teal.modules.clinical (version 0.9.0)

template_events_col_by_grade: Template: Adverse Events Grouped by Grade with Threshold

Description

Creates a valid expression to generate a table to summarize adverse events grouped by grade.

Usage

template_events_col_by_grade(
  dataname,
  parentname,
  arm_var,
  grading_groups = list(`Any Grade (%)` = c("1", "2", "3", "4", "5"), `Grade 1-2 (%)` =
    c("1", "2"), `Grade 3-4 (%)` = c("3", "4"), `Grade 5 (%)` = "5"),
  add_total = TRUE,
  total_label = default_total_label(),
  id = "USUBJID",
  hlt,
  llt,
  label_hlt = NULL,
  label_llt = NULL,
  grade = "AETOXGR",
  label_grade = NULL,
  prune_freq = 0.1,
  prune_diff = 0,
  na_level = default_na_str(),
  drop_arm_levels = TRUE,
  basic_table_args = teal.widgets::basic_table_args()
)

Value

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

Arguments

dataname

(character)
analysis data used in teal module.

parentname

(character)
parent analysis data used in teal module, usually this refers to ADSL.

arm_var

(character)
variable names that can be used as arm_var.

grading_groups

(list)
named list of grading groups.

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").

id

(character)
name of variable to uniquely identify patients in datasets.

hlt

(character)
name of the variable with high level term for events.

llt

(character)
name of the variable with low level term for events.

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.

grade

(character)
name of grade variable to base grading_groups on.

label_grade

(character)
label of the grade variable from dataname.

prune_freq

(number)
threshold to use for trimming table using event incidence rate in any column.

prune_diff

(number)
threshold to use for trimming table using as criteria difference in rates between any two columns.

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").

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.

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_events_by_grade()