tm_t_ancova: teal Module: ANCOVA Summary

Description

This module produces a table to summarize analysis of variance, consistent with the TLG Catalog template for AOVT01 available here when multiple endpoints are selected.

Usage

tm_t_ancova(
  label,
  dataname,
  parentname = ifelse(inherits(arm_var, "data_extract_spec"),
    teal.transform::datanames_input(arm_var), "ADSL"),
  arm_var,
  arm_ref_comp = NULL,
  aval_var,
  cov_var,
  include_interact = FALSE,
  interact_var = NULL,
  interact_y = FALSE,
  avisit,
  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()
)

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.
aval_var: (teal.transform::choices_selected())
object with all available choices and pre-selected option for the analysis variable.
cov_var: (teal.transform::choices_selected())
object with all available choices and preselected option for the covariates variables.
include_interact: (logical)
whether an interaction term should be included in the model.
interact_var: (character)
name of the variable that should have interactions with arm. If the interaction is not needed, the default option is NULL.
interact_y: (character)
a selected item from the interact_var column which will be used to select the specific ANCOVA results when interact_var is discrete. If the interaction is not needed, the default option is FALSE.
avisit: (teal.transform::choices_selected())
value of analysis visit AVISIT of interest.
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: 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

When a single endpoint is selected, both unadjusted and adjusted comparison are provided. This modules expects that the analysis data has the following variables:

AVISIT: variable used to filter for analysis visits.
PARAMCD: variable used to filter for endpoints, after filtering for paramcd and avisit, one observation per patient is expected for the analysis to be meaningful.

Examples

Run this code

ADSL <- tmc_ex_adsl
ADQS <- tmc_ex_adqs

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

app <- init(
  data = cdisc_data(
    ADSL = ADSL,
    ADQS = ADQS,
    code = "
      ADSL <- tmc_ex_adsl
      ADQS <- tmc_ex_adqs
    "
  ),
  modules = modules(
    tm_t_ancova(
      label = "ANCOVA Table",
      dataname = "ADQS",
      avisit = choices_selected(
        choices = value_choices(ADQS, "AVISIT"),
        selected = "WEEK 1 DAY 8"
      ),
      arm_var = choices_selected(
        choices = variable_choices(ADSL, c("ARM", "ACTARMCD", "ARMCD")),
        selected = "ARMCD"
      ),
      arm_ref_comp = arm_ref_comp,
      aval_var = choices_selected(
        choices = variable_choices(ADQS, c("CHG", "AVAL")),
        selected = "CHG"
      ),
      cov_var = choices_selected(
        choices = variable_choices(ADQS, c("BASE", "STRATA1", "SEX")),
        selected = "STRATA1"
      ),
      paramcd = choices_selected(
        choices = value_choices(ADQS, "PARAMCD", "PARAM"),
        selected = "FKSI-FWB"
      ),
      interact_var = choices_selected(
        choices = variable_choices(ADQS, c("BASE", "STRATA1", "SEX")),
        selected = "STRATA1"
      )
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}