module_arguments: Standard Module Arguments

In teal.modules.clinical: 'teal' Modules for Standard Clinical Outputs

Standard Module Arguments

Description

The documentation to this function lists all the arguments in teal modules that are used repeatedly to express an analysis.

Arguments

arm_ref_comp	(list) optional, if specified it must be a named list with each element corresponding to an arm variable in ADSL and the element must be another list (possibly with delayed teal.transform::variable_choices() or delayed teal.transform::value_choices() with the elements named ref and comp that the defined the default reference and comparison arms when the arm variable is changed.
arm_var	(teal.transform::choices_selected()) object with all available choices and preselected option for variable names that can be used as arm_var. It defines the grouping variable in the results table.
atirel	(teal.transform::choices_selected()) object with all available choices and preselected option for the ATIREL variable from dataname.
aval_var	(teal.transform::choices_selected()) object with all available choices and pre-selected option for the analysis variable.
avalu_var	(teal.transform::choices_selected()) object with all available choices and preselected option for the analysis unit variable.
avisit	(teal.transform::choices_selected()) value of analysis visit AVISIT of interest.
baseline_var	(teal.transform::choices_selected()) object with all available choices and preselected option for variable values that can be used as baseline_var.
by_vars	(teal.transform::choices_selected()) object with all available choices and preselected option for variable names used to split the summary by rows.
cmdecod	(teal.transform::choices_selected()) object with all available choices and preselected option for the CMDECOD variable from dataname.
cmindc	(teal.transform::choices_selected()) object with all available choices and preselected option for the CMINDC variable from dataname.
cmstdy	(teal.transform::choices_selected()) object with all available choices and preselected option for the CMSTDY variable from dataname.
cnsr_var	(teal.transform::choices_selected()) object with all available choices and preselected option for the censoring variable.
conf_level	(teal.transform::choices_selected()) object with all available choices and pre-selected option for the confidence level, each within range of (0, 1).
cov_var	(teal.transform::choices_selected()) object with all available choices and preselected option for the covariates variables.
dataname	(character) analysis data used in teal module.
default_responses	(list or character) defines the default codes for the response variable in the module per value of paramcd. A passed vector is transmitted for all paramcd values. A passed list must be named and contain arrays, each name corresponding to a single value of paramcd. Each array may contain default response values or named arrays rsp of default selected response values and levels of default level choices.
fixed_symbol_size	(logical) 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.
font_size	(numeric) numeric vector of length 3 of current, minimum and maximum font size values.
hlt	(teal.transform::choices_selected()) name of the variable with high level term for events.
id_var	(teal.transform::choices_selected()) object specifying the variable name for subject id.
interact_var	(character) name of the variable that should have interactions with arm. If the interaction is not needed, the default option is NULL.
interact_y	(character) a selected item from the interact_var column which will be used to select the specific ANCOVA results when interact_var is discrete. If the interaction is not needed, the default option is FALSE.
label	(character) menu item label of the module in the teal app.
llt	(teal.transform::choices_selected()) name of the variable with low level term for events.
paramcd	(teal.transform::choices_selected()) object with all available choices and preselected option for the parameter code variable from dataname.
parentname	(character) parent analysis data used in teal module, usually this refers to ADSL.
patient_col	(character) name of patient ID variable.
plot_height	(numeric) optional 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.
plot_width	(numeric) optional vector of length three with c(value, min, max). Specifies the width of the main plot and renders a slider on the plot to interactively adjust the plot width.
post_output	(shiny.tag) optional, with text placed after the output to put the output into context. For example the shiny::helpText() elements are useful.
pre_output	(shiny.tag) optional, with text placed before the output to put the output into context. For example a title.
strata_var	(teal.transform::choices_selected()) names of the variables for stratified analysis.
summarize_vars	(teal.transform::choices_selected()) names of the variables that should be summarized.
subgroup_var	(teal.transform::choices_selected()) object with all available choices and preselected option for variable names that can be used as the default subgroups.
time_points	(teal.transform::choices_selected()) object with all available choices and preselected option for time points that can be used in tern::surv_timepoint().
time_unit_var	(teal.transform::choices_selected()) object with all available choices and pre-selected option for the time unit variable.
treatment_flag	(teal.transform::choices_selected()) value indicating on treatment records in treatment_flag_var.
treatment_flag_var	(teal.transform::choices_selected()) on treatment flag variable.
useNA	(character) whether missing data (NA) should be displayed as a level.
visit_var	(teal.transform::choices_selected()) object with all available choices and preselected option for variable names that can be used as visit variable. Must be a factor in dataname.
worst_flag_indicator	(teal.transform::choices_selected()) value indicating worst grade.
worst_flag_var	(teal.transform::choices_selected()) object with all available choices and preselected option for variable names that can be used as worst flag variable.
decorators	(named list of lists of teal_transform_module) optional, decorator for tables or plots included in the module output reported. The decorators are applied to the respective output objects. See section "Decorating Module" below for more details.

Details

• Although this function just returns 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 roxygen argument description with: ⁠@inheritParams module_arguments⁠

• Parameters with identical descriptions & input types to those in the Standard Template Arguments section are excluded to reduce duplication as each module function inherits parameters from its corresponding template function.

Value

a teal_module object.

See Also

The TLG Catalog where additional example apps implementing this module can be found.

teal.modules.clinical documentation built on April 4, 2025, 12:35 a.m.