teal Module: Logistic Regression

Usage

tm_t_logistic(
  label,
  dataname,
  parentname = ifelse(inherits(arm_var, "data_extract_spec"),
    teal.transform::datanames_input(arm_var), "ADSL"),
  arm_var = NULL,
  arm_ref_comp = NULL,
  paramcd,
  cov_var = NULL,
  avalc_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    "AVALC"), "AVALC", fixed = TRUE),
  conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =
    TRUE),
  pre_output = NULL,
  post_output = NULL,
  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() or NULL)
object with all available choices and preselected option for variable names that can be used as arm_var. This defines the grouping variable(s) in the results table. If there are two elements selected for arm_var, the second variable will be nested under the first variable. If NULL, no arm/treatment variable is included in the logistic model.

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.

paramcd

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

cov_var

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

avalc_var

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

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).

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.

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 (ElementaryTable - 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

library(dplyr)

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADRS <- tmc_ex_adrs %>%
    filter(PARAMCD %in% c("BESRSPI", "INVET"))
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADRS <- data[["ADRS"]]

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 = data,
  modules = modules(
    tm_t_logistic(
      label = "Logistic Regression",
      dataname = "ADRS",
      arm_var = choices_selected(
        choices = variable_choices(ADRS, c("ARM", "ARMCD")),
        selected = "ARM"
      ),
      arm_ref_comp = arm_ref_comp,
      paramcd = choices_selected(
        choices = value_choices(ADRS, "PARAMCD", "PARAM"),
        selected = "BESRSPI"
      ),
      cov_var = choices_selected(
        choices = c("SEX", "AGE", "BMRKR1", "BMRKR2"),
        selected = "SEX"
      )
    )
  )
)
#> Initializing tm_t_logistic
#> Initializing reporter_previewer_module
if (interactive()) {
  shinyApp(app$ui, app$server)
}