tm_t_summary {teal.modules.clinical} | R Documentation |
teal Module: Summary of Variables
Description
This module produces a table to summarize variables.
Usage
tm_t_summary(
label,
dataname,
parentname = ifelse(inherits(arm_var, "data_extract_spec"),
teal.transform::datanames_input(arm_var), "ADSL"),
arm_var,
summarize_vars,
add_total = TRUE,
total_label = default_total_label(),
useNA = c("ifany", "no"),
na_level = default_na_str(),
numeric_stats = c("n", "mean_sd", "mean_ci", "median", "median_ci", "quantiles",
"range", "geom_mean"),
denominator = c("N", "n", "omit"),
drop_arm_levels = 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.
|
summarize_vars |
(teal.transform::choices_selected() ) names of
the variables that should be summarized.
|
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") .
|
useNA |
(character ) whether missing data (NA ) should be displayed as a level.
|
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") .
|
numeric_stats |
(character ) names of statistics to display for numeric summary variables. Available
statistics are n , mean_sd , mean_ci , median , median_ci , quantiles , range , and geom_mean .
|
denominator |
(character ) chooses how percentages are calculated. With option N , the reference
population from the column total is used as the denominator. With option n , the number of non-missing
records in this row and column intersection is used as the denominator. If omit is chosen, then the
percentage is omitted.
|
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.
|
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
# Preparation of the test case - use `EOSDY` and `DCSREAS` variables to demonstrate missing data.
ADSL <- tmc_ex_adsl
ADSL$EOSDY[1] <- NA_integer_
app <- init(
data = cdisc_data(
ADSL = ADSL,
code = "
ADSL <- tmc_ex_adsl
ADSL$EOSDY[1] <- NA_integer_
"
),
modules = modules(
tm_t_summary(
label = "Demographic Table",
dataname = "ADSL",
arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
add_total = TRUE,
summarize_vars = choices_selected(
c("SEX", "RACE", "BMRKR2", "EOSDY", "DCSREAS", "AGE"),
c("SEX", "RACE")
),
useNA = "ifany"
)
)
)
if (interactive()) {
shinyApp(app$ui, app$server)
}
[Package
teal.modules.clinical version 0.9.1
Index]