teal Module: Exposure Table for Risk management plan

The module produces an exposure table for risk management plan.

tm_t_exposure(
  label,
  dataname,
  parentname = ifelse(inherits(col_by_var, "data_extract_spec"),
    teal.transform::datanames_input(col_by_var), "ADSL"),
  row_by_var,
  col_by_var,
  paramcd = teal.transform::choices_selected(choices =
    teal.transform::value_choices(dataname, "PARAMCD", "PARAM"), selected = "TDURD"),
  paramcd_label = "PARAM",
  id_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    subset = "USUBJID"), selected = "USUBJID", fixed = TRUE),
  parcat,
  aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    subset = "AVAL"), selected = "AVAL", fixed = TRUE),
  avalu_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    subset = "AVALU"), selected = "AVALU", fixed = TRUE),
  add_total,
  total_label = default_total_label(),
  add_total_row = TRUE,
  total_row_label = "Total number of patients and patient time*",
  na_level = tern::default_na_str(),
  pre_output = NULL,
  post_output = NULL,
  basic_table_args = teal.widgets::basic_table_args(),
  transformators = list(),
  decorators = list()
)

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.

row_by_var

(teal.transform::choices_selected())
object with all available choices and preselected option for variable names that can be used to split rows.

col_by_var

(teal.transform::choices_selected())
object with all available choices and preselected option for variable names that can be used to split columns.

paramcd

(teal.transform::choices_selected())
object with all available choices and preselected option for the parameter code variable from dataname.

paramcd_label

(character)
the column from the dataset where the value will be used to label the argument paramcd.

id_var

(teal.transform::choices_selected())
object specifying the variable name for subject id.

parcat

(teal.transform::choices_selected())
object with all available choices and preselected option for parameter category values.

aval_var

(teal.transform::choices_selected())
object with all available choices and pre-selected option for the analysis variable.

avalu_var

(teal.transform::choices_selected())
object with all available choices and preselected option for the analysis unit variable.

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").

add_total_row

(flag)
whether a "total" level should be added after the others which includes all the levels that constitute the split. A custom label can be set for this level via the total_row_label argument.

total_row_label

(character)
string to display as total row label if row is enabled (see add_total_row).

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").

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").

transformators

(list of teal_transform_module) that will be applied to transform module's data input. To learn more check vignette("transform-input-data", package = "teal").

decorators

(named list of lists of teal_transform_module) optional, decorator for tables or plots included in the module output reported. The decorators are applied to the respective output objects.

See section "Decorating Module" below for more details.

Value

a teal_module object.

Decorating Module

This module generates the following objects, which can be modified in place using decorators:

• table (ElementaryTable as created from rtables::build_table)

A Decorator is applied to the specific output using a named list of teal_transform_module objects. The name of this list corresponds to the name of the output to which the decorator is applied. See code snippet below:

tm_t_exposure(
   ..., # arguments for module
   decorators = list(
     table = teal_transform_module(...) # applied only to `table` output
   )
)

For additional details and examples of decorators, refer to the vignette vignette("decorate-module-output", package = "teal.modules.clinical").

To learn more please refer to the vignette vignette("transform-module-output", package = "teal") or the teal::teal_transform_module() documentation.

See also

The TLG Catalog where additional example apps implementing this module can be found.

Examples in Shinylive

example-1

Open in Shinylive

Examples

library(dplyr)

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADEX <- tmc_ex_adex

  set.seed(1, kind = "Mersenne-Twister")
  .labels <- col_labels(ADEX, fill = FALSE)
  ADEX <- ADEX %>%
    distinct(USUBJID, .keep_all = TRUE) %>%
    mutate(
      PARAMCD = "TDURD",
      PARAM = "Overall duration (days)",
      AVAL = sample(x = seq(1, 200), size = n(), replace = TRUE),
      AVALU = "Days"
    ) %>%
    bind_rows(ADEX)
  col_labels(ADEX) <- .labels
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

app <- init(
  data = data,
  modules = modules(
    tm_t_exposure(
      label = "Duration of Exposure Table",
      dataname = "ADEX",
      paramcd = choices_selected(
        choices = value_choices(data[["ADEX"]], "PARAMCD", "PARAM"),
        selected = "TDURD"
      ),
      col_by_var = choices_selected(
        choices = variable_choices(data[["ADEX"]], subset = c("SEX", "ARM")),
        selected = "SEX"
      ),
      row_by_var = choices_selected(
        choices = variable_choices(data[["ADEX"]], subset = c("RACE", "REGION1", "STRATA1", "SEX")),
        selected = "RACE"
      ),
      parcat = choices_selected(
        choices = value_choices(data[["ADEX"]], "PARCAT2"),
        selected = "Drug A"
      ),
      add_total = FALSE
    )
  ),
  filter = teal_slices(teal_slice("ADSL", "SAFFL", selected = "Y"))
)
#> Initializing tm_t_exposure
if (interactive()) {
  shinyApp(app$ui, app$server)
}