tests/testthat/test-derive_vars_max_flag.R

In admiralvaccine: Vaccine Extension Package for ADaM in 'R' Asset Library

## Test 1: Derive maximum severity flag variables

test_that("derive_vars_max_flag Test 1: Derive maximum severity flag variables", {
  input <- tibble::tribble(
    ~USUBJID, ~FAOBJ, ~FATESTCD, ~FATPTREF, ~AVAL, ~FATPT, ~PARAMCD,
    "ABC101", "REDNESS", "DIAMETER", "VACC 1", 10, "DAY 1", "DIARE",
    "ABC101", "REDNESS", "DIAMETER", "VACC 1", 7, "DAY 2", "DIARE",
    "ABC101", "REDNESS", "DIAMETER", "VACC 2", 3, "DAY 1", "DIARE",
    "ABC101", "REDNESS", "DIAMETER", "VACC 2", 8, "DAY 2", "DIARE",
    "ABC101", "FATIQUE", "SEV", "VACC 1", 1, "DAY 1", "SEVFAT",
    "ABC101", "FATIQUE", "SEV", "VACC 1", 1, "DAY 2", "SEVFAT",
    "ABC101", "FATIQUE", "SEV", "VACC 2", 2, "DAY 1", "SEVFAT",
    "ABC101", "FATIQUE", "SEV", "VACC 2", 3, "DAY 2", "SEVFAT"
  )

  expected1 <- input %>%
    arrange(desc(AVAL), FATPT) %>%
    group_by(USUBJID, FAOBJ, FATPTREF) %>%
    mutate(temp = row_number()) %>%
    mutate(flag1 = if_else(temp == 1, "Y", NA_character_)) %>%
    arrange(FAOBJ, FATESTCD) %>%
    select(-temp)

  expected2 <- input %>%
    arrange(desc(AVAL), FATPT) %>%
    group_by(USUBJID, FAOBJ) %>%
    mutate(temp = row_number()) %>%
    mutate(flag2 = if_else(temp == 1, "Y", NA_character_)) %>%
    arrange(FAOBJ, FATESTCD) %>%
    ungroup() %>%
    select(-temp)

  expected_output <- merge(expected1, expected2) %>%
    rename(ANL01FL = flag1, ANL02FL = flag2)

  actual_output <- derive_vars_max_flag(
    dataset = input,
    flag1 = "ANL01FL",
    flag2 = "ANL02FL"
  )

  expect_dfs_equal(
    expected_output,
    actual_output,
    keys = c(
      "USUBJID", "FAOBJ", "AVAL", "FATPT",
      "FATESTCD", "FATPTREF", "ANL01FL", "ANL02FL"
    )
  )
})

## Test 2: Derive maximum severity flag variable per event

test_that("derive_vars_max_flag Test 2: Derive maximum severity flag variable per event", {
  input <- tibble::tribble(
    ~USUBJID, ~FAOBJ, ~FATESTCD, ~FATPTREF, ~AVAL, ~FATPT, ~PARAMCD,
    "ABC101", "REDNESS", "DIAMETER", "VACC 1", 10, "DAY 1", "DIARE",
    "ABC101", "REDNESS", "DIAMETER", "VACC 1", 7, "DAY 2", "DIARE",
    "ABC101", "REDNESS", "DIAMETER", "VACC 2", 3, "DAY 1", "DIARE",
    "ABC101", "REDNESS", "DIAMETER", "VACC 2", 8, "DAY 2", "DIARE",
    "ABC101", "FATIQUE", "SEV", "VACC 1", 1, "DAY 1", "SEVFAT",
    "ABC101", "FATIQUE", "SEV", "VACC 1", 1, "DAY 2", "SEVFAT",
    "ABC101", "FATIQUE", "SEV", "VACC 2", 2, "DAY 1", "SEVFAT",
    "ABC101", "FATIQUE", "SEV", "VACC 2", 3, "DAY 2", "SEVFAT"
  )

  expected_output <- input %>%
    arrange(desc(AVAL), FATPT) %>%
    group_by(USUBJID, FAOBJ, FATPTREF) %>%
    mutate(temp = row_number()) %>%
    mutate(flag1 = if_else(temp == 1, "Y", NA_character_)) %>%
    arrange(FAOBJ, FATESTCD) %>%
    select(-temp) %>%
    rename(ANL01FL = flag1)


  actual_output <- derive_vars_max_flag(
    dataset = input,
    flag1 = "ANL01FL",
    flag2 = NULL
  )

  expect_dfs_equal(
    expected_output,
    actual_output,
    keys = c(
      "USUBJID", "FAOBJ", "AVAL", "FATPT",
      "FATESTCD", "FATPTREF"
    )
  )
})

## Test 3: Check if the records with AVAL = NA are not flagged

test_that("derive_vars_max_flag Test 3: check if the records with AVAL = NA are not flagged", {
  input <- tibble::tribble(
    ~USUBJID, ~FAOBJ, ~FATESTCD, ~FATPTREF, ~AVAL, ~FATPT, ~PARAMCD,
    "ABC101", "REDNESS", "DIAMETER", "VACC 1", 10, "DAY 1", "DIARE",
    "ABC101", "REDNESS", "DIAMETER", "VACC 1", 7, "DAY 2", "DIARE",
    "ABC101", "REDNESS", "DIAMETER", "VACC 2", 3, "DAY 1", "DIARE",
    "ABC101", "REDNESS", "DIAMETER", "VACC 2", 8, "DAY 2", "DIARE",
    "ABC101", "FATIQUE", "SEV", "VACC 1", 1, "DAY 1", "SEVFAT",
    "ABC101", "FATIQUE", "SEV", "VACC 1", 1, "DAY 2", "SEVFAT",
    "ABC101", "FATIQUE", "SEV", "VACC 2", 2, "DAY 1", "SEVFAT",
    "ABC101", "FATIQUE", "SEV", "VACC 2", 3, "DAY 2", "SEVFAT",
    "ABC101", "REDNESS", "OCCUR", "VACC 1", NA, "DAY 1", "LOCISR",
    "ABC101", "REDNESS", "OCCUR", "VACC 1", NA, "DAY 2", "LOCISR",
    "ABC101", "REDNESS", "OCCUR", "VACC 2", NA, "DAY 1", "LOCISR",
    "ABC101", "REDNESS", "OCCUR", "VACC 2", NA, "DAY 2", "LOCISR"
  )

  input <- input %>% filter(!is.na(PARAMCD) & FATESTCD != "OCCUR")

  expected_output <- input %>%
    arrange(desc(AVAL), FATPT) %>%
    group_by(USUBJID, FAOBJ) %>%
    mutate(temp = row_number()) %>%
    mutate(ANL02FL = if_else(temp == 1, "Y", NA_character_)) %>%
    arrange(FAOBJ, FATESTCD) %>%
    ungroup() %>%
    select(-temp)


  actual_output <- derive_vars_max_flag(
    dataset = input,
    flag1 = NULL,
    flag2 = "ANL02FL"
  )

  expect_dfs_equal(
    expected_output,
    actual_output,
    keys = c(
      "USUBJID", "FAOBJ", "AVAL", "FATPT",
      "FATESTCD", "FATPTREF"
    )
  )
})

## Test 4: Check for error if both flags are NULL

test_that("derive_vars_max_flag Test 4: Check for error if both flags are NULL", {
  input <- tibble::tribble(
    ~USUBJID, ~FAOBJ, ~FATESTCD, ~FATPTREF, ~AVAL, ~FATPT, ~PARAMCD,
    "ABC101", "REDNESS", "DIAMETER", "VACC 1", 10, "DAY 1", "DIARE",
    "ABC101", "REDNESS", "DIAMETER", "VACC 1", 7, "DAY 2", "DIARE",
    "ABC101", "REDNESS", "DIAMETER", "VACC 2", 3, "DAY 1", "DIARE",
    "ABC101", "REDNESS", "DIAMETER", "VACC 2", 8, "DAY 2", "DIARE",
    "ABC101", "FATIQUE", "SEV", "VACC 1", 1, "DAY 1", "SEVFAT",
    "ABC101", "FATIQUE", "SEV", "VACC 1", 1, "DAY 2", "SEVFAT",
    "ABC101", "FATIQUE", "SEV", "VACC 2", 2, "DAY 1", "SEVFAT",
    "ABC101", "FATIQUE", "SEV", "VACC 2", 3, "DAY 2", "SEVFAT"
  )

  testthat::expect_error(
    derive_vars_max_flag(
      dataset = input,
      flag1 = NULL,
      flag2 = NULL
    ),
    regexp = paste("Both flag names cannot be NULL")
  )
})