template_arguments: 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.

Value

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

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