tm_t_ancova {teal.modules.clinical}

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()
)

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

(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.

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

(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").

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.

Value

a teal_module object.

See Also

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

Examples

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)
}