Exercise 2

Enhance your application with pre-built modules!

Reference:

• teal.modules.general::tm_data_table() to create a data previewer module
• teal.modules.clinical::tm_t_summary() to create a demographic summary table:
  • please read the documentation - especially arm_var and summarize_vars argument and what data type it takes
  • use both "ARM" and "ARMCD" as arm_var
  • use "SEX", "AGE" and "RACE" as summarize_vars

Example

library(dplyr)
library(teal.modules.general)
library(teal.modules.clinical)

# Prepare data object
data <- teal_data()
data <- within(data, {
  ADSL <- rADSL
})
join_keys(data) <- default_cdisc_join_keys["ADSL"]


# Prepare module inputs
ADSL <- data[["ADSL"]]

cs_arm_var <- choices_selected(
  choices = variable_choices(ADSL, subset = c("ARMCD", "ARM")),
  selected = "ARM"
)

demog_vars_adsl <- ADSL |>
  select(where(is.numeric) | where(is.factor)) |>
  names()


# Create app
app <- init(
  data = data,
  modules = list(
    tm_data_table("Data Table"),
    tm_t_summary(
      label = "Demographic Table",
      dataname = "ADSL",
      arm_var = cs_arm_var,
      summarize_vars = choices_selected(
        choices = variable_choices(ADSL, demog_vars_adsl),
        selected = c("SEX", "AGE", "RACE")
      )
    )
  )
)

if (Sys.getenv("QUARTO_ROOT") == "") {
  shinyApp(app$ui, app$server)
}

App

Exercise

Open editor in Shinylive

The module output requires further tweaks:

• We dont’ want to have “ALL PATIENT” column - let’s remove it. Please read function documentation and identify the argument to be changed.

  Answer

  tm_t_summary(
    ...,
    add_total = FALSE
  )

• It is possible to select “ARM” in the “Summarize Variables” input which does not make much sense. Let’s limit the selection to only a few interesting columns of your choice. Which object to change?

  Answer

  # explicit
  demog_vars_adsl <- c("AGE", "SEX", "RACE", ...)
  # alternatively: exclude
  demog_vars_adsl <- ... |> setdiff(c("AGE", ...))

• Let’s create two modules in the same application - one with “ARM” column as arm_var and the other with “ARMCD”.

  Answer

  app <- init(
    ...
    modules = list(
      ...,
      tm_t_summary(
        ...,
        arm_var = choices_selected("ARM", "ARM", fixed = TRUE)
      ),
      tm_t_summary(
        ...,
        arm_var = choices_selected("ARMCD", "ARMCD", fixed = TRUE)
      )
    )
  )