` of interest.
@@ -117,6 +125,12 @@ NULL
 #'   all available choices and preselected option for variable values that can be used as `baseline_var`.
 #' @param by_vars (`choices_selected` or `data_extract_spec`)\cr object with all available choices and preselected
 #'   option for variable names used to split the summary by rows.
+#' @param cmdecod ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#'   available choices and preselected option for the `CMDECOD` variable from `dataname`.
+#' @param cmindc ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#'   available choices and preselected option for the `CMINDC` variable from `dataname`.
+#' @param cmstdy ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#'   available choices and preselected option for the `CMSTDY` variable from `dataname`.
 #' @param cnsr_var (`choices_selected` or `data_extract_spec`)\cr object with all available choices and preselected
 #'   option for the censoring variable.
 #' @param conf_level (`choices_selected`)\cr object with all available choices and preselected option for the
@@ -131,6 +145,7 @@ NULL
 #'   values and `levels` of default level choices.
 #' @param fixed_symbol_size (`logical`)\cr When (`TRUE`), the same symbol size is used for plotting each estimate.
 #'   Otherwise, the symbol size will be proportional to the sample size in each each subgroup.
+#' @param font_size (`numeric`)\cr numeric vector of length 3 of current, minimum and maximum font size values.
 #' @param hlt (`choices_selected` or `data_extract_spec`)\cr name of the variable with high level term for events.
 #' @param id_var (`choices_selected` or `data_extract_spec`)\cr object specifying the variable name for subject id.
 #' @param interact_var (`character`)\cr name of the variable that should have interactions
@@ -142,6 +157,7 @@ NULL
 #' @param llt (`choices_selected` or `data_extract_spec`)\cr name of the variable with low level term for events.
 #' @param paramcd (`choices_selected` or `data_extract_spec`)\cr variable value designating the studied parameter.
 #' @param parentname (`character`)\cr parent analysis data used in teal module, usually this refers to `ADSL`.
+#' @param patient_col (`character`)\cr name of patient ID variable.
 #' @param plot_height optional, (`numeric`)\cr a vector of length three with `c(value, min, max)`. Specifies the
 #'   height of the main plot and renders a slider on the plot to interactively adjust the plot height.
 #' @param plot_width optional, (`numeric`)\cr a vector of length three with `c(value, min, max)`. Specifies the width
diff --git a/R/tm_g_pp_therapy.R b/R/tm_g_pp_therapy.R
index 8504b26c12..654426cd28 100644
--- a/R/tm_g_pp_therapy.R
+++ b/R/tm_g_pp_therapy.R
@@ -1,22 +1,20 @@
-#' Template: Therapy
+#' Template: Patient Profile Therapy Plot
 #'
-#' Creates a therapy template call.
+#' Creates a valid expression to generate a [ggplot2::ggplot()] patient profile therapy plot using ADaM datasets.
 #'
 #' @inheritParams template_arguments
-#' @param atirel (`character`)\cr name of time relation of medication variable.
-#' @param cmdecod (`character`)\cr name of standardized medication name variable.
-#' @param cmindc (`character`)\cr name of indication variable.
 #' @param cmdose (`character`)\cr name of dose per administration variable.
 #' @param cmtrt (`character`)\cr name of reported name of drug, med, or therapy variable.
 #' @param cmdosu (`character`)\cr name of dose units variable.
 #' @param cmroute (`character`)\cr name of route of administration variable.
 #' @param cmdosfrq (`character`)\cr name of dosing frequency per interval variable.
-#' @param cmstdy (`character`)\cr name of study day of start of medication variable.
 #' @param cmendy (`character`)\cr name of study day of end of medication variable.
-#' @param patient_id (`character`)\cr patient ID.
-#' @param font_size (`numeric`)\cr numeric vector of length 3 for current, min and max font size values.
-#' @keywords internal
 #'
+#' @inherit template_arguments return
+#'
+#' @seealso [tm_g_pp_therapy()]
+#'
+#' @keywords internal
 template_therapy <- function(dataname = "ANL",
                              atirel = "ATIREL",
                              cmdecod = "CMDECOD",
@@ -230,36 +228,26 @@ template_therapy <- function(dataname = "ANL",
   y
 }
 
-#' Teal Module: Patient Profile Therapy Teal Module
+#' teal Module: Patient Profile Therapy Plot
 #'
-#' This teal module produces a patient profile therapy plot using `ADaM` datasets.
+#' This module produces a [ggplot2::ggplot()] type patient profile therapy plot using ADaM datasets.
 #'
 #' @inheritParams module_arguments
 #' @inheritParams template_therapy
-#' @param patient_col (`character`)\cr patient ID column to be used.
-#' @param atirel ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr
-#' `ATIREL` column of the `ADCM` dataset.
-#' @param cmdecod ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr
-#' `CMDECOD` column of the `ADCM` dataset.
-#' @param cmdose ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr
-#' `CMDOSE` column of the `ADCM` dataset.
-#' @param cmtrt ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr
-#' `CMTRT` column of the `ADCM` dataset.
-#' @param cmdosu ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr
-#' `CMDOSU` column of the `ADCM` dataset.
-#' @param cmroute ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr
-#' `CMROUTE` column of the `ADCM` dataset.
-#' @param cmdosfrq ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr
-#' `CMDOSFRQ` column of the `ADCM` dataset.
-#' @param cmstdy ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr
-#' `CMSTDY` column of the `ADCM` dataset.
-#' @param cmendy ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr
-#' `CMENDY` column of the `ADCM` dataset.
-#' @param cmindc ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr
-#' `CMINDC` column of the `ADCM` dataset.
-#' @param font_size (`numeric`)\cr numeric vector of length 3 for current, min and max font size values.
+#' @param cmdose ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#'   available choices and preselected option for the `CMDOSE` variable from `dataname`.
+#' @param cmtrt ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#'   available choices and preselected option for the `CMTRT` variable from `dataname`.
+#' @param cmdosu ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#'   available choices and preselected option for the `CMDOSU` variable from `dataname`.
+#' @param cmroute ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#'   available choices and preselected option for the `CMROUTE` variable from `dataname`.
+#' @param cmdosfrq ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#'   available choices and preselected option for the `CMDOSFRQ` variable from `dataname`.
+#' @param cmendy ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#'   available choices and preselected option for the `CMENDY` variable from `dataname`.
 #'
-#' @export
+#' @inherit module_arguments return
 #'
 #' @examples
 #' library(nestcolor)
@@ -339,6 +327,7 @@ template_therapy <- function(dataname = "ANL",
 #'   shinyApp(app$ui, app$server)
 #' }
 #'
+#' @export
 tm_g_pp_therapy <- function(label,
                             dataname = "ADCM",
                             parentname = "ADSL",
@@ -412,6 +401,7 @@ tm_g_pp_therapy <- function(label,
   )
 }
 
+#' @keywords internal
 ui_g_therapy <- function(id, ...) {
   ui_args <- list(...)
   is_single_dataset_value <- teal.transform::is_single_dataset(
@@ -531,7 +521,7 @@ ui_g_therapy <- function(id, ...) {
   )
 }
 
-
+#' @keywords internal
 srv_g_therapy <- function(id,
                           data,
                           reporter,
diff --git a/man/module_arguments.Rd b/man/module_arguments.Rd
index e17351692d..ec1e646c46 100644
--- a/man/module_arguments.Rd
+++ b/man/module_arguments.Rd
@@ -16,6 +16,9 @@ It defines the grouping variable(s) in the results table.
 If there are two elements selected for \code{arm_var},
 second variable will be nested under the first variable.}
 
+\item{atirel}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr object with all
+available choices and preselected option for the \code{ATIREL} variable from \code{dataname}.}
+
 \item{aval_var}{(\code{choices_selected} or \code{data_extract_spec})\cr object with all available choices and preselected
 option for the analysis variable.}
 
@@ -27,6 +30,15 @@ all available choices and preselected option for variable values that can be use
 \item{by_vars}{(\code{choices_selected} or \code{data_extract_spec})\cr object with all available choices and preselected
 option for variable names used to split the summary by rows.}
 
+\item{cmdecod}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr object with all
+available choices and preselected option for the \code{CMDECOD} variable from \code{dataname}.}
+
+\item{cmindc}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr object with all
+available choices and preselected option for the \code{CMINDC} variable from \code{dataname}.}
+
+\item{cmstdy}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr object with all
+available choices and preselected option for the \code{CMSTDY} variable from \code{dataname}.}
+
 \item{cnsr_var}{(\code{choices_selected} or \code{data_extract_spec})\cr object with all available choices and preselected
 option for the censoring variable.}
 
@@ -46,6 +58,8 @@ values and \code{levels} of default level choices.}
 \item{fixed_symbol_size}{(\code{logical})\cr When (\code{TRUE}), the same symbol size is used for plotting each estimate.
 Otherwise, the symbol size will be proportional to the sample size in each each subgroup.}
 
+\item{font_size}{(\code{numeric})\cr numeric vector of length 3 of current, minimum and maximum font size values.}
+
 \item{hlt}{(\code{choices_selected} or \code{data_extract_spec})\cr name of the variable with high level term for events.}
 
 \item{id_var}{(\code{choices_selected} or \code{data_extract_spec})\cr object specifying the variable name for subject id.}
@@ -65,6 +79,8 @@ needed, the default option is \code{FALSE}.}
 
 \item{parentname}{(\code{character})\cr parent analysis data used in teal module, usually this refers to \code{ADSL}.}
 
+\item{patient_col}{(\code{character})\cr name of patient ID variable.}
+
 \item{plot_height}{optional, (\code{numeric})\cr a vector of length three with \code{c(value, min, max)}. Specifies the
 height of the main plot and renders a slider on the plot to interactively adjust the plot height.}
 
diff --git a/man/template_arguments.Rd b/man/template_arguments.Rd
index 7aa0f33bd6..9e8ef4cd07 100644
--- a/man/template_arguments.Rd
+++ b/man/template_arguments.Rd
@@ -10,6 +10,8 @@
 
 \item{arm_var}{(\code{character})\cr variable names that can be used as \code{arm_var}.}
 
+\item{atirel}{(\code{character})\cr name of time relation of medication variable.}
+
 \item{aval}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Please use the \code{aval_var} argument instead.}
 
 \item{avalu}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Please use the \code{avalu_var} argument instead.}
@@ -28,6 +30,12 @@ For more details, see the vignette: \code{vignette("custom-basic-table-arguments
 
 \item{by_vars}{(\code{character})\cr variable names used to split the summary by rows.}
 
+\item{cmdecod}{(\code{character})\cr name of standardized medication name variable.}
+
+\item{cmindc}{(\code{character})\cr name of indication variable.}
+
+\item{cmstdy}{(\code{character})\cr name of study relative day of start of medication variable.}
+
 \item{cnsr_var}{(\code{character})\cr name of the censoring variable.}
 
 \item{combine_comp_arms}{(\code{logical})\cr triggers the combination of comparison arms.}
@@ -51,6 +59,8 @@ percentage is omitted.}
 When \code{TRUE}, \code{arm_var} levels are set to those used in the \code{dataname} dataset. When \code{FALSE},
 \code{arm_var} levels are set to those used in the \code{parantname} dataset.}
 
+\item{font_size}{(\code{numeric})\cr font size value.}
+
 \item{ggplot2_args}{optional, (\code{ggplot2_args})\cr object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings
 for the module plot. The argument is merged with option \code{teal.ggplot2_args} and with default module arguments
 (hard coded in the module body).
@@ -71,6 +81,8 @@ specific \code{ANCOVA} results. If the interaction is not needed, the default op
 
 \item{llt}{(\code{character})\cr name of the variable with low level term for events.}
 
+\item{patient_id}{(\code{character})\cr patient ID.}
+
 \item{na_level}{(\code{string})\cr used to replace all \code{NA} or empty values
 in character or factor variables in the data. Defaults to \code{"<Missing>"}. To set a
 default \code{na_level} to apply in all modules, run \code{set_default_na_str("new_default")}.}
diff --git a/man/template_g_km.Rd b/man/template_g_km.Rd
index 35d72b182c..ca8a921f22 100644
--- a/man/template_g_km.Rd
+++ b/man/template_g_km.Rd
@@ -61,7 +61,7 @@ an optimal tick position on the x axis.}
 object with all available choices and preselected option
 for variable names that can be used for facet plotting.}
 
-\item{font_size}{(\code{number})\cr font size to be used.}
+\item{font_size}{(\code{numeric})\cr font size value.}
 
 \item{conf_level}{(\code{numeric})\cr value for the confidence level within the range of (0, 1).}
 
diff --git a/man/template_therapy.Rd b/man/template_therapy.Rd
index 53248b12d0..1ca697aed9 100644
--- a/man/template_therapy.Rd
+++ b/man/template_therapy.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/tm_g_pp_therapy.R
 \name{template_therapy}
 \alias{template_therapy}
-\title{Template: Therapy}
+\title{Template: Patient Profile Therapy Plot}
 \usage{
 template_therapy(
   dataname = "ANL",
@@ -40,13 +40,13 @@ template_therapy(
 
 \item{cmdosfrq}{(\code{character})\cr name of dosing frequency per interval variable.}
 
-\item{cmstdy}{(\code{character})\cr name of study day of start of medication variable.}
+\item{cmstdy}{(\code{character})\cr name of study relative day of start of medication variable.}
 
 \item{cmendy}{(\code{character})\cr name of study day of end of medication variable.}
 
 \item{patient_id}{(\code{character})\cr patient ID.}
 
-\item{font_size}{(\code{numeric})\cr numeric vector of length 3 for current, min and max font size values.}
+\item{font_size}{(\code{numeric})\cr font size value.}
 
 \item{ggplot2_args}{optional, (\code{ggplot2_args})\cr object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings
 for the module plot. The argument is merged with option \code{teal.ggplot2_args} and with default module arguments
@@ -54,7 +54,13 @@ for the module plot. The argument is merged with option \code{teal.ggplot2_args}
 
 For more details, see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.}
 }
+\value{
+a \code{list} of expressions to generate a table or plot object.
+}
 \description{
-Creates a therapy template call.
+Creates a valid expression to generate a \code{\link[ggplot2:ggplot]{ggplot2::ggplot()}} patient profile therapy plot using ADaM datasets.
+}
+\seealso{
+\code{\link[=tm_g_pp_therapy]{tm_g_pp_therapy()}}
 }
 \keyword{internal}
diff --git a/man/tm_g_pp_therapy.Rd b/man/tm_g_pp_therapy.Rd
index 04054d4e65..3925da1ac5 100644
--- a/man/tm_g_pp_therapy.Rd
+++ b/man/tm_g_pp_therapy.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/tm_g_pp_therapy.R
 \name{tm_g_pp_therapy}
 \alias{tm_g_pp_therapy}
-\title{Teal Module: Patient Profile Therapy Teal Module}
+\title{teal Module: Patient Profile Therapy Plot}
 \usage{
 tm_g_pp_therapy(
   label,
@@ -34,39 +34,39 @@ tm_g_pp_therapy(
 
 \item{parentname}{(\code{character})\cr parent analysis data used in teal module, usually this refers to \code{ADSL}.}
 
-\item{patient_col}{(\code{character})\cr patient ID column to be used.}
+\item{patient_col}{(\code{character})\cr name of patient ID variable.}
 
-\item{atirel}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr
-\code{ATIREL} column of the \code{ADCM} dataset.}
+\item{atirel}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr object with all
+available choices and preselected option for the \code{ATIREL} variable from \code{dataname}.}
 
-\item{cmdecod}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr
-\code{CMDECOD} column of the \code{ADCM} dataset.}
+\item{cmdecod}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr object with all
+available choices and preselected option for the \code{CMDECOD} variable from \code{dataname}.}
 
-\item{cmindc}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr
-\code{CMINDC} column of the \code{ADCM} dataset.}
+\item{cmindc}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr object with all
+available choices and preselected option for the \code{CMINDC} variable from \code{dataname}.}
 
-\item{cmdose}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr
-\code{CMDOSE} column of the \code{ADCM} dataset.}
+\item{cmdose}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr object with all
+available choices and preselected option for the \code{CMDOSE} variable from \code{dataname}.}
 
-\item{cmtrt}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr
-\code{CMTRT} column of the \code{ADCM} dataset.}
+\item{cmtrt}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr object with all
+available choices and preselected option for the \code{CMTRT} variable from \code{dataname}.}
 
-\item{cmdosu}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr
-\code{CMDOSU} column of the \code{ADCM} dataset.}
+\item{cmdosu}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr object with all
+available choices and preselected option for the \code{CMDOSU} variable from \code{dataname}.}
 
-\item{cmroute}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr
-\code{CMROUTE} column of the \code{ADCM} dataset.}
+\item{cmroute}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr object with all
+available choices and preselected option for the \code{CMROUTE} variable from \code{dataname}.}
 
-\item{cmdosfrq}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr
-\code{CMDOSFRQ} column of the \code{ADCM} dataset.}
+\item{cmdosfrq}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr object with all
+available choices and preselected option for the \code{CMDOSFRQ} variable from \code{dataname}.}
 
-\item{cmstdy}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr
-\code{CMSTDY} column of the \code{ADCM} dataset.}
+\item{cmstdy}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr object with all
+available choices and preselected option for the \code{CMSTDY} variable from \code{dataname}.}
 
-\item{cmendy}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr
-\code{CMENDY} column of the \code{ADCM} dataset.}
+\item{cmendy}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr object with all
+available choices and preselected option for the \code{CMENDY} variable from \code{dataname}.}
 
-\item{font_size}{(\code{numeric})\cr numeric vector of length 3 for current, min and max font size values.}
+\item{font_size}{(\code{numeric})\cr numeric vector of length 3 of current, minimum and maximum font size values.}
 
 \item{plot_height}{optional, (\code{numeric})\cr a vector of length three with \code{c(value, min, max)}. Specifies the
 height of the main plot and renders a slider on the plot to interactively adjust the plot height.}
@@ -86,8 +86,11 @@ for the module plot. The argument is merged with option \code{teal.ggplot2_args}
 
 For more details, see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.}
 }
+\value{
+a \code{teal_module} object.
+}
 \description{
-This teal module produces a patient profile therapy plot using \code{ADaM} datasets.
+This module produces a \code{\link[ggplot2:ggplot]{ggplot2::ggplot()}} type patient profile therapy plot using ADaM datasets.
 }
 \examples{
 library(nestcolor)

From 46145dd8d1c3b3bc109b3ddbdb50cf958c68d42c Mon Sep 17 00:00:00 2001
From: Emily de la Rua <emily.de_la_rua@contractors.roche.com>
Date: Thu, 1 Feb 2024 18:23:51 -0500
Subject: [PATCH 2/3] Update title

---
 R/tm_g_pp_therapy.R     | 9 +++++----
 man/template_therapy.Rd | 5 +++--
 man/tm_g_pp_therapy.Rd  | 4 ++--
 3 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/R/tm_g_pp_therapy.R b/R/tm_g_pp_therapy.R
index 654426cd28..0fcf150a7b 100644
--- a/R/tm_g_pp_therapy.R
+++ b/R/tm_g_pp_therapy.R
@@ -1,6 +1,7 @@
-#' Template: Patient Profile Therapy Plot
+#' Template: Patient Profile Therapy Table and Plot
 #'
-#' Creates a valid expression to generate a [ggplot2::ggplot()] patient profile therapy plot using ADaM datasets.
+#' Creates a valid expression to generate a patient profile therapy table and [ggplot2::ggplot()] plot using ADaM
+#' datasets.
 #'
 #' @inheritParams template_arguments
 #' @param cmdose (`character`)\cr name of dose per administration variable.
@@ -228,9 +229,9 @@ template_therapy <- function(dataname = "ANL",
   y
 }
 
-#' teal Module: Patient Profile Therapy Plot
+#' teal Module: Patient Profile Therapy Table and Plot
 #'
-#' This module produces a [ggplot2::ggplot()] type patient profile therapy plot using ADaM datasets.
+#' This module produces a patient profile therapy table and [ggplot2::ggplot()] type plot using ADaM datasets.
 #'
 #' @inheritParams module_arguments
 #' @inheritParams template_therapy
diff --git a/man/template_therapy.Rd b/man/template_therapy.Rd
index 1ca697aed9..f56ccbca6d 100644
--- a/man/template_therapy.Rd
+++ b/man/template_therapy.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/tm_g_pp_therapy.R
 \name{template_therapy}
 \alias{template_therapy}
-\title{Template: Patient Profile Therapy Plot}
+\title{Template: Patient Profile Therapy Table and Plot}
 \usage{
 template_therapy(
   dataname = "ANL",
@@ -58,7 +58,8 @@ For more details, see the vignette: \code{vignette("custom-ggplot2-arguments", p
 a \code{list} of expressions to generate a table or plot object.
 }
 \description{
-Creates a valid expression to generate a \code{\link[ggplot2:ggplot]{ggplot2::ggplot()}} patient profile therapy plot using ADaM datasets.
+Creates a valid expression to generate a patient profile therapy table and \code{\link[ggplot2:ggplot]{ggplot2::ggplot()}} plot using ADaM
+datasets.
 }
 \seealso{
 \code{\link[=tm_g_pp_therapy]{tm_g_pp_therapy()}}
diff --git a/man/tm_g_pp_therapy.Rd b/man/tm_g_pp_therapy.Rd
index 3925da1ac5..807555e2be 100644
--- a/man/tm_g_pp_therapy.Rd
+++ b/man/tm_g_pp_therapy.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/tm_g_pp_therapy.R
 \name{tm_g_pp_therapy}
 \alias{tm_g_pp_therapy}
-\title{teal Module: Patient Profile Therapy Plot}
+\title{teal Module: Patient Profile Therapy Table and Plot}
 \usage{
 tm_g_pp_therapy(
   label,
@@ -90,7 +90,7 @@ For more details, see the vignette: \code{vignette("custom-ggplot2-arguments", p
 a \code{teal_module} object.
 }
 \description{
-This module produces a \code{\link[ggplot2:ggplot]{ggplot2::ggplot()}} type patient profile therapy plot using ADaM datasets.
+This module produces a patient profile therapy table and \code{\link[ggplot2:ggplot]{ggplot2::ggplot()}} type plot using ADaM datasets.
 }
 \examples{
 library(nestcolor)

From f69df3834d04bf3b61933c6df6bec725a804ee42 Mon Sep 17 00:00:00 2001
From: Emily de la Rua <emily.de_la_rua@contractors.roche.com>
Date: Fri, 2 Feb 2024 11:24:48 -0500
Subject: [PATCH 3/3] Update docs

---
 man/template_arguments.Rd | 2 --
 1 file changed, 2 deletions(-)

diff --git a/man/template_arguments.Rd b/man/template_arguments.Rd
index 7da0a458b9..261cde7fa0 100644
--- a/man/template_arguments.Rd
+++ b/man/template_arguments.Rd
@@ -82,8 +82,6 @@ specific \code{ANCOVA} results. If the interaction is not needed, the default op
 
 \item{llt}{(\code{character})\cr name of the variable with low level term for events.}
 
-\item{patient_id}{(\code{character})\cr patient ID.}
-
 \item{na_level}{(\code{string})\cr used to replace all \code{NA} or empty values
 in character or factor variables in the data. Defaults to \code{"<Missing>"}. To set a
 default \code{na_level} to apply in all modules, run \code{set_default_na_str("new_default")}.}