teal.modules.clinical (version 0.9.0)

tm_t_tte: teal Module: Time-To-Event Table

Description

This module produces a time-to-event analysis summary table, consistent with the TLG Catalog template for TTET01 available here.

Usage

tm_t_tte(
  label,
  dataname,
  parentname = ifelse(inherits(arm_var, "data_extract_spec"),
    teal.transform::datanames_input(arm_var), "ADSL"),
  arm_var,
  arm_ref_comp = NULL,
  paramcd,
  strata_var,
  aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    "AVAL"), "AVAL", fixed = TRUE),
  cnsr_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    "CNSR"), "CNSR", fixed = TRUE),
  conf_level_coxph = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order
    = TRUE),
  conf_level_survfit = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95,
    keep_order = TRUE),
  time_points,
  time_unit_var =
    teal.transform::choices_selected(teal.transform::variable_choices(dataname, "AVALU"),
    "AVALU", fixed = TRUE),
  event_desc_var = teal.transform::choices_selected("EVNTDESC", "EVNTDESC", fixed = TRUE),
  add_total = FALSE,
  total_label = default_total_label(),
  na_level = default_na_str(),
  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.

arm_ref_comp

optional, (list)
If specified it must be a named list with each element corresponding to an arm variable in ADSL and the element must be another list (possibly with delayed teal.transform::variable_choices() or delayed teal.transform::value_choices() with the elements named ref and comp that the defined the default reference and comparison arms when the arm variable is changed.

paramcd

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

strata_var

(teal.transform::choices_selected())
names of the variables for stratified analysis.

aval_var

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

cnsr_var

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

conf_level_coxph

(teal.transform::choices_selected())
object with all available choices and pre-selected option for confidence level, each within range of (0, 1).

conf_level_survfit

(teal.transform::choices_selected())
object with all available choices and pre-selected option for confidence level, each within range of (0, 1).

time_points

(teal.transform::choices_selected())
object with all available choices and preselected option for time points that can be used in tern::surv_timepoint().

time_unit_var

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

event_desc_var

(character or data_extract_spec())
variable name with the event description information, optional.

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").

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

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").

Details

• The core functionality of this module is based on coxph_pairwise(), surv_timepoint(), and surv_time() from the tern package.

• The arm and stratification variables are taken from the parentname data.

• The following variables are used in the module:

  • AVAL: time to event

  • CNSR: 1 if record in AVAL is censored, 0 otherwise

  • PARAMCD: variable used to filter for endpoint (e.g. OS). After filtering for PARAMCD one observation per patient is expected

See Also

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

Examples

ADSL <- tmc_ex_adsl
ADTTE <- tmc_ex_adtte

arm_ref_comp <- list(
  ACTARMCD = list(
    ref = "ARM B",
    comp = c("ARM A", "ARM C")
  ),
  ARM = list(
    ref = "B: Placebo",
    comp = c("A: Drug X", "C: Combination")
  )
)

app <- init(
  data = cdisc_data(
    ADSL = ADSL,
    ADTTE = ADTTE,
    code = "
      ADSL <- tmc_ex_adsl
      ADTTE <- tmc_ex_adtte
    "
  ),
  modules = modules(
    tm_t_tte(
      label = "Time To Event Table",
      dataname = "ADTTE",
      arm_var = choices_selected(
        variable_choices(ADSL, c("ARM", "ARMCD", "ACTARMCD")),
        "ARM"
      ),
      arm_ref_comp = arm_ref_comp,
      paramcd = choices_selected(
        value_choices(ADTTE, "PARAMCD", "PARAM"),
        "OS"
      ),
      strata_var = choices_selected(
        variable_choices(ADSL, c("SEX", "BMRKR2")),
        "SEX"
      ),
      time_points = choices_selected(c(182, 243), 182),
      event_desc_var = choices_selected(
        variable_choices(ADTTE, "EVNTDESC"),
        "EVNTDESC",
        fixed = TRUE
      )
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}