teal.modules.clinical (version 0.10.0)

tm_g_forest_tte: teal Module: Forest Survival Plot

Description

This module produces a grid-style forest plot for time-to-event data with ADaM structure.

Usage

tm_g_forest_tte(
  label,
  dataname,
  parentname = ifelse(inherits(arm_var, "data_extract_spec"),
    teal.transform::datanames_input(arm_var), "ADSL"),
  arm_var,
  arm_ref_comp = NULL,
  subgroup_var,
  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),
  stats = c("n_tot_events", "n_events", "median", "hr", "ci"),
  riskdiff = NULL,
  conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =
    TRUE),
  time_unit_var =
    teal.transform::choices_selected(teal.transform::variable_choices(dataname, "AVALU"),
    "AVALU", fixed = TRUE),
  fixed_symbol_size = TRUE,
  plot_height = c(500L, 200L, 2000L),
  plot_width = c(1500L, 800L, 3000L),
  rel_width_forest = c(25L, 0L, 100L),
  font_size = c(15L, 1L, 30L),
  pre_output = NULL,
  post_output = NULL,
  ggplot2_args = teal.widgets::ggplot2_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.

arm_ref_comp

(list) optional,
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.

subgroup_var

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

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.

stats

(character)
the names of statistics to be reported among:

• n_tot_events: Total number of events per group.

• n_events: Number of events per group.

• n_tot: Total number of observations per group.

• n: Number of observations per group.

• median: Median survival time.

• hr: Hazard ratio.

• ci: Confidence interval of hazard ratio.

• pval: p-value of the effect. Note, one of the statistics n_tot and n_tot_events, as well as both hr and ci are required.

riskdiff

(list)
if a risk (proportion) difference column should be added, a list of settings to apply within the column. See tern::control_riskdiff() for details. If NULL, no risk difference column will be added.

conf_level

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

time_unit_var

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

fixed_symbol_size

(logical)
When (TRUE), the same symbol size is used for plotting each estimate. Otherwise, the symbol size will be proportional to the sample size in each each subgroup.

plot_height

(numeric) optional
vector of length three with c(value, min, max). Specifies the height of the main plot and renders a slider on the plot to interactively adjust the plot height.

plot_width

(numeric) optional
vector of length three with c(value, min, max). Specifies the width of the main plot and renders a slider on the plot to interactively adjust the plot width.

rel_width_forest

(proportion)
proportion of total width to allocate to the forest plot. Relative width of table is then 1 - rel_width_forest. If as_list = TRUE, this parameter is ignored.

font_size

(numeric(1))
font size.

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.

ggplot2_args

(ggplot2_args) optional
object created by teal.widgets::ggplot2_args() with settings for the module plot. The argument is merged with option teal.ggplot2_args and with default module arguments (hard coded in the module body). For more details, see the vignette: vignette("custom-ggplot2-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:

• plot (ggplot)

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_g_forest_tte(
   ..., # arguments for module
   decorators = list(
     plot = teal_transform_module(...) # applied only to `plot` 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

library(nestcolor)
library(dplyr)

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADTTE <- tmc_ex_adtte
  ADSL$RACE <- droplevels(ADSL$RACE) %>% with_label("Race")
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADTTE <- data[["ADTTE"]]

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

app <- init(
  data = data,
  modules = modules(
    tm_g_forest_tte(
      label = "Forest Survival",
      dataname = "ADTTE",
      arm_var = choices_selected(
        variable_choices(ADSL, c("ARM", "ARMCD")),
        "ARMCD"
      ),
      arm_ref_comp = arm_ref_comp,
      paramcd = choices_selected(
        value_choices(ADTTE, "PARAMCD", "PARAM"),
        "OS"
      ),
      subgroup_var = choices_selected(
        variable_choices(ADSL, names(ADSL)),
        c("BMRKR2", "SEX")
      ),
      strata_var = choices_selected(
        variable_choices(ADSL, c("STRATA1", "STRATA2")),
        "STRATA2"
      )
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}