template_events_col_by_grade {teal.modules.clinical} | R Documentation |
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()
)
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 |
(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") .
|
Value
a list
of expressions to generate a table or plot object.
See Also
tm_t_events_by_grade()
[Package
teal.modules.clinical version 0.9.1
Index]