tests/testthat/test-derive_vars_dy.R

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

## Test 1: Single --DT input when ref date is --DTM ----
test_that("derive_vars_dy Test 1: Single --DT input when ref date is --DTM", {
  datain <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~TRTSDTM, ~ASTDT,
    "TEST01", "PAT01", "2014-01-17T23:59:59", "2014-01-18",
  ) %>%
    mutate(
      TRTSDTM = lubridate::as_datetime(TRTSDTM),
      ASTDT = lubridate::ymd(ASTDT)
    )

  expected_output <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~TRTSDTM, ~ASTDT, ~ASTDY,
    "TEST01", "PAT01", "2014-01-17T23:59:59", "2014-01-18", 2
  ) %>%
    mutate(
      TRTSDTM = lubridate::as_datetime(TRTSDTM),
      ASTDT = lubridate::ymd(ASTDT)
    )

  actual_output <- derive_vars_dy(datain,
    reference_date = TRTSDTM,
    source_vars = exprs(ASTDT)
  )

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

## Test 2: DT input, ref date DTM, DY var specified ----
test_that("derive_vars_dy Test 2: DT input, ref date DTM, DY var specified", {
  datain <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~TRTSDTM, ~ASTDT, ~AENDT, ~DTHDT,
    "TEST01", "PAT01", "2014-01-17T23:59:59", "2014-01-18", "2014-01-20", "2014-02-01",
    "TEST01", "PAT02", "2014-01-17T23:59:59", "2014-01-17", "2014-01-20", "2014-03-01",
    "TEST01", "PAT03", "2014-01-17T23:59:59", "2014-01-15", "2014-01-20", "2014-05-01"
  ) %>%
    mutate(
      TRTSDTM = lubridate::as_datetime(TRTSDTM),
      ASTDT = lubridate::ymd(ASTDT),
      AENDT = lubridate::ymd(AENDT),
      DTHDT = lubridate::ymd(DTHDT)
    )

  expected_output <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~TRTSDTM, ~ASTDT, ~AENDT, ~DTHDT, ~TRTSDY, ~ASTDY, ~AENDY, ~DEATHDY,
    "TEST01", "PAT01", "2014-01-17T23:59:59", "2014-01-18", "2014-01-20", "2014-02-01", 1, 2, 4, 16,
    "TEST01", "PAT02", "2014-01-17T23:59:59", "2014-01-17", "2014-01-20", "2014-03-01", 1, 1, 4, 44,
    "TEST01", "PAT03", "2014-01-17T23:59:59", "2014-01-15", "2014-01-20", "2014-05-01", 1, -2, 4, 105, # nolint
  ) %>%
    mutate(
      TRTSDTM = lubridate::as_datetime(TRTSDTM),
      ASTDT = lubridate::ymd(ASTDT),
      AENDT = lubridate::ymd(AENDT),
      DTHDT = lubridate::ymd(DTHDT)
    )

  actual_output <- derive_vars_dy(datain,
    reference_date = TRTSDTM,
    source_vars = exprs(TRTSDTM, ASTDT, AENDT, DEATHDY = DTHDT)
  )

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

## Test 3: Combo of --DT/--DTM input when ref date is --DTM ----
test_that("derive_vars_dy Test 3: Combo of --DT/--DTM input when ref date is --DTM", {
  datain <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~TRTSDTM, ~ASTDTM, ~AENDT,
    "TEST01", "PAT01", "2014-01-17T23:59:59", "2014-01-18T13:09:O9", "2014-01-20"
  ) %>%
    mutate(
      TRTSDTM = lubridate::as_datetime(TRTSDTM),
      ASTDTM = lubridate::as_datetime(ASTDTM),
      AENDT = lubridate::ymd(AENDT)
    )

  expected_output <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~TRTSDTM, ~ASTDTM, ~AENDT, ~TRTSDY, ~ASTDY, ~AENDY,
    "TEST01", "PAT01", "2014-01-17T23:59:59", "2014-01-18T13:09:O9", "2014-01-20", 1, 2, 4
  ) %>%
    mutate(
      TRTSDTM = lubridate::as_datetime(TRTSDTM),
      ASTDTM = lubridate::as_datetime(ASTDTM),
      AENDT = lubridate::ymd(AENDT)
    )

  actual_output <- derive_vars_dy(datain,
    reference_date = TRTSDTM,
    source_vars = exprs(TRTSDTM, ASTDTM, AENDT)
  )

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

## Test 4: Single --DT input when ref date is --DT ----
test_that("derive_vars_dy Test 4: Single --DT input when ref date is --DT", {
  datain <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~TRTSDT, ~ASTDT,
    "TEST01", "PAT01", "2014-01-17", "2014-01-18",
  ) %>%
    mutate(
      TRTSDT = lubridate::ymd(TRTSDT),
      ASTDT = lubridate::ymd(ASTDT)
    )

  expected_output <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~TRTSDT, ~ASTDT, ~ASTDY,
    "TEST01", "PAT01", "2014-01-17", "2014-01-18", 2
  ) %>%
    mutate(
      TRTSDT = lubridate::ymd(TRTSDT),
      ASTDT = lubridate::ymd(ASTDT)
    )

  actual_output <- derive_vars_dy(datain,
    reference_date = TRTSDT,
    source_vars = exprs(ASTDT)
  )

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

## Test 5: Multiple --DT input when ref date is --DT ----
test_that("derive_vars_dy Test 5: Multiple --DT input when ref date is --DT", {
  datain <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~TRTSDT, ~ASTDT, ~AENDT,
    "TEST01", "PAT01", "2014-01-17", "2014-01-18", "2014-01-20"
  ) %>%
    mutate(
      TRTSDT = lubridate::ymd(TRTSDT),
      ASTDT = lubridate::ymd(ASTDT),
      AENDT = lubridate::ymd(AENDT)
    )

  expected_output <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~TRTSDT, ~ASTDT, ~AENDT, ~TRTSDY, ~ASTDY, ~AENDY,
    "TEST01", "PAT01", "2014-01-17", "2014-01-18", "2014-01-20", 1, 2, 4
  ) %>%
    mutate(
      TRTSDT = lubridate::ymd(TRTSDT),
      ASTDT = lubridate::ymd(ASTDT),
      AENDT = lubridate::ymd(AENDT)
    )

  actual_output <- derive_vars_dy(datain,
    reference_date = TRTSDT,
    source_vars = exprs(TRTSDT, ASTDT, AENDT)
  )

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

## Test 6: Combo of --DT/--DTM input when ref date is --DT ----
test_that("derive_vars_dy Test 6: Combo of --DT/--DTM input when ref date is --DT", {
  datain <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~TRTSDT, ~ASTDTM, ~AENDT,
    "TEST01", "PAT01", "2014-01-17", "2014-01-18T13:09:O9", "2014-01-20"
  ) %>%
    mutate(
      TRTSDT = lubridate::ymd(TRTSDT),
      ASTDTM = lubridate::as_datetime(ASTDTM),
      AENDT = lubridate::ymd(AENDT)
    )

  expected_output <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~TRTSDT, ~ASTDTM, ~AENDT, ~TRTSDY, ~ASTDY, ~AENDY,
    "TEST01", "PAT01", "2014-01-17", "2014-01-18T13:09:O9", "2014-01-20", 1, 2, 4
  ) %>%
    mutate(
      TRTSDT = lubridate::ymd(TRTSDT),
      ASTDTM = lubridate::as_datetime(ASTDTM),
      AENDT = lubridate::ymd(AENDT)
    )

  actual_output <- derive_vars_dy(datain,
    reference_date = TRTSDT,
    source_vars = exprs(TRTSDT, ASTDTM, AENDT)
  )

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

## Test 7: All dates as --DTM ----
test_that("derive_vars_dy Test 7: All dates as --DTM", {
  datain <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~TRTSDTM, ~ASTDTM, ~AENDTM,
    "TEST01", "PAT01", "2014-01-17T16:34:O9", "2014-01-18T13:09:O9", "2014-01-20T08:29:05"
  ) %>%
    mutate(
      TRTSDTM = lubridate::as_datetime(TRTSDTM),
      ASTDTM = lubridate::as_datetime(ASTDTM),
      AENDTM = lubridate::as_datetime(AENDTM)
    )

  expected_output <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~TRTSDTM, ~ASTDTM, ~AENDTM, ~TRTSDY, ~ASTDY, ~AENDY,
    "TEST01", "PAT01", "2014-01-17T16:34:O9", "2014-01-18T13:09:O9", "2014-01-20T08:29:05", 1, 2, 4
  ) %>%
    mutate(
      TRTSDTM = lubridate::as_datetime(TRTSDTM),
      ASTDTM = lubridate::as_datetime(ASTDTM),
      AENDTM = lubridate::as_datetime(AENDTM)
    )

  actual_output <- derive_vars_dy(datain,
    reference_date = TRTSDTM,
    source_vars = exprs(TRTSDTM, ASTDTM, AENDTM)
  )

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

## Test 8: error if source variables do not end in DT or DTM ----
test_that("derive_vars_dy Test 8: error if source variables do not end in DT or DTM", {
  datain <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~TRTSDTW,              ~ASTDTW,               ~AENDTW,
    "TEST01", "PAT01",  "2014-01-17T16:34:O9", "2014-01-18T13:09:O9", "2014-01-20T08:29:05"
  )

  expect_snapshot(
    derive_vars_dy(datain,
      reference_date = TRTSDTW,
      source_vars = exprs(TRTSDTW, ASTDTW, AENDTW)
    ),
    error = TRUE
  )
})

## Test 9: Single named --DT input when ref date is --DTM ----
test_that("derive_vars_dy Test 9: Single named --DT input when ref date is --DTM", {
  datain <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~TRTSDTM, ~ASTDT,
    "TEST01", "PAT01", "2014-01-17T23:59:59", "2014-01-18",
  ) %>%
    mutate(
      TRTSDTM = lubridate::as_datetime(TRTSDTM),
      ASTDT = lubridate::ymd(ASTDT)
    )

  expected_output <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~TRTSDTM, ~ASTDT, ~ASTDY,
    "TEST01", "PAT01", "2014-01-17T23:59:59", "2014-01-18", 2
  ) %>%
    mutate(
      TRTSDTM = lubridate::as_datetime(TRTSDTM),
      ASTDT = lubridate::ymd(ASTDT)
    )

  actual_output <- derive_vars_dy(datain,
    reference_date = TRTSDTM,
    source_vars = exprs(ASTDY = ASTDT)
  )

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

## Test 10: no error if input with variable end with `_temp` ----
test_that("derive_vars_dy Test 10: no error if input with variable end with `_temp`", {
  datain <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~TRTSDTM, ~ASTDT, ~test_temp,
    "TEST01", "PAT01", "2014-01-17T23:59:59", "2014-01-18", "test"
  ) %>%
    mutate(
      TRTSDTM = lubridate::as_datetime(TRTSDTM),
      ASTDT = lubridate::ymd(ASTDT)
    )

  expected_output <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~TRTSDTM, ~ASTDT, ~test_temp, ~ASTDY,
    "TEST01", "PAT01", "2014-01-17T23:59:59", "2014-01-18", "test", 2
  ) %>%
    mutate(
      TRTSDTM = lubridate::as_datetime(TRTSDTM),
      ASTDT = lubridate::ymd(ASTDT)
    )

  actual_output <- derive_vars_dy(datain,
    reference_date = TRTSDTM,
    source_vars = exprs(ASTDT)
  )

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