tests/testthat/test-who.R

In icd: Comorbidity Calculations and Tools for ICD-9 and ICD-10 Codes

context("WHO")

test_that("No ranges or NA in code section of WHO data", {
  skip_multi()
  skip_missing_dat("icd10who2016")
  skip_missing_dat("icd10who2008fr")
  for (nm in c("icd10who2016", "icd10who2008fr")) {
    if (!.exists_in_cache(nm)) {
      skip(paste(nm, "not available for testing."))
    }
    i <- get_icd_data(nm)
    # structure tests
    expect_true(is.data.frame(i), info = nm)
    expect_false(any(grepl("-", i$code)), info = nm)
    expect_false(any(is.na(i$code)), info = nm)
    expect_false(any(is.na(i$leaf)), info = nm)
    expect_false(any(is.na(i$desc)), info = nm)
    expect_false(any(is.na(i$three_digit)), info = nm)
    expect_false(any(is.na(i$major)), info = nm)
    # sub_sub_chapter may be NA
    expect_false(any(is.na(i$sub_chapter)), info = nm)
    expect_false(any(is.na(i$chapter)), info = nm)
    # data tests
    expect_true(!anyDuplicated(i$code), info = nm)
  }
})

test_that("HIV is problematic for some reason", {
  skip_multi()
  skip_missing_dat("icd10who2016")
  b21 <- .dl_icd10who_children("B21")
  expect_match(b21$ID, "^B21\\.[0-9]$")
})

test_that("Some codes beginning with Roman numerals were missed", {
  test_that("we do download the relevant blocks", {
    skip_multi()
    skip_if_offline()
    expect_true(nrow(.dl_icd10who_children("I10-I15")) > 1)
    expect_true(nrow(.dl_icd10who_walk("I10-I15")) > 1)
  })
  skip_missing_icd10who()
  expect_equal_no_icd(
    explain_code(as.icd10who(c("V13", "X13", "I10"))),
    c(
      "Essential (primary) hypertension",
      "Pedal cyclist injured in collision with car, pick-up truck or van",
      "Contact with steam and hot vapours"
    )
  )
  expect_equal_no_icd(
    explain_code(as.icd10who(c("V13", "X13", "I10")), lang = "fr"),
    c(
      "Hypertension essentielle (primitive)",
      "Cycliste bless\u00e9 dans une collision avec une automobile ou une camionnette",
      "Contact avec de la vapeur d'eau et des vapeurs br\u00fblantes"
    )
  )
})