tests/testthat/test-derive_param_wbc_abs.R

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

test_that("Test 1: Test adding absolute records for each by group", {
  input <- tibble::tribble(
    ~USUBJID, ~PARAMCD, ~AVAL, ~PARAM, ~VISIT,
    "P01", "WBC", 33, "Leukocyte Count (10^9/L)", "CYCLE 1 DAY 1",
    "P01", "WBC", 38, "Leukocyte Count (10^9/L)", "CYCLE 2 DAY 1",
    "P01", "LYMLE", 0.9, "Lymphocytes (fraction of 1)", "CYCLE 1 DAY 1",
    "P01", "LYMLE", 0.6, "Lymphocytes (fraction of 1)", "CYCLE 2 DAY 1"
  )
  expected_output <- tibble::tribble(
    ~USUBJID, ~PARAMCD, ~AVAL, ~PARAM, ~VISIT, ~DTYPE,
    "P01", "WBC", 33, "Leukocyte Count (10^9/L)", "CYCLE 1 DAY 1", NA_character_,
    "P01", "WBC", 38, "Leukocyte Count (10^9/L)", "CYCLE 2 DAY 1", NA_character_,
    "P01", "LYMLE", 0.9, "Lymphocytes (fraction of 1)", "CYCLE 1 DAY 1", NA_character_,
    "P01", "LYMLE", 0.6, "Lymphocytes (fraction of 1)", "CYCLE 2 DAY 1", NA_character_,
    "P01", "LYMPH", 29.7, "Lymphocytes Abs (10^9/L)", "CYCLE 1 DAY 1", "CALCULATION",
    "P01", "LYMPH", 22.8, "Lymphocytes Abs (10^9/L)", "CYCLE 2 DAY 1", "CALCULATION"
  )

  expect_equal(
    derive_param_wbc_abs(
      dataset = input,
      by_vars = exprs(USUBJID, VISIT),
      set_values_to = exprs(
        PARAMCD = "LYMPH",
        PARAM = "Lymphocytes Abs (10^9/L)",
        DTYPE = "CALCULATION"
      ),
      get_unit_expr = extract_unit(PARAM),
      wbc_code = "WBC",
      diff_code = "LYMLE",
      diff_type = "fraction"
    ),
    expected_output
  )
})

test_that("Test 2: Test when only one of WBC/differential is present", {
  input <- tibble::tribble(
    ~USUBJID, ~PARAMCD, ~AVAL, ~PARAM, ~VISIT,
    "P01", "WBC", 33, "Leukocyte Count (10^9/L)", "CYCLE 1 DAY 1",
    "P01", "WBC", 38, "Leukocyte Count (10^9/L)", "CYCLE 2 DAY 1",
    "P01", "LYMLE", 0.9, "Lymphocytes (fraction of 1)", "CYCLE 2 DAY 1",
    "P01", "LYMLE", 0.8, "Lymphocytes (fraction of 1)", "CYCLE 3 DAY 1"
  )
  expected_output <- tibble::tribble(
    ~USUBJID, ~PARAMCD, ~AVAL, ~PARAM, ~VISIT, ~DTYPE,
    "P01", "WBC", 33, "Leukocyte Count (10^9/L)", "CYCLE 1 DAY 1", NA_character_,
    "P01", "WBC", 38, "Leukocyte Count (10^9/L)", "CYCLE 2 DAY 1", NA_character_,
    "P01", "LYMLE", 0.9, "Lymphocytes (fraction of 1)", "CYCLE 2 DAY 1", NA_character_,
    "P01", "LYMLE", 0.8, "Lymphocytes (fraction of 1)", "CYCLE 3 DAY 1", NA_character_,
    "P01", "LYMPH", 34.2, "Lymphocytes Abs (10^9/L)", "CYCLE 2 DAY 1", "CALCULATION"
  )

  expect_equal(
    derive_param_wbc_abs(
      dataset = input,
      by_vars = exprs(USUBJID, VISIT),
      set_values_to = exprs(
        PARAMCD = "LYMPH",
        PARAM = "Lymphocytes Abs (10^9/L)",
        DTYPE = "CALCULATION"
      ),
      get_unit_expr = extract_unit(PARAM),
      wbc_code = "WBC",
      diff_code = "LYMLE",
      diff_type = "fraction"
    ),
    expected_output
  )
})

test_that("Test 3: Test when absolute record already present in source dataset 1", {
  input <- tibble::tribble(
    ~USUBJID, ~PARAMCD, ~AVAL, ~PARAM, ~VISIT,
    "P01", "WBC", 33, "Leukocyte Count (10^9/L)", "CYCLE 1 DAY 1",
    "P01", "WBC", 38, "Leukocyte Count (10^9/L)", "CYCLE 2 DAY 1",
    "P01", "LYMPH", 27, "Lymphocytes Abs (10^9/L)", "CYCLE 2 DAY 1",
    "P01", "LYMLE", 0.7, "Lymphocytes (fraction of 1)", "CYCLE 2 DAY 1",
    "P01", "LYMLE", 0.8, "Lymphocytes (fraction of 1)", "CYCLE 3 DAY 1"
  )
  expected_output <- tibble::tribble(
    ~USUBJID, ~PARAMCD, ~AVAL, ~PARAM, ~VISIT,
    "P01", "WBC", 33, "Leukocyte Count (10^9/L)", "CYCLE 1 DAY 1",
    "P01", "WBC", 38, "Leukocyte Count (10^9/L)", "CYCLE 2 DAY 1",
    "P01", "LYMPH", 27, "Lymphocytes Abs (10^9/L)", "CYCLE 2 DAY 1",
    "P01", "LYMLE", 0.7, "Lymphocytes (fraction of 1)", "CYCLE 2 DAY 1",
    "P01", "LYMLE", 0.8, "Lymphocytes (fraction of 1)", "CYCLE 3 DAY 1"
  )

  expect_message(
    expect_equal(
      derive_param_wbc_abs(
        dataset = input,
        by_vars = exprs(USUBJID, VISIT),
        set_values_to = exprs(
          PARAMCD = "LYMPH",
          PARAM = "Lymphocytes Abs (10^9/L)",
          DTYPE = "CALCULATION"
        ),
        get_unit_expr = extract_unit(PARAM),
        wbc_code = "WBC",
        diff_code = "LYMLE",
        diff_type = "fraction"
      ),
      expected_output
    ),
    "No source records meet condition for calculation, therefore no new records created"
  )
})

test_that("Test 4: Test when absolute record already present in source dataset 2", {
  input <- tibble::tribble(
    ~USUBJID, ~PARAMCD, ~AVAL, ~PARAM, ~VISIT,
    "P01", "WBC", 33, "Leukocyte Count (10^9/L)", "CYCLE 1 DAY 1",
    "P01", "WBC", 38, "Leukocyte Count (10^9/L)", "CYCLE 2 DAY 1",
    "P01", "LYMPH", 27, "Lymphocytes Abs (10^9/L)", "CYCLE 2 DAY 1",
    "P01", "LYMLE", 0.7, "Lymphocytes (fraction of 1)", "CYCLE 2 DAY 1",
    "P01", "LYMLE", 0.9, "Lymphocytes (fraction of 1)", "CYCLE 1 DAY 1"
  )

  expected_output <- tibble::tribble(
    ~USUBJID, ~PARAMCD, ~AVAL, ~PARAM, ~VISIT, ~DTYPE,
    "P01", "WBC", 33, "Leukocyte Count (10^9/L)", "CYCLE 1 DAY 1", NA_character_,
    "P01", "WBC", 38, "Leukocyte Count (10^9/L)", "CYCLE 2 DAY 1", NA_character_,
    "P01", "LYMPH", 27, "Lymphocytes Abs (10^9/L)", "CYCLE 2 DAY 1", NA_character_,
    "P01", "LYMLE", 0.7, "Lymphocytes (fraction of 1)", "CYCLE 2 DAY 1", NA_character_,
    "P01", "LYMLE", 0.9, "Lymphocytes (fraction of 1)", "CYCLE 1 DAY 1", NA_character_,
    "P01", "LYMPH", 29.7, "Lymphocytes Abs (10^9/L)", "CYCLE 1 DAY 1", "CALCULATION"
  )

  expect_equal(
    derive_param_wbc_abs(
      dataset = input,
      by_vars = exprs(USUBJID, VISIT),
      set_values_to = exprs(
        PARAMCD = "LYMPH",
        PARAM = "Lymphocytes Abs (10^9/L)",
        DTYPE = "CALCULATION"
      ),
      get_unit_expr = extract_unit(PARAM),
      wbc_code = "WBC",
      diff_code = "LYMLE",
      diff_type = "fraction"
    ),
    expected_output
  )
})


test_that("Test 5: Test percent differential type", {
  input <- tibble::tribble(
    ~USUBJID, ~PARAMCD, ~AVAL, ~PARAM, ~VISIT,
    "P01", "WBC", 33, "Leukocyte Count (10^9/L)", "CYCLE 1 DAY 1",
    "P01", "WBC", 38, "Leukocyte Count (10^9/L)", "CYCLE 2 DAY 1",
    "P01", "LYMPH", 27, "Lymphocytes Abs (10^9/L)", "CYCLE 2 DAY 1",
    "P01", "LYMLE", 70, "Lymphocytes (%)", "CYCLE 2 DAY 1",
    "P01", "LYMLE", 90, "Lymphocytes (%)", "CYCLE 1 DAY 1"
  )

  expected_output <- tibble::tribble(
    ~USUBJID, ~PARAMCD, ~AVAL, ~PARAM, ~VISIT, ~DTYPE,
    "P01", "WBC", 33, "Leukocyte Count (10^9/L)", "CYCLE 1 DAY 1", NA_character_,
    "P01", "WBC", 38, "Leukocyte Count (10^9/L)", "CYCLE 2 DAY 1", NA_character_,
    "P01", "LYMPH", 27, "Lymphocytes Abs (10^9/L)", "CYCLE 2 DAY 1", NA_character_,
    "P01", "LYMLE", 70, "Lymphocytes (%)", "CYCLE 2 DAY 1", NA_character_,
    "P01", "LYMLE", 90, "Lymphocytes (%)", "CYCLE 1 DAY 1", NA_character_,
    "P01", "LYMPH", 29.7, "Lymphocytes Abs (10^9/L)", "CYCLE 1 DAY 1", "CALCULATION"
  )

  expect_equal(
    derive_param_wbc_abs(
      dataset = input,
      by_vars = exprs(USUBJID, VISIT),
      set_values_to = exprs(
        PARAMCD = "LYMPH",
        PARAM = "Lymphocytes Abs (10^9/L)",
        DTYPE = "CALCULATION"
      ),
      get_unit_expr = extract_unit(PARAM),
      wbc_code = "WBC",
      diff_code = "LYMLE",
      diff_type = "percent"
    ),
    expected_output
  )
})