template_abnormality: Template: Abnormality Summary Table

View source: R/tm_t_abnormality.R

template_abnormalityR Documentation

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.