template_arguments: Standard Template Arguments

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

Standard Template Arguments

Description

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

Arguments

add_total	(logical) whether to include column with total number of patients.
anl_name	(character) analysis data used in teal module.
arm_var	(character) variable names that can be used as arm_var.
atirel	(character) name of time relation of medication variable.
aval	Please use the aval_var argument instead.
avalu	Please use the avalu_var argument instead.
avalu_var	(character) name of the analysis value unit variable.
aval_var	(character) name of the analysis value variable.
baseline_var	(character) name of the variable for baseline values of the analysis variable.
base_var	Please use the baseline_var argument instead.
basic_table_args	(basic_table_args) optional object created by teal.widgets::basic_table_args() with settings for the module table. The argument is merged with option teal.basic_table_args and with default module arguments (hard coded in the module body). For more details, see the vignette: vignette("custom-basic-table-arguments", package = "teal.widgets").
by_vars	(character) variable names used to split the summary by rows.
cmdecod	(character) name of standardized medication name variable.
cmindc	(character) name of indication variable.
cmstdy	(character) name of study relative day of start of medication variable.
cnsr_var	(character) name of the censoring variable.
combine_comp_arms	(logical) triggers the combination of comparison arms.
compare_arm	(logical) triggers the comparison between study arms.
comp_arm	(character) the level of comparison arm in case of arm comparison.
conf_level	(numeric) value for the confidence level within the range of (0, 1).
control	(list) list of settings for the analysis.
cov_var	(character) names of the covariates variables.
dataname	(character) analysis data used in teal module.
denominator	(character) chooses how percentages are calculated. With option N, the reference population from the column total is used as the denominator. With option n, the number of non-missing records in this row and column intersection is used as the denominator. If omit is chosen, then the percentage is omitted.
drop_arm_levels	(logical) whether to drop unused levels of arm_var. If TRUE, arm_var levels are set to those used in the dataname dataset. If FALSE, arm_var levels are set to those used in the parentname dataset. If dataname and parentname are the same, then drop_arm_levels is set to TRUE and user input for this parameter is ignored.
event_type	(character) type of event that is summarized (e.g. adverse event, treatment). Default is "event".
font_size	(numeric) font size value.
ggplot2_args	(ggplot2_args) optional 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). For more details, see the vignette: vignette("custom-ggplot2-arguments", package = "teal.widgets").
hlt	(character) name of the variable with high level term for events.
id_var	(character) the variable name for subject id.
include_interact	(logical) whether an interaction term should be included in the model.
label_hlt	(string) label of the hlt variable from dataname. The label will be extracted from the module.
label_llt	(string) label of the llt variable from dataname. The label will be extracted from the module.
llt	(character) name of the variable with low level term for events.
na_level	(string) 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").
na.rm	(logical) whether NA values should be removed prior to analysis.
numeric_stats	(character) names of statistics to display for numeric summary variables. Available statistics are n, mean_sd, mean_ci, median, median_ci, quantiles, range, and geom_mean.
paramcd	(character) name of the parameter code variable.
parentname	(character) parent analysis data used in teal module, usually this refers to ADSL.
patient_id	(character) patient ID.
prune_diff	(number) threshold to use for trimming table using as criteria difference in rates between any two columns.
prune_freq	(number) threshold to use for trimming table using event incidence rate in any column.
ref_arm	(character) the level of reference arm in case of arm comparison.
sort_criteria	(character) how to sort the final table. Default option freq_desc sorts on column sort_freq_col by decreasing number of patients with event. Alternative option alpha sorts events alphabetically.
strata_var	(character) names of the variables for stratified analysis.
subgroup_var	(character) with variable names that can be used as subgroups.
sum_vars	(character) names of the variables that should be summarized.
time_points	(character) time points that can be used in tern::surv_timepoint().
time_unit_var	(character) name of the variable representing time units.
title	(character) title of the output.
total_label	(string) string to display as total column/row label if column/row is enabled (see add_total). Defaults to "All Patients". To set a new default total_label to apply in all modules, run set_default_total_label("new_default").
treatment_flag	(character) name of the value indicating on treatment records in treatment_flag_var.
treatment_flag_var	(character) name of the on treatment flag variable.
useNA	(character) whether missing data (NA) should be displayed as a level.
var_labels	(named character) optional variable labels for relabeling the analysis variables.
visit_var	(character) variable names that can be used as visit variable. Must be a factor in dataname.
worst_flag_indicator	(character) value indicating worst grade.
worst_flag_var	(character) name of the worst flag variable.

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 template_arguments⁠

Value

a list of expressions to generate a table or plot object.

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