tm_t_events {teal.modules.clinical} | R Documentation |
teal Module: Events by Term
Description
This module produces a table of events by term.
Usage
tm_t_events(
label,
dataname,
parentname = ifelse(inherits(arm_var, "data_extract_spec"),
teal.transform::datanames_input(arm_var), "ADSL"),
arm_var,
hlt,
llt,
add_total = TRUE,
total_label = default_total_label(),
na_level = default_na_str(),
event_type = "event",
sort_criteria = c("freq_desc", "alpha"),
sort_freq_col = total_label,
prune_freq = 0,
prune_diff = 0,
drop_arm_levels = TRUE,
incl_overall_sum = TRUE,
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args()
)
Arguments
label |
(character ) menu item label of the module in the teal app.
|
dataname |
(character ) analysis data used in teal module.
|
parentname |
(character ) parent analysis data used in teal module, usually this refers to ADSL .
|
arm_var |
(teal.transform::choices_selected() ) object with all
available choices and preselected option for variable names that can be used as arm_var .
It defines the grouping variable(s) in the results table.
If there are two elements selected for arm_var ,
second variable will be nested under the first variable.
|
hlt |
(teal.transform::choices_selected() ) name of the variable
with high level term for events.
|
llt |
(teal.transform::choices_selected() ) name of the variable
with low level term for events.
|
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") .
|
event_type |
(character ) type of event that is summarized (e.g. adverse event, treatment). Default
is "event" .
|
sort_criteria |
(character ) how to sort the final table. Default option freq_desc sorts
on column sort_freq_col by decreasing number of patients with event. Alternative option alpha sorts events
alphabetically.
|
sort_freq_col |
(character ) column to sort by frequency on if sort_criteria is set to freq_desc .
|
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.
|
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.
|
incl_overall_sum |
(flag ) whether two rows which summarize the overall number of adverse events
should be included at the top of the table.
|
pre_output |
(shiny.tag ) optional, with text placed before the output to put the output into context.
For example a title.
|
post_output |
(shiny.tag ) optional, with text placed after the output to put the output into context.
For example the shiny::helpText() elements are useful.
|
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 teal_module
object.
See Also
The TLG Catalog where additional example
apps implementing this module can be found.
Examples
ADSL <- tmc_ex_adsl
ADAE <- tmc_ex_adae
app <- init(
data = cdisc_data(
ADSL = ADSL,
ADAE = ADAE,
code = "
ADSL <- tmc_ex_adsl
ADAE <- tmc_ex_adae
"
),
modules = modules(
tm_t_events(
label = "Adverse Event Table",
dataname = "ADAE",
arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
llt = choices_selected(
choices = variable_choices(ADAE, c("AETERM", "AEDECOD")),
selected = c("AEDECOD")
),
hlt = choices_selected(
choices = variable_choices(ADAE, c("AEBODSYS", "AESOC")),
selected = "AEBODSYS"
),
add_total = TRUE,
event_type = "adverse event"
)
)
)
if (interactive()) {
shinyApp(app$ui, app$server)
}
[Package
teal.modules.clinical version 0.9.1
Index]