template_abnormality: Template: Abnormality Summary Table

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

Template: Abnormality Summary Table

Description

Creates a valid expression to generate a table to summarize abnormality.

Usage

template_abnormality(
  parentname,
  dataname,
  arm_var,
  id_var = "USUBJID",
  by_vars,
  abnormal = list(low = c("LOW", "LOW LOW"), high = c("HIGH", "HIGH HIGH")),
  grade = "ANRIND",
  baseline_var = "BNRIND",
  treatment_flag_var = "ONTRTFL",
  treatment_flag = "Y",
  add_total = FALSE,
  total_label = default_total_label(),
  exclude_base_abn = FALSE,
  drop_arm_levels = TRUE,
  na_level = default_na_str(),
  basic_table_args = teal.widgets::basic_table_args(),
  tbl_title
)

Arguments

parentname	(character) parent analysis data used in teal module, usually this refers to ADSL.
dataname	(character) analysis data used in teal module.
arm_var	(character) variable names that can be used as arm_var.
id_var	(character) the variable name for subject id.
by_vars	(character) variable names used to split the summary by rows.
abnormal	(⁠named list⁠) indicating abnormality direction and grades.
grade	(character) name of the variable used to specify the abnormality grade. Variable must be factor.
baseline_var	(character) name of the variable specifying baseline abnormality grade.
treatment_flag_var	(character) name of the on treatment flag variable.
treatment_flag	(character) name of the value indicating on treatment records in treatment_flag_var.
add_total	(logical) whether to include column with total number of patients.
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").
exclude_base_abn	(logical) whether to exclude patients who had abnormal values at baseline.
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.
na_level	(character) the NA level in the input dataset, defaults to "<Missing>".
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").
tbl_title	(character) Title with label of variables from by bars

Value

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

See Also

tm_t_abnormality()

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