tests/testthat/test-derive_vars_atc.R

In Roche-GSK/admiral: ADaM in R Asset Library

## Test 1: ATC variables are merged properly ----
test_that("derive_vars_atc Test 1: ATC variables are merged properly", {
  cm <- tibble::tribble(
    ~STUDYID,  ~USUBJID,       ~CMGRPID, ~CMREFID,  ~CMDECOD,
    "STUDY01", "BP40257-1001", "14",     "1192056", "PARACETAMOL",
    "STUDY01", "BP40257-1001", "18",     "2007001", "SOLUMEDROL",
    "STUDY01", "BP40257-1002", "19",     "2791596", "SPIRONOLACTONE"
  )
  facm <- tibble::tribble(
    ~STUDYID,  ~USUBJID,       ~FAGRPID, ~FAREFID,  ~FATESTCD,  ~FASTRESC,
    "STUDY01", "BP40257-1001", "1",      "1192056", "CMATC1CD", "N",
    "STUDY01", "BP40257-1001", "1",      "1192056", "CMATC2CD", "N02",
    "STUDY01", "BP40257-1001", "1",      "1192056", "CMATC3CD", "N02B",
    "STUDY01", "BP40257-1001", "1",      "1192056", "CMATC4CD", "N02BE",
    "STUDY01", "BP40257-1001", "1",      "2007001", "CMATC1CD", "D",
    "STUDY01", "BP40257-1001", "1",      "2007001", "CMATC2CD", "D10",
    "STUDY01", "BP40257-1001", "1",      "2007001", "CMATC3CD", "D10A",
    "STUDY01", "BP40257-1001", "1",      "2007001", "CMATC4CD", "D10AA",
    "STUDY01", "BP40257-1001", "2",      "2007001", "CMATC1CD", "D",
    "STUDY01", "BP40257-1001", "2",      "2007001", "CMATC2CD", "D07",
    "STUDY01", "BP40257-1001", "2",      "2007001", "CMATC3CD", "D07A",
    "STUDY01", "BP40257-1001", "2",      "2007001", "CMATC4CD", "D07AA",
    "STUDY01", "BP40257-1001", "3",      "2007001", "CMATC1CD", "H",
    "STUDY01", "BP40257-1001", "3",      "2007001", "CMATC2CD", "H02",
    "STUDY01", "BP40257-1001", "3",      "2007001", "CMATC3CD", "H02A",
    "STUDY01", "BP40257-1001", "3",      "2007001", "CMATC4CD", "H02AB",
    "STUDY01", "BP40257-1002", "1",      "2791596", "CMATC1CD", "C",
    "STUDY01", "BP40257-1002", "1",      "2791596", "CMATC2CD", "C03",
    "STUDY01", "BP40257-1002", "1",      "2791596", "CMATC3CD", "C03D",
    "STUDY01", "BP40257-1002", "1",      "2791596", "CMATC4CD", "C03DA"
  )
  # nolint start
  expected_output <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~CMGRPID, ~CMREFID, ~CMDECOD, ~ATC1CD, ~ATC2CD, ~ATC3CD, ~ATC4CD,
    "STUDY01", "BP40257-1001", "14", "1192056", "PARACETAMOL", "N", "N02", "N02B", "N02BE",
    "STUDY01", "BP40257-1001", "18", "2007001", "SOLUMEDROL", "D", "D07", "D07A", "D07AA",
    "STUDY01", "BP40257-1001", "18", "2007001", "SOLUMEDROL", "D", "D10", "D10A", "D10AA",
    "STUDY01", "BP40257-1001", "18", "2007001", "SOLUMEDROL", "H", "H02", "H02A", "H02AB",
    "STUDY01", "BP40257-1002", "19", "2791596", "SPIRONOLACTONE", "C", "C03", "C03D", "C03DA"
  )
  # nolint end
  actual_output <- derive_vars_atc(
    dataset = cm,
    dataset_facm = facm,
    id_vars = exprs(FAGRPID)
  )

  expect_dfs_equal(expected_output, actual_output, keys = c("USUBJID", "CMDECOD", "ATC4CD"))
})

## Test 2: error if facm not unique ----
test_that("derive_vars_atc Test 2: error if facm not unique", {
  cm <- tibble::tribble(
    ~STUDYID,  ~USUBJID,       ~CMGRPID, ~CMREFID,  ~CMDECOD,
    "STUDY01", "BP40257-1001", "14",     "1192056", "PARACETAMOL",
    "STUDY01", "BP40257-1001", "18",     "2007001", "SOLUMEDROL",
    "STUDY01", "BP40257-1002", "19",     "2791596", "SPIRONOLACTONE"
  )
  facm <- tibble::tribble(
    ~STUDYID,  ~USUBJID,       ~FAGRPID, ~FAREFID,  ~FATESTCD,  ~FASTRESC,
    "STUDY01", "BP40257-1001", "1",      "1192056", "CMATC1CD", "N",
    "STUDY01", "BP40257-1001", "1",      "1192056", "CMATC2CD", "N02",
    "STUDY01", "BP40257-1001", "1",      "1192056", "CMATC3CD", "N02B",
    "STUDY01", "BP40257-1001", "1",      "1192056", "CMATC4CD", "N02BE",
    "STUDY01", "BP40257-1001", "1",      "2007001", "CMATC1CD", "D",
    "STUDY01", "BP40257-1001", "1",      "2007001", "CMATC2CD", "D10",
    "STUDY01", "BP40257-1001", "1",      "2007001", "CMATC3CD", "D10A",
    "STUDY01", "BP40257-1001", "1",      "2007001", "CMATC4CD", "D10AA",
    "STUDY01", "BP40257-1001", "2",      "2007001", "CMATC1CD", "D",
    "STUDY01", "BP40257-1001", "2",      "2007001", "CMATC2CD", "D07",
    "STUDY01", "BP40257-1001", "2",      "2007001", "CMATC3CD", "D07A",
    "STUDY01", "BP40257-1001", "2",      "2007001", "CMATC4CD", "D07AA",
    "STUDY01", "BP40257-1001", "3",      "2007001", "CMATC1CD", "H",
    "STUDY01", "BP40257-1001", "3",      "2007001", "CMATC2CD", "H02",
    "STUDY01", "BP40257-1001", "3",      "2007001", "CMATC3CD", "H02A",
    "STUDY01", "BP40257-1001", "3",      "2007001", "CMATC4CD", "H02AB",
    "STUDY01", "BP40257-1002", "1",      "2791596", "CMATC1CD", "C",
    "STUDY01", "BP40257-1002", "1",      "2791596", "CMATC2CD", "C03",
    "STUDY01", "BP40257-1002", "1",      "2791596", "CMATC3CD", "C03D",
    "STUDY01", "BP40257-1002", "1",      "2791596", "CMATC4CD", "C03DA"
  )

  expect_snapshot(
    derive_vars_atc(
      dataset = cm,
      dataset_facm = facm
    ),
    error = TRUE
  )
})