teal Module: Generalized Estimating Equations (GEE) analysis

This module produces an analysis table using Generalized Estimating Equations (GEE).

Usage

tm_a_gee(
  label,
  dataname,
  parentname = ifelse(inherits(arm_var, "data_extract_spec"),
    teal.transform::datanames_input(arm_var), "ADSL"),
  aval_var,
  id_var,
  arm_var,
  visit_var,
  cov_var,
  arm_ref_comp = NULL,
  paramcd,
  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(),
  transformators = list(),
  decorators = list()
)

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.

aval_var

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

id_var

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

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.

cov_var

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

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.

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").

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.

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())

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_a_gee(
   ..., # arguments for module
   decorators = list(
     table = teal_transform_module(...) # applied to the `table` 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

Examples

library(dplyr)
#> 
#> Attaching package: ‘dplyr’
#> The following object is masked from ‘package:testthat’:
#> 
#>     matches
#> The following objects are masked from ‘package:stats’:
#> 
#>     filter, lag
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, setdiff, setequal, union

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADQS <- tmc_ex_adqs %>%
    filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
    mutate(
      AVISIT = as.factor(AVISIT),
      AVISITN = rank(AVISITN) %>%
        as.factor() %>%
        as.numeric() %>%
        as.factor(),
      AVALBIN = AVAL < 50 # Just as an example to get a binary endpoint.
    ) %>%
    droplevels()
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

app <- init(
  data = data,
  modules = modules(
    tm_a_gee(
      label = "GEE",
      dataname = "ADQS",
      aval_var = choices_selected("AVALBIN", fixed = TRUE),
      id_var = choices_selected(c("USUBJID", "SUBJID"), "USUBJID"),
      arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
      visit_var = choices_selected(c("AVISIT", "AVISITN"), "AVISIT"),
      paramcd = choices_selected(
        choices = value_choices(data[["ADQS"]], "PARAMCD", "PARAM"),
        selected = "FKSI-FWB"
      ),
      cov_var = choices_selected(c("BASE", "AGE", "SEX", "BASE:AVISIT"), NULL)
    )
  )
)
#> Initializing tm_a_gee (prototype)
if (interactive()) {
  shinyApp(app$ui, app$server)
}