teal.modules.clinical (version 0.10.0)

template_abnormality: 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
)

Value

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

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

See Also

tm_t_abnormality()