teal.modules.clinical (version 0.9.0)

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()
)

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(s) in the results table. If there are two elements selected for arm_var, second variable will be nested under the first variable.

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

optional, (shiny.tag)
with text placed before the output to put the output into context. For example a title.

post_output

optional, (shiny.tag)
with text placed after the output to put the output into context. For example the shiny::helpText() elements are useful.

basic_table_args

optional, (basic_table_args)
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").

See Also

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

Examples

ADSL <- tmc_ex_adsl
ADEG <- tmc_ex_adeg

app <- init(
  data = cdisc_data(
    ADSL = ADSL,
    ADEG = ADEG,
    code = "
      ADSL <- tmc_ex_adsl
      ADEG <- tmc_ex_adeg
    "
  ),
  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)
}