Exercise 2

Enhance your application with pre-built modules!

• use teal.modules.general::tm_front_page() to create the first “welcome screen” of the application
• use teal.modules.general::tm_data_table() to create a data previewer module
• use 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

Code

library(dplyr)
library(random.cdisc.data)
library(nestcolor)
library(teal.modules.general)
library(teal.modules.clinical)

## Data reproducible code ----
data <- teal_data()
data <- within(data, {
  ADSL <- radsl(cached = TRUE)
  adsl_labels <- col_labels(ADSL, fill = FALSE)

  char_vars_asl <- names(Filter(isTRUE, sapply(ADSL, is.character)))
})
# set datanames
datanames <- c("ADSL")
datanames(data) <- datanames
# set join_keys
join_keys(data) <- default_cdisc_join_keys[datanames]


## Reusable Configuration For Modules
ADSL <- data[["ADSL"]]

arm_vars <- c("ARMCD", "ARM")

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


date_vars_asl <- names(ADSL)[vapply(ADSL, function(x) inherits(x, c("Date", "POSIXct", "POSIXlt")), logical(1))]
demog_vars_asl <- names(ADSL)[!(names(ADSL) %in% c("USUBJID", "STUDYID", date_vars_asl))]


header <- tags$span(
  style = "display: flex; align-items: center; justify-content: space-between; margin: 10px 0 10px 0;",
  tags$span("Exercise 1", style = "font-size: 30px;"),
)

footer <- tags$p(
  "This teal app is brought to you by PhUSE SDE Basel",
)


app <- init(
  data = data,
  modules = modules(
    tm_front_page(
      label = "App Info",
      header_text = c(
        "Info about input data source" =
          "This app uses CDISC ADaM datasets randomly generated by `random.cdisc.data` R packages"
      ),
      tables = list(`NEST packages used in this demo app` = data.frame(
        Packages = c("teal.modules.general", "teal.modules.clinical", "random.cdisc.data")
      ))
    ),
    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_asl),
        selected = c("SEX", "AGE", "RACE")
      )
    )
  ),
  title = build_app_title("Basic Teal Demo App"),
  header = header,
  footer = footer
)

[INFO] 2024-10-20 10:32:43.0237 pid:6025 token:[] teal.modules.general Initializing tm_front_page
[INFO] 2024-10-20 10:32:43.0265 pid:6025 token:[] teal.modules.general Initializing tm_data_table

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

URL

Open in Shinylive

App