tests/testthat/test-aet04.R

In chevron: Standard TLGs for Clinical Trials Reporting

test_that("aet04 can handle NA values", {
  proc_data <- syn_data
  proc_data$adae <- proc_data$adae %>%
    mutate(
      AEBODSYS = with_label(NA_character_, var_labels_for(syn_data$adae, "AEBODSYS")),
      AEDECOD = with_label(NA_character_, var_labels_for(syn_data$adae, "AEDECOD"))
    )

  res1 <- expect_silent(run(aet04, proc_data))
  expect_snapshot(cat(export_as_txt(res1, lpp = 100)))
  skip_on_os("windows")
  grade_groups <- list(
    "Grade 1-2" = c("1", "2"),
    "Grade 3-4" = c("3", "4"),
    "Grade 5" = c("5")
  )
  res2 <- expect_silent(run(aet04, proc_data, grade_groups = grade_groups))
  expect_identical(res1, res2)

  grade_groups <- list(
    "Grade 1-2" = c("1", "2"),
    "Grade 3-5" = c("3", "4", "5")
  )
  res3 <- expect_silent(run(aet04, proc_data, grade_groups = grade_groups))
  expect_snapshot(cat(export_as_txt(res3, lpp = 100)))
})

test_that("aet04 can handle some NA values", {
  skip_on_os("windows")
  proc_data <- syn_data
  proc_data$adae[1:2, c("AEBODSYS", "AEDECOD")] <- NA
  res1 <- expect_silent(run(aet04, proc_data))
  expect_snapshot(cat(export_as_txt(res1, lpp = 100)))

  grade_groups <- list(
    "Grade 1-2" = c("1", "2"),
    "Grade 3-4" = c("3", "4"),
    "Grade 5" = c("5")
  )
  res2 <- expect_silent(run(aet04, proc_data, grade_groups = grade_groups))
  expect_identical(res1, res2)

  grade_groups <- list(
    "Grade 1-2" = c("1", "2"),
    "Grade 3-5" = c("3", "4", "5")
  )
  res3 <- expect_silent(run(aet04, proc_data, grade_groups = grade_groups))
  expect_snapshot(cat(export_as_txt(res3, lpp = 100)))
})