teal Module: Grade Summary Table

This module produces a summary table of worst grades per subject by visit and parameter.

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()
)

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.
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").

Value

a teal_module object.

Examples

ADSL <- tmc_ex_adsl
ADLB <- tmc_ex_adlb

app <- init(
  data = cdisc_data(
    ADSL = ADSL,
    ADLB = ADLB,
    code = "
      ADSL <- tmc_ex_adsl
      ADLB <- tmc_ex_adlb
    "
  ),
  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
if (interactive()) {
  shinyApp(app$ui, app$server)
}

Usage

Arguments

Value

See also

Examples