teal.modules.clinical (version 0.10.0)

tm_t_shift_by_arm: teal Module: Shift by Arm

Description

This module produces a summary table of analysis indicator levels by arm.

Usage

tm_t_shift_by_arm(
  label,
  dataname,
  parentname = ifelse(inherits(arm_var, "data_extract_spec"),
    teal.transform::datanames_input(arm_var), "ADSL"),
  arm_var,
  paramcd,
  visit_var,
  aval_var,
  base_var = lifecycle::deprecated(),
  baseline_var,
  treatment_flag_var =
    teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =
    "ONTRTFL"), selected = "ONTRTFL"),
  treatment_flag = teal.transform::choices_selected("Y"),
  useNA = c("ifany", "no"),
  na_level = default_na_str(),
  add_total = FALSE,
  total_label = default_total_label(),
  pre_output = NULL,
  post_output = NULL,
  basic_table_args = teal.widgets::basic_table_args(),
  transformators = list(),
  decorators = list()
)

Value

a teal_module object.

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 in the results table.

paramcd

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

visit_var

(teal.transform::choices_selected())
object with all available choices and preselected option for variable names that can be used as visit variable. Must be a factor in dataname.

aval_var

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

base_var

Please use the baseline_var argument instead.

baseline_var

(teal.transform::choices_selected())
object with all available choices and preselected option for variable values that can be used as baseline_var.

treatment_flag_var

(teal.transform::choices_selected())
on treatment flag variable.

treatment_flag

(teal.transform::choices_selected())
value indicating on treatment records in treatment_flag_var.

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").

add_total

(logical)
whether to include row 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").

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.

Decorating Module

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

• table (TableTree - output of 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_shift_by_arm(
   ..., # 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.

Examples in Shinylive

example-1

Open in Shinylive

See Also

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

Examples

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADEG <- tmc_ex_adeg
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADEG <- data[["ADEG"]]

app <- init(
  data = data,
  modules = modules(
    tm_t_shift_by_arm(
      label = "Shift by Arm Table",
      dataname = "ADEG",
      arm_var = choices_selected(
        variable_choices(ADSL, subset = c("ARM", "ARMCD")),
        selected = "ARM"
      ),
      paramcd = choices_selected(
        value_choices(ADEG, "PARAMCD"),
        selected = "HR"
      ),
      visit_var = choices_selected(
        value_choices(ADEG, "AVISIT"),
        selected = "POST-BASELINE MINIMUM"
      ),
      aval_var = choices_selected(
        variable_choices(ADEG, subset = "ANRIND"),
        selected = "ANRIND",
        fixed = TRUE
      ),
      baseline_var = choices_selected(
        variable_choices(ADEG, subset = "BNRIND"),
        selected = "BNRIND",
        fixed = TRUE
      ),
      useNA = "ifany"
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}