teal Module: Grade Summary Table

Usage

tm_t_shift_by_grade(
  label,
  dataname,
  parentname = ifelse(inherits(arm_var, "data_extract_spec"),
    teal.transform::datanames_input(arm_var), "ADSL"),
  arm_var,
  visit_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    subset = "AVISIT"), selected = "AVISIT", fixed = TRUE),
  paramcd,
  worst_flag_var =
    teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =
    c("WGRLOVFL", "WGRLOFL", "WGRHIVFL", "WGRHIFL")), selected = "WGRLOVFL"),
  worst_flag_indicator =
    teal.transform::choices_selected(teal.transform::value_choices(dataname, "WGRLOVFL"),
    selected = "Y", fixed = TRUE),
  anl_toxgrade_var =
    teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =
    c("ATOXGR")), selected = c("ATOXGR"), fixed = TRUE),
  base_toxgrade_var =
    teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =
    c("BTOXGR")), selected = c("BTOXGR"), fixed = TRUE),
  id_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    subset = "USUBJID"), selected = "USUBJID", fixed = TRUE),
  add_total = FALSE,
  total_label = default_total_label(),
  drop_arm_levels = TRUE,
  pre_output = NULL,
  post_output = NULL,
  na_level = default_na_str(),
  code_missing_baseline = FALSE,
  basic_table_args = teal.widgets::basic_table_args(),
  decorators = NULL
)

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.

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.

paramcd

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

worst_flag_var

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

worst_flag_indicator

(teal.transform::choices_selected())
value indicating worst grade.

anl_toxgrade_var

(teal.transform::choices_selected())
variable for analysis toxicity grade.

base_toxgrade_var

(teal.transform::choices_selected())
variable for baseline toxicity grade.

id_var

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

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").

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.

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").

code_missing_baseline

(logical)
whether missing baseline grades should be counted as grade 0.

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").

decorators

" (list of teal_transform_module, named list of teal_transform_module or" NULL) optional, if not NULL, decorator for tables or plots included in the module. When a named list of teal_transform_module, the decorators are applied to the respective output objects.

Otherwise, the decorators are applied to all objects, which is equivalent as using the name default.

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 (TableTree - output of rtables::build_table)

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

See also

Examples in Shinylive

example-1

Open in Shinylive

Examples

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

ADSL <- data[["ADSL"]]
ADLB <- data[["ADLB"]]

app <- init(
  data = data,
  modules = modules(
    tm_t_shift_by_grade(
      label = "Grade Laboratory Abnormality Table",
      dataname = "ADLB",
      arm_var = choices_selected(
        choices = variable_choices(ADSL, subset = c("ARM", "ARMCD")),
        selected = "ARM"
      ),
      paramcd = choices_selected(
        choices = value_choices(ADLB, "PARAMCD", "PARAM"),
        selected = "ALT"
      ),
      worst_flag_var = choices_selected(
        choices = variable_choices(ADLB, subset = c("WGRLOVFL", "WGRLOFL", "WGRHIVFL", "WGRHIFL")),
        selected = c("WGRLOVFL")
      ),
      worst_flag_indicator = choices_selected(
        value_choices(ADLB, "WGRLOVFL"),
        selected = "Y", fixed = TRUE
      ),
      anl_toxgrade_var = choices_selected(
        choices = variable_choices(ADLB, subset = c("ATOXGR")),
        selected = c("ATOXGR"),
        fixed = TRUE
      ),
      base_toxgrade_var = choices_selected(
        choices = variable_choices(ADLB, subset = c("BTOXGR")),
        selected = c("BTOXGR"),
        fixed = TRUE
      ),
      add_total = FALSE
    )
  ),
  filter = teal_slices(teal_slice("ADSL", "SAFFL", selected = "Y"))
)
#> Initializing tm_t_shift_by_grade
#> Initializing reporter_previewer_module
if (interactive()) {
  shinyApp(app$ui, app$server)
}