template_arguments.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/argument_convention.R
\name{template_arguments}
\alias{template_arguments}
\title{Standard Template Arguments}
\arguments{
\item{add_total}{(\code{logical})\cr whether to include column with total number of patients.}

\item{anl_name}{(\code{character})\cr analysis data used in teal module.}

\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.}

\item{avalu_var}{(\code{character})\cr name of the analysis value unit variable.}

\item{aval_var}{(\code{character})\cr name of the analysis value variable.}

\item{baseline_var}{(\code{character})\cr name of the variable for baseline values of the analysis variable.}

\item{base_var}{\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{baseline_var} argument instead.}

\item{basic_table_args}{(\code{basic_table_args}) optional\cr object created by \code{\link[teal.widgets:basic_table_args]{teal.widgets::basic_table_args()}}
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{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.}

\item{compare_arm}{(\code{logical})\cr triggers the comparison between study arms.}

\item{comp_arm}{(\code{character})\cr the level of comparison arm in case of arm comparison.}

\item{conf_level}{(\code{numeric})\cr value for the confidence level within the range of (0, 1).}

\item{control}{(\code{list})\cr list of settings for the analysis.}

\item{cov_var}{(\code{character})\cr names of the covariates variables.}

\item{dataname}{(\code{character})\cr analysis data used in teal module.}

\item{denominator}{(\code{character})\cr chooses how percentages are calculated. With option \code{N}, the reference
population from the column total is used as the denominator. With option \code{n}, the number of non-missing
records in this row and column intersection is used as the denominator. If \code{omit} is chosen, then the
percentage is omitted.}

\item{drop_arm_levels}{(\code{logical})\cr whether to drop unused levels of \code{arm_var}. If \code{TRUE}, \code{arm_var} levels are
set to those used in the \code{dataname} dataset. If \code{FALSE}, \code{arm_var} levels are set to those used in the
\code{parentname} dataset. If \code{dataname} and \code{parentname} are the same, then \code{drop_arm_levels} is set to \code{TRUE} and
user input for this parameter is ignored.}

\item{event_type}{(\code{character})\cr type of event that is summarized (e.g. adverse event, treatment). Default
is \code{"event"}.}

\item{font_size}{(\code{numeric})\cr font size value.}

\item{ggplot2_args}{(\code{ggplot2_args}) optional\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).
For more details, see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.}

\item{hlt}{(\code{character})\cr name of the variable with high level term for events.}

\item{id_var}{(\code{character})\cr the variable name for subject id.}

\item{include_interact}{(\code{logical})\cr whether an interaction term should be included in the model.}

\item{label_hlt}{(\code{string})\cr label of the \code{hlt} variable from \code{dataname}. The label will be extracted from the
module.}

\item{label_llt}{(\code{string})\cr label of the \code{llt} variable from \code{dataname}. The label will be extracted from the
module.}

\item{llt}{(\code{character})\cr name of the variable with low level term for events.}

\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")}.}

\item{na.rm}{(\code{logical})\cr whether \code{NA} values should be removed prior to analysis.}

\item{numeric_stats}{(\code{character})\cr names of statistics to display for numeric summary variables. Available
statistics are \code{n}, \code{mean_sd}, \code{mean_ci}, \code{median}, \code{median_ci}, \code{quantiles}, \code{range}, and \code{geom_mean}.}

\item{paramcd}{(\code{character})\cr name of the parameter code variable.}

\item{parentname}{(\code{character})\cr parent analysis data used in teal module, usually this refers to \code{ADSL}.}

\item{patient_id}{(\code{character})\cr patient ID.}

\item{prune_diff}{(\code{number})\cr threshold to use for trimming table using as criteria difference in
rates between any two columns.}

\item{prune_freq}{(\code{number})\cr threshold to use for trimming table using event incidence rate in any column.}

\item{ref_arm}{(\code{character})\cr the level of reference arm in case of arm comparison.}

\item{sort_criteria}{(\code{character})\cr how to sort the final table. Default option \code{freq_desc} sorts
on column \code{sort_freq_col} by decreasing number of patients with event. Alternative option \code{alpha} sorts events
alphabetically.}

\item{strata_var}{(\code{character})\cr names of the variables for stratified analysis.}

\item{subgroup_var}{(\code{character})\cr with variable names that can be used as subgroups.}

\item{sum_vars}{(\code{character})\cr names of the variables that should be summarized.}

\item{time_points}{(\code{character})\cr time points that can be used in \code{\link[tern:survival_timepoint]{tern::surv_timepoint()}}.}

\item{time_unit_var}{(\code{character})\cr name of the variable representing time units.}

\item{title}{(\code{character})\cr title of the output.}

\item{total_label}{(\code{string})\cr string to display as total column/row label if column/row is
enabled (see \code{add_total}). Defaults to \code{"All Patients"}. To set a new default \code{total_label} to
apply in all modules, run \code{set_default_total_label("new_default")}.}

\item{treatment_flag}{(\code{character})\cr name of the value indicating on treatment
records in \code{treatment_flag_var}.}

\item{treatment_flag_var}{(\code{character})\cr name of the on treatment flag variable.}

\item{useNA}{(\code{character})\cr whether missing data (\code{NA}) should be displayed as a level.}

\item{var_labels}{(named \code{character}) optional\cr variable labels for relabeling the analysis variables.}

\item{visit_var}{(\code{character})\cr variable names that can be used as \code{visit} variable. Must be a factor in
\code{dataname}.}

\item{worst_flag_indicator}{(\code{character})\cr value indicating worst grade.}

\item{worst_flag_var}{(\code{character})\cr name of the worst flag variable.}
}
\value{
a \code{list} of expressions to generate a table or plot object.
}
\description{
The documentation to this function lists all the arguments in teal module
templates that are used repeatedly to express an analysis.
}
\details{
Although this function just returns \code{NULL} it has two uses, for
the teal module users it provides a documentation of arguments that are
commonly and consistently used in the framework. For the developer it adds a
single reference point to import the \code{roxygen} argument description with:
\verb{@inheritParams template_arguments}
}
\keyword{internal}