teal Module: Mixed Model Repeated Measurements (MMRM) Analysis

This module produces analysis tables and plots for Mixed Model Repeated Measurements.

Usage

tm_a_mmrm(
  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,
  method = teal.transform::choices_selected(c("Satterthwaite", "Kenward-Roger",
    "Kenward-Roger-Linear"), "Satterthwaite", keep_order = TRUE),
  conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =
    TRUE),
  plot_height = c(700L, 200L, 2000L),
  plot_width = NULL,
  total_label = default_total_label(),
  pre_output = NULL,
  post_output = NULL,
  basic_table_args = teal.widgets::basic_table_args(),
  ggplot2_args = teal.widgets::ggplot2_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.
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(s) in the results table. If there are two elements selected for arm_var, second variable will be nested under the first variable.
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: 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.
paramcd: (teal.transform::choices_selected())
object with all available choices and preselected option for the parameter code variable from dataname.
method: (teal.transform::choices_selected())
object with all available choices and pre-selected option for the adjustment method.
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).
plot_height: optional, (numeric)
a 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: optional, (numeric)
a 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.
total_label: (string)
string to display as total column/row label if column/row is enabled (see add_total). Defaults to "All Patients". To set a new default total_label to apply in all modules, run set_default_total_label("new_default").
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").
ggplot2_args: (ggplot2_args)
optional, object created by teal.widgets::ggplot2_args() with settings for all the plots or named list of ggplot2_args objects for plot-specific settings. List names should match the following: c("default", "lsmeans", "diagnostic"). 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 help vignette: vignette("custom-ggplot2-arguments", package = "teal.widgets").

Value

a teal_module object.

Note

The ordering of the input data sets can lead to slightly different numerical results or different convergence behavior. This is a known observation with the used package lme4. However, once convergence is achieved, the results are reliable up to numerical precision.

Examples

library(dplyr)
arm_ref_comp <- list(
  ARMCD = list(
    ref = "ARM B",
    comp = c("ARM A", "ARM C")
  )
)

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADQS <- tmc_ex_adqs %>%
    filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
    filter(AVISIT %in% c("WEEK 1 DAY 8", "WEEK 2 DAY 15", "WEEK 3 DAY 22")) %>%
    mutate(
      AVISIT = as.factor(AVISIT),
      AVISITN = rank(AVISITN) %>%
        as.factor() %>%
        as.numeric() %>%
        as.factor() #' making consecutive numeric factor
    )
})

datanames <- c("ADSL", "ADQS")
datanames(data) <- datanames
join_keys(data) <- default_cdisc_join_keys[datanames]
app <- init(
  data = data,
  modules = modules(
    tm_a_mmrm(
      label = "MMRM",
      dataname = "ADQS",
      aval_var = choices_selected(c("AVAL", "CHG"), "AVAL"),
      id_var = choices_selected(c("USUBJID", "SUBJID"), "USUBJID"),
      arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
      visit_var = choices_selected(c("AVISIT", "AVISITN"), "AVISIT"),
      arm_ref_comp = arm_ref_comp,
      paramcd = choices_selected(
        choices = value_choices(data[["ADQS"]], "PARAMCD", "PARAM"),
        selected = "FKSI-FWB"
      ),
      cov_var = choices_selected(c("BASE", "AGE", "SEX", "BASE:AVISIT"), NULL)
    )
  )
)
#> [INFO] 2024-02-26 01:42:30.8314 pid:1518 token:[] teal.modules.clinical Initializing tm_a_mmrm
if (interactive()) {
  shinyApp(app$ui, app$server)
}