tests/testthat/test-derive_var_base.R

In epijim/admiral: ADaM in R Asset Library

test_that("`target` is set to `source` where `ABLFL == 'Y'`", {
  input <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~PARAMCD,  ~ASEQ, ~AVAL, ~ABLFL, ~BASETYPE,
    "TEST01", "PAT01",  "PARAM01", 1,     10.12, "Y",    "LAST",
    "TEST01", "PAT01",  "PARAM01", 2,      9.7,  "",     "LAST",
    "TEST01", "PAT01",  "PARAM01", 3,     15.01, "",     "LAST",
    "TEST01", "PAT01",  "PARAM02", 1,      8.35, "Y",    "LAST",
    "TEST01", "PAT01",  "PARAM02", 2,     NA,    "",     "LAST",
    "TEST01", "PAT01",  "PARAM02", 3,      8.35, "",     "LAST",

    "TEST01", "PAT02",  "PARAM01", 1,     29,    "Y",    "LAST",
    "TEST01", "PAT02",  "PARAM01", 2,     19.7,  "",     "LAST",
    "TEST01", "PAT02",  "PARAM01", 3,     18.01, "",     "LAST",
    "TEST01", "PAT02",  "PARAM02", 1,      8.9,  "Y",    "LAST",
    "TEST01", "PAT02",  "PARAM02", 2,      9,    "",     "LAST",
    "TEST01", "PAT02",  "PARAM02", 3,      5.35, "",     "LAST"
  )
  expected_output <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~PARAMCD,  ~ASEQ, ~AVAL, ~ABLFL, ~BASETYPE, ~BASE,
    "TEST01", "PAT01",  "PARAM01", 1,     10.12, "Y",    "LAST",     10.12,
    "TEST01", "PAT01",  "PARAM01", 2,      9.7,  "",     "LAST",     10.12,
    "TEST01", "PAT01",  "PARAM01", 3,     15.01, "",     "LAST",     10.12,
    "TEST01", "PAT01",  "PARAM02", 1,      8.35, "Y",    "LAST",      8.35,
    "TEST01", "PAT01",  "PARAM02", 2,     NA,    "",     "LAST",      8.35,
    "TEST01", "PAT01",  "PARAM02", 3,      8.35, "",     "LAST",      8.35,

    "TEST01", "PAT02",  "PARAM01", 1,     29,    "Y",    "LAST",     29,
    "TEST01", "PAT02",  "PARAM01", 2,     19.7,  "",     "LAST",     29,
    "TEST01", "PAT02",  "PARAM01", 3,     18.01, "",     "LAST",     29,
    "TEST01", "PAT02",  "PARAM02", 1,      8.9,  "Y",    "LAST",      8.9,
    "TEST01", "PAT02",  "PARAM02", 2,      9,    "",     "LAST",      8.9,
    "TEST01", "PAT02",  "PARAM02", 3,      5.35, "",     "LAST",      8.9
  )
  actual_output <- derive_var_base(
    input,
    by_vars = vars(USUBJID, PARAMCD, BASETYPE),
    source_var = AVAL,
    new_var = BASE
  )

  expect_dfs_equal(
    expected_output,
    actual_output,
    keys = c("STUDYID", "USUBJID", "PARAMCD", "ASEQ")
  )
})

test_that("`target` is set to `NA` if a baseline record is missing", {
  input <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~PARAMCD,  ~ASEQ, ~AVAL, ~ABLFL, ~BASETYPE,
    "TEST01", "PAT01",  "PARAM01", 1,     10.12, "Y",    "LAST",
    "TEST01", "PAT01",  "PARAM01", 2,      9.7,  "",     "LAST",
    "TEST01", "PAT01",  "PARAM01", 3,     15.01, "",     "LAST",
    "TEST01", "PAT01",  "PARAM02", 1,      4.9,  "",     "LAST",
    "TEST01", "PAT01",  "PARAM02", 2,      7.1,  "",     "LAST",
    "TEST01", "PAT01",  "PARAM02", 3,      8.35, "",     "LAST"
  )
  expected_output <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~PARAMCD,  ~ASEQ, ~AVAL, ~ABLFL, ~BASETYPE, ~BASE,
    "TEST01", "PAT01",  "PARAM01", 1,     10.12, "Y",    "LAST",    10.12,
    "TEST01", "PAT01",  "PARAM01", 2,      9.7,  "",     "LAST",    10.12,
    "TEST01", "PAT01",  "PARAM01", 3,     15.01, "",     "LAST",    10.12,
    "TEST01", "PAT01",  "PARAM02", 1,      4.9,  "",     "LAST",    NA,
    "TEST01", "PAT01",  "PARAM02", 2,      7.1,  "",     "LAST",    NA,
    "TEST01", "PAT01",  "PARAM02", 3,      8.35, "",     "LAST",    NA
  )
  actual_output <- derive_var_base(
    input,
    by_vars = vars(USUBJID, PARAMCD, BASETYPE),
    source_var = AVAL,
    new_var = BASE
  )

  expect_dfs_equal(
    actual_output,
    expected_output,
    keys = c("STUDYID", "USUBJID", "PARAMCD", "ASEQ")
  )
})

test_that("only the `target` variable is added to the input dataset", {
  input <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~PARAMCD,  ~ASEQ, ~AVAL, ~ABLFL, ~BASETYPE, ~ANL01FL,
    "TEST01", "PAT01",  "PARAM01", 1,     10.12, "Y",    "LAST",    "Y",
    "TEST01", "PAT01",  "PARAM01", 2,      9.7,  "",     "LAST",    "Y",
    "TEST01", "PAT01",  "PARAM01", 3,     15.01, "",     "LAST",    "Y",
    "TEST01", "PAT01",  "PARAM02", 1,      8.35, "Y",    "LAST",    "Y",
    "TEST01", "PAT01",  "PARAM02", 2,     NA,    "",     "LAST",    "Y",
    "TEST01", "PAT01",  "PARAM02", 3,      8.35, "",     "LAST",    "Y"
  )
  expected_output <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~PARAMCD,  ~ASEQ, ~AVAL, ~ABLFL, ~BASETYPE, ~ANL01FL, ~BASE,
    "TEST01", "PAT01",  "PARAM01", 1,     10.12, "Y",    "LAST",    "Y",      10.12,
    "TEST01", "PAT01",  "PARAM01", 2,      9.7,  "",     "LAST",    "Y",      10.12,
    "TEST01", "PAT01",  "PARAM01", 3,     15.01, "",     "LAST",    "Y",      10.12,
    "TEST01", "PAT01",  "PARAM02", 1,      8.35, "Y",    "LAST",    "Y",       8.35,
    "TEST01", "PAT01",  "PARAM02", 2,     NA,    "",     "LAST",    "Y",       8.35,
    "TEST01", "PAT01",  "PARAM02", 3,      8.35, "",     "LAST",    "Y",       8.35
  )
  actual_output <- derive_var_base(
    input,
    by_vars = vars(USUBJID, PARAMCD, BASETYPE),
    source_var = AVAL,
    new_var = BASE
  )

  expect_dfs_equal(
    actual_output,
    expected_output,
    keys = c("STUDYID", "USUBJID", "PARAMCD", "ASEQ")
  )
})

test_that("An error is thrown if a subject has multiple records per `PARAMCD` and `BASETYPE`", {
  input <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~PARAMCD,  ~AVALC,   ~ABLFL, ~BASETYPE,
    "TEST01", "PAT01",  "PARAM01", "LOW",    "Y",    "LAST",
    "TEST01", "PAT01",  "PARAM01", "MEDIUM", "Y",    "LAST",
    "TEST01", "PAT01",  "PARAM01", "LOW",    "",     "LAST",
    "TEST01", "PAT01",  "PARAM01", "MEDIUM", "",     "LAST",
    "TEST01", "PAT02",  "PARAM02", "HIGH",   "Y",    "LAST",
    "TEST01", "PAT02",  "PARAM02", "HIGH",   "Y",    "LAST",
    "TEST01", "PAT02",  "PARAM02", "MEDIUM", "",     "LAST",
  )

  expect_error(
    derive_var_base(
      input,
      by_vars = vars(USUBJID, PARAMCD, BASETYPE),
      source_var = AVALC,
      new_var = BASEC
    ),
    "Dataset contains multiple baseline records."
  )
})