teal.modules.clinical (version 0.9.0)

template_shift_by_grade: Template: Grade Summary Table

Description

Creates a valid expression to generate a grade summary table.

Usage

template_shift_by_grade(
  parentname,
  dataname,
  arm_var = "ARM",
  id_var = "USUBJID",
  visit_var = "AVISIT",
  worst_flag_var = c("WGRLOVFL", "WGRLOFL", "WGRHIVFL", "WGRHIFL"),
  worst_flag_indicator = "Y",
  anl_toxgrade_var = "ATOXGR",
  base_toxgrade_var = "BTOXGR",
  paramcd = "PARAMCD",
  drop_arm_levels = TRUE,
  add_total = FALSE,
  total_label = default_total_label(),
  na_level = default_na_str(),
  code_missing_baseline = FALSE,
  basic_table_args = teal.widgets::basic_table_args()
)

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.

visit_var

(character)
variable names that can be used as visit variable. Must be a factor in dataname.

worst_flag_var

(character)
name of the worst flag variable.

worst_flag_indicator

(character)
value indicating worst grade.

anl_toxgrade_var

(character)
name of the variable indicating the analysis toxicity grade.

base_toxgrade_var

(character)
name of the variable indicating the baseline toxicity grade.

paramcd

(character)
name of the parameter code variable.

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.

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").

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").

code_missing_baseline

(logical)
whether missing baseline grades should be counted as grade 0.

basic_table_args

optional, (basic_table_args)
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").

See Also

tm_t_shift_by_grade()