tests/testthat/test-derive_var_shift.R

In admiral: ADaM in R Asset Library

# derive_var_shift ----

## Test 1: Shift based on character variables ----
test_that("derive_var_shift Test 1: Shift based on character variables", {
  input <- tibble::tribble(
    ~USUBJID, ~PARAMCD, ~AVAL, ~ABLFL, ~BNRIND, ~ANRIND,
    "P01", "ALB", 33, "Y", "LOW", "LOW",
    "P01", "ALB", 38, NA, "LOW", "NORMAL",
    "P02", "ALB", 37, "Y", "NORMAL", "NORMAL",
    "P02", "ALB", 49, NA, "NORMAL", "HIGH",
    "P02", "SODIUM", 147, "Y", "HIGH", "HIGH"
  )
  expected_output <- tibble::tribble(
    ~USUBJID, ~PARAMCD, ~AVAL, ~ABLFL, ~BNRIND, ~ANRIND, ~SHIFT1,
    "P01", "ALB", 33, "Y", "LOW", "LOW", "LOW to LOW",
    "P01", "ALB", 38, NA, "LOW", "NORMAL", "LOW to NORMAL",
    "P02", "ALB", 37, "Y", "NORMAL", "NORMAL", "NORMAL to NORMAL",
    "P02", "ALB", 49, NA, "NORMAL", "HIGH", "NORMAL to HIGH",
    "P02", "SODIUM", 147, "Y", "HIGH", "HIGH", "HIGH to HIGH"
  )

  expect_equal(
    derive_var_shift(
      input,
      new_var = SHIFT1,
      from_var = BNRIND,
      to_var = ANRIND
    ),
    expected_output
  )
})


## Test 2: Shift based on character variables with missing values ----
test_that("derive_var_shift Test 2: Shift based on character variables with missing values", {
  input <- tibble::tribble(
    ~USUBJID, ~PARAMCD, ~AVAL, ~ABLFL, ~BNRIND, ~ANRIND,
    "P01", "ALB", 33, "Y", "LOW", "LOW",
    "P01", "ALB", 38, NA, "LOW", "NORMAL",
    "P01", "ALB", NA, NA, "LOW", NA,
    "P02", "ALB", NA, "Y", NA, NA,
    "P02", "ALB", 49, NA, NA, "HIGH",
    "P02", "SODIUM", 147, "Y", "HIGH", "HIGH"
  )
  expected_output <- tibble::tribble(
    ~USUBJID, ~PARAMCD, ~AVAL, ~ABLFL, ~BNRIND, ~ANRIND, ~SHIFT1,
    "P01", "ALB", 33, "Y", "LOW", "LOW", "LOW to LOW",
    "P01", "ALB", 38, NA, "LOW", "NORMAL", "LOW to NORMAL",
    "P01", "ALB", NA, NA, "LOW", NA, "LOW to NULL",
    "P02", "ALB", NA, "Y", NA, NA, "NULL to NULL",
    "P02", "ALB", 49, NA, NA, "HIGH", "NULL to HIGH",
    "P02", "SODIUM", 147, "Y", "HIGH", "HIGH", "HIGH to HIGH"
  )

  expect_equal(
    derive_var_shift(
      input,
      new_var = SHIFT1,
      from_var = BNRIND,
      to_var = ANRIND
    ),
    expected_output
  )
})


## Test 3: Shift based on numeric variables with missing values ----
test_that("derive_var_shift Test 3: Shift based on numeric variables with missing values", {
  input <- tibble::tribble(
    ~USUBJID, ~PARAMCD, ~AVAL, ~ABLFL, ~BASE,
    "P01", "ALB", 33.1, "Y", 33.1,
    "P01", "ALB", 38.5, NA, 33.1,
    "P01", "ALB", NA, NA, 33.1,
    "P02", "ALB", NA, "Y", NA,
    "P02", "ALB", 49.0, NA, NA,
    "P02", "SODIUM", 147.5, "Y", 147.5
  ) %>% convert_blanks_to_na()
  expected_output <- tibble::tribble(
    ~USUBJID, ~PARAMCD, ~AVAL, ~ABLFL, ~BASE, ~SHIFT2,
    "P01", "ALB", 33.1, "Y", 33.1, "33.1 to 33.1",
    "P01", "ALB", 38.5, NA, 33.1, "33.1 to 38.5",
    "P01", "ALB", NA, NA, 33.1, "33.1 to NULL",
    "P02", "ALB", NA, "Y", NA, "NULL to NULL",
    "P02", "ALB", 49, NA, NA, "NULL to 49",
    "P02", "SODIUM", 147.5, "Y", 147.5, "147.5 to 147.5"
  )

  expect_equal(
    derive_var_shift(
      input,
      new_var = SHIFT2,
      from_var = BASE,
      to_var = AVAL
    ),
    expected_output
  )
})

## Test 4: Shift with user-specified missing_value and sep_val ----
test_that("derive_var_shift Test 4: Shift with user-specified missing_value and sep_val", {
  input <- tibble::tribble(
    ~USUBJID, ~PARAMCD, ~AVAL, ~ABLFL, ~BNRIND, ~ANRIND,
    "P01", "ALB", 33, "Y", "LOW", "LOW",
    "P01", "ALB", 38, NA, "LOW", "NORMAL",
    "P01", "ALB", NA, NA, "LOW", NA,
    "P02", "ALB", NA, "Y", NA, NA,
    "P02", "ALB", 49, NA, NA, "HIGH",
    "P02", "SODIUM", 147, "Y", "HIGH", "HIGH"
  )
  expected_output <- tibble::tribble(
    ~USUBJID, ~PARAMCD, ~AVAL, ~ABLFL, ~BNRIND, ~ANRIND, ~SHIFT1,
    "P01", "ALB", 33, "Y", "LOW", "LOW", "LOW - LOW",
    "P01", "ALB", 38, NA, "LOW", "NORMAL", "LOW - NORMAL",
    "P01", "ALB", NA, NA, "LOW", NA, "LOW - MISSING",
    "P02", "ALB", NA, "Y", NA, NA, "MISSING - MISSING",
    "P02", "ALB", 49, NA, NA, "HIGH", "MISSING - HIGH",
    "P02", "SODIUM", 147, "Y", "HIGH", "HIGH", "HIGH - HIGH"
  )

  expect_equal(
    derive_var_shift(
      input,
      new_var = SHIFT1,
      from_var = BNRIND,
      to_var = ANRIND,
      missing_value = "MISSING",
      sep_val = " - "
    ),
    expected_output
  )
})

## Test 5: Test deprecation warning of na_val argument ----
test_that("derive_var_shift Test 5: Test deprecation warning of na_val argument", {
  input <- tibble::tribble(
    ~USUBJID, ~PARAMCD, ~AVAL, ~ABLFL, ~BNRIND, ~ANRIND,
    "P01", "ALB", 33, "Y", "LOW", "LOW",
    "P01", "ALB", 38, NA, "LOW", "NORMAL",
    "P01", "ALB", NA, NA, "LOW", NA,
    "P02", "ALB", NA, "Y", NA, NA,
    "P02", "ALB", 49, NA, NA, "HIGH",
    "P02", "SODIUM", 147, "Y", "HIGH", "HIGH"
  )

  expect_warning(
    derive_var_shift(
      input,
      new_var = SHIFT1,
      from_var = BNRIND,
      to_var = ANRIND,
      na_val = "MISSING",
      sep_val = " - "
    ),
    class = "lifecycle_warning_deprecated"
  )
})