tests/testthat/test-derive_derived_param.R

In epijim/admiral: ADaM in R Asset Library

test_that("new observations are derived correctly", {
  input <- tibble::tribble(
    ~USUBJID,      ~PARAMCD, ~PARAM,                            ~AVAL, ~AVALU, ~VISIT,
    "01-701-1015", "DIABP",  "Diastolic Blood Pressure (mmHg)",  51,   "mmHg", "BASELINE",
    "01-701-1015", "DIABP",  "Diastolic Blood Pressure (mmHg)",  50,   "mmHg", "WEEK 2",
    "01-701-1015", "SYSBP",  "Systolic Blood Pressure (mmHg)",  121,   "mmHg", "BASELINE",
    "01-701-1015", "SYSBP",  "Systolic Blood Pressure (mmHg)",  121,   "mmHg", "WEEK 2",
    "01-701-1028", "DIABP",  "Diastolic Blood Pressure (mmHg)",  79,   "mmHg", "BASELINE",
    "01-701-1028", "DIABP",  "Diastolic Blood Pressure (mmHg)",  80,   "mmHg", "WEEK 2",
    "01-701-1028", "SYSBP",  "Systolic Blood Pressure (mmHg)",  130,   "mmHg", "BASELINE",
    "01-701-1028", "SYSBP",  "Systolic Blood Pressure (mmHg)",  132,   "mmHg", "WEEK 2"
  )

  new_obs <-
    inner_join(input %>% filter(PARAMCD == "DIABP") %>% select(USUBJID, VISIT, AVAL),
               input %>% filter(PARAMCD == "SYSBP") %>% select(USUBJID, VISIT, AVAL),
               by = c("USUBJID", "VISIT"),
               suffix = c(".DIABP", ".SYSBP")) %>%
    mutate(AVAL = (2 * AVAL.DIABP + AVAL.SYSBP) / 3,
           PARAMCD = "MAP",
           PARAM = "Mean arterial pressure (mmHg)",
           AVALU = "mmHg") %>%
    select(-AVAL.DIABP, -AVAL.SYSBP)
  expected_output <- bind_rows(input, new_obs)

  expect_dfs_equal(
    derive_derived_param(
      input,
      parameters = c("SYSBP", "DIABP"),
      by_vars = vars(USUBJID, VISIT),
      analysis_value = (AVAL.SYSBP + 2 * AVAL.DIABP) / 3,
      set_values_to = vars(
        PARAMCD = "MAP",
        PARAM = "Mean arterial pressure (mmHg)",
        AVALU = "mmHg"
      )
    )
    ,
    expected_output,
    keys = c("USUBJID", "PARAMCD", "VISIT")
  )
})

test_that("new observations are derived correctly with constant parameters", {
    input <- tibble::tribble(
    ~USUBJID,      ~PARAMCD, ~PARAM,        ~AVAL, ~AVALU, ~VISIT,
    "01-701-1015", "HEIGHT", "Height (cm)", 147,   "cm",   "SCREENING",
    "01-701-1015", "WEIGHT", "Weight (kg)",  54.0, "kg",   "SCREENING",
    "01-701-1015", "WEIGHT", "Weight (kg)",  54.4, "kg",   "BASELINE",
    "01-701-1015", "WEIGHT", "Weight (kg)",  53.1, "kg",   "WEEK 2",
    "01-701-1028", "HEIGHT", "Height (cm)", 163,   "cm",   "SCREENING",
    "01-701-1028", "WEIGHT", "Weight (kg)",  78.5, "kg",   "SCREENING",
    "01-701-1028", "WEIGHT", "Weight (kg)",  80.3, "kg",   "BASELINE",
    "01-701-1028", "WEIGHT", "Weight (kg)",  80.7, "kg",   "WEEK 2"
  )

  new_obs <-
    inner_join(input %>% filter(PARAMCD == "HEIGHT") %>% select(USUBJID, AVAL),
               input %>% filter(PARAMCD == "WEIGHT") %>% select(USUBJID, VISIT, AVAL),
               by = c("USUBJID"),
               suffix = c(".HEIGHT", ".WEIGHT")) %>%
    mutate(AVAL = AVAL.WEIGHT / (AVAL.HEIGHT / 100) ^ 2,
           PARAMCD = "BMI",
           PARAM = "Body Mass Index (kg/m2)",
           AVALU = "kg/m2") %>%
    select(-AVAL.HEIGHT, -AVAL.WEIGHT)
  expected_output <- bind_rows(input, new_obs)

  expect_dfs_equal(
    derive_derived_param(
      input,
      parameters = c("WEIGHT"),
      by_vars = vars(USUBJID, VISIT),
      constant_parameters = c("HEIGHT"),
      constant_by_vars = vars(USUBJID),
      analysis_value = AVAL.WEIGHT / (AVAL.HEIGHT / 100) ^ 2,
      set_values_to = vars(
        PARAMCD = "BMI",
        PARAM = "Body Mass Index (kg/m2)",
        AVALU = "kg/m2"
      )
    ),
    expected_output,
    keys = c("USUBJID", "PARAMCD", "VISIT")
  )
})

test_that("no new observations are added if filtered dataset is empty", {
  input <- tibble::tribble(
    ~USUBJID,      ~PARAMCD, ~PARAM,                            ~AVAL, ~AVALU, ~VISIT,
    "01-701-1015", "DIABP",  "Diastolic Blood Pressure (mmHg)",  51,   "mmHg", "BASELINE",
    "01-701-1015", "DIABP",  "Diastolic Blood Pressure (mmHg)",  50,   "mmHg", "WEEK 2",
    "01-701-1015", "SYSBP",  "Systolic Blood Pressure (mmHg)",  121,   "mmHg", "BASELINE",
    "01-701-1015", "SYSBP",  "Systolic Blood Pressure (mmHg)",  121,   "mmHg", "WEEK 2",
    "01-701-1028", "DIABP",  "Diastolic Blood Pressure (mmHg)",  79,   "mmHg", "BASELINE",
    "01-701-1028", "DIABP",  "Diastolic Blood Pressure (mmHg)",  80,   "mmHg", "WEEK 2",
    "01-701-1028", "SYSBP",  "Systolic Blood Pressure (mmHg)",  130,   "mmHg", "BASELINE",
    "01-701-1028", "SYSBP",  "Systolic Blood Pressure (mmHg)",  132,   "mmHg", "WEEK 2"
  )

  expect_warning(
    derive_derived_param(
      input,
      filter = VISIT == "WEEK 24",
      parameters = c("SYSBP", "DIABP"),
      by_vars = vars(USUBJID, VISIT),
      analysis_value = (AVAL.SYSBP + 2 * AVAL.DIABP) / 3,
      set_values_to = vars(
        PARAMCD = "MAP",
        PARAM = "Mean arterial pressure (mmHg)",
        AVALU = "mmHg"
      )
    )
    ,
    "The input dataset does not contain any observations fullfiling the filter condition .*"
  ) %>%
    expect_dfs_equal(input,
                     keys = c("USUBJID", "PARAMCD", "VISIT"))
})

test_that("no new observations are added if a parameter is missing", {
  input <- tibble::tribble(
    ~USUBJID,      ~PARAMCD, ~PARAM,                            ~AVAL, ~AVALU, ~VISIT,
    "01-701-1015", "DIABP",  "Diastolic Blood Pressure (mmHg)",  51,   "mmHg", "BASELINE",
    "01-701-1015", "DIABP",  "Diastolic Blood Pressure (mmHg)",  50,   "mmHg", "WEEK 2",
    "01-701-1015", "SYSBP",  "Systolic Blood Pressure (mmHg)",  121,   "mmHg", "BASELINE",
    "01-701-1015", "SYSBP",  "Systolic Blood Pressure (mmHg)",  121,   "mmHg", "WEEK 2",
    "01-701-1028", "DIABP",  "Diastolic Blood Pressure (mmHg)",  79,   "mmHg", "BASELINE",
    "01-701-1028", "DIABP",  "Diastolic Blood Pressure (mmHg)",  80,   "mmHg", "WEEK 2",
    "01-701-1028", "SYSBP",  "Systolic Blood Pressure (mmHg)",  130,   "mmHg", "BASELINE",
    "01-701-1028", "SYSBP",  "Systolic Blood Pressure (mmHg)",  132,   "mmHg", "WEEK 2"
  )

  expect_warning(
    derive_derived_param(
      input,
      filter = PARAMCD == "DIABP",
      parameters = c("SYSBP", "DIABP"),
      by_vars = vars(USUBJID, VISIT),
      analysis_value = (AVAL.SYSBP + 2 * AVAL.DIABP) / 3,
      set_values_to = vars(
        PARAMCD = "MAP",
        PARAM = "Mean arterial pressure (mmHg)",
        AVALU = "mmHg"
      )
    )
    ,
    "The input dataset does not contain any observations fullfiling the filter condition .*"
  ) %>%
    expect_dfs_equal(input,
                     keys = c("USUBJID", "PARAMCD", "VISIT"))
})