tests/testthat/test-derive_var_extreme_flag.R

In epijim/admiral: ADaM in R Asset Library

input_worst_flag <- tibble::tribble(
  ~STUDYID, ~USUBJID, ~PARAMCD,  ~AVISIT,    ~ADT,                 ~AVAL,
  "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-27"), 15.0,
  "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0,
  "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0,
  "TEST01", "PAT01",  "PARAM01", "WEEK 1",   as.Date("2021-04-27"), 10.0,
  "TEST01", "PAT01",  "PARAM01", "WEEK 2",   as.Date("2021-04-30"), 12.0,

  "TEST01", "PAT02",  "PARAM01", "SCREENING", as.Date("2021-04-27"), 15.0,
  "TEST01", "PAT02",  "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0,
  "TEST01", "PAT02",  "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0,
  "TEST01", "PAT02",  "PARAM01", "WEEK 1",   as.Date("2021-04-27"), 10.0,
  "TEST01", "PAT02",  "PARAM01", "WEEK 2",   as.Date("2021-04-30"), 12.0,

  "TEST01", "PAT01",  "PARAM02", "SCREENING", as.Date("2021-04-27"), 15.0,
  "TEST01", "PAT01",  "PARAM02", "SCREENING", as.Date("2021-04-25"), 14.0,
  "TEST01", "PAT01",  "PARAM02", "SCREENING", as.Date("2021-04-23"), 15.0,
  "TEST01", "PAT01",  "PARAM02", "BASELINE", as.Date("2021-04-27"), 10.0,
  "TEST01", "PAT01",  "PARAM02", "WEEK 2",   as.Date("2021-04-30"), 12.0,

  "TEST01", "PAT02",  "PARAM02", "SCREENING", as.Date("2021-04-27"), 15.0,
  "TEST01", "PAT02",  "PARAM02", "BASELINE", as.Date("2021-04-25"), 14.0,
  "TEST01", "PAT02",  "PARAM02", "WEEK 1",   as.Date("2021-04-23"), 15.0,
  "TEST01", "PAT02",  "PARAM02", "WEEK 1",   as.Date("2021-04-27"), 10.0,
  "TEST01", "PAT02",  "PARAM02", "BASELINE", as.Date("2021-04-30"), 12.0,

  "TEST01", "PAT02",  "PARAM03", "SCREENING", as.Date("2021-04-27"), 15.0,
  "TEST01", "PAT02",  "PARAM03", "BASELINE", as.Date("2021-04-25"), 14.0,
  "TEST01", "PAT02",  "PARAM03", "WEEK 1",   as.Date("2021-04-23"), 15.0,
  "TEST01", "PAT02",  "PARAM03", "WEEK 1",   as.Date("2021-04-27"), 10.0,
  "TEST01", "PAT02",  "PARAM03", "BASELINE", as.Date("2021-04-30"), 12.0
)

test_that("first observation for each group is flagged", {
  input <- tibble::tribble(
    ~USUBJID, ~AVISITN, ~AVAL,
    1, 1, 12,
    1, 3, 9,
    2, 2, 42,
    3, 3, 14,
    3, 3, 10
  )

  expected_output <- input %>% mutate(firstfl = c("Y", NA, "Y", "Y", NA))

  actual_output <- derive_var_extreme_flag(
    input,
    by_vars = vars(USUBJID),
    order = vars(AVISITN, desc(AVAL)),
    new_var = firstfl,
    mode = "first"
  )

  expect_dfs_equal(
    base = expected_output,
    compare = actual_output,
    keys = c("USUBJID", "AVISITN", "AVAL")
  )
})

test_that("last observation for each group is flagged, filter works", {
  input <- tibble::tribble(
    ~USUBJID, ~AVISITN, ~AVAL,
    1, 1, 12,
    1, 3, 9,
    2, 2, 42,
    3, 3, 14,
    3, 3, 10
  )

  expected_output <- input %>% mutate(lastfl = c(NA, "Y", NA, NA, "Y"))

  actual_output <- derive_var_extreme_flag(
    input,
    by_vars = vars(USUBJID),
    order = vars(AVISITN, desc(AVAL)),
    new_var = lastfl,
    mode = "last",
    filter = USUBJID != 2
  )

  expect_dfs_equal(
    base = expected_output,
    compare = actual_output,
    keys = c("USUBJID", "AVISITN", "AVAL")
  )
})

test_that("ABLFL = Y using last observation within a subset", {
  input <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~PARAMCD,  ~AVISIT,    ~ADT,                 ~AVAL,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-27"), 15.0,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0,
    "TEST01", "PAT01",  "PARAM01", "WEEK 1",   as.Date("2021-04-27"), 10.0,
    "TEST01", "PAT01",  "PARAM01", "WEEK 2",   as.Date("2021-04-30"), 12.0,

    "TEST01", "PAT02",  "PARAM01", "SCREEN",   as.Date("2021-04-27"), 15.0,
    "TEST01", "PAT02",  "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0,
    "TEST01", "PAT02",  "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0,
    "TEST01", "PAT02",  "PARAM01", "WEEK 1",   as.Date("2021-04-27"), 10.0,
    "TEST01", "PAT02",  "PARAM01", "WEEK 2",   as.Date("2021-04-30"), 12.0,

    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-27"), 15.0,
    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-25"), 14.0,
    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-23"), 15.0,
    "TEST01", "PAT01",  "PARAM02", "BASELINE", as.Date("2021-04-27"), 10.0,
    "TEST01", "PAT01",  "PARAM02", "WEEK 2",   as.Date("2021-04-30"), 12.0,

    "TEST01", "PAT02",  "PARAM02", "SCREEN",   as.Date("2021-04-27"), 15.0,
    "TEST01", "PAT02",  "PARAM02", "BASELINE", as.Date("2021-04-25"), 14.0,
    "TEST01", "PAT02",  "PARAM02", "WEEK 1",   as.Date("2021-04-23"), 15.0,
    "TEST01", "PAT02",  "PARAM02", "WEEK 1",   as.Date("2021-04-27"), 10.0,
    "TEST01", "PAT02",  "PARAM02", "BASELINE", as.Date("2021-04-30"), 12.0

  )
  expected_output <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~PARAMCD,  ~AVISIT,    ~ADT,                 ~AVAL, ~ABLFL,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-27"), 15.0, "Y",
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0, NA,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0, NA,
    "TEST01", "PAT01",  "PARAM01", "WEEK 1",   as.Date("2021-04-27"), 10.0, NA,
    "TEST01", "PAT01",  "PARAM01", "WEEK 2",   as.Date("2021-04-30"), 12.0, NA,

    "TEST01", "PAT02",  "PARAM01", "SCREEN",   as.Date("2021-04-27"), 15.0, NA,
    "TEST01", "PAT02",  "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0, "Y",
    "TEST01", "PAT02",  "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0, NA,
    "TEST01", "PAT02",  "PARAM01", "WEEK 1",   as.Date("2021-04-27"), 10.0, NA,
    "TEST01", "PAT02",  "PARAM01", "WEEK 2",   as.Date("2021-04-30"), 12.0, NA,

    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-27"), 15.0, NA,
    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-25"), 14.0, NA,
    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-23"), 15.0, NA,
    "TEST01", "PAT01",  "PARAM02", "BASELINE", as.Date("2021-04-27"), 10.0, "Y",
    "TEST01", "PAT01",  "PARAM02", "WEEK 2",   as.Date("2021-04-30"), 12.0, NA,

    "TEST01", "PAT02",  "PARAM02", "SCREEN",   as.Date("2021-04-27"), 15.0, NA,
    "TEST01", "PAT02",  "PARAM02", "BASELINE", as.Date("2021-04-25"), 14.0, NA,
    "TEST01", "PAT02",  "PARAM02", "WEEK 1",   as.Date("2021-04-23"), 15.0, NA,
    "TEST01", "PAT02",  "PARAM02", "WEEK 1",   as.Date("2021-04-27"), 10.0, NA,
    "TEST01", "PAT02",  "PARAM02", "BASELINE", as.Date("2021-04-30"), 12.0, "Y"
  )

  actual_output <- derive_var_extreme_flag(
    input,
    by_vars = vars(USUBJID, PARAMCD),
    order = vars(ADT),
    new_var = ABLFL,
    mode = "last",
    filter = AVISIT == "BASELINE"
  )

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

test_that("ABLFL = Y worst observation = HI within a subset", {
  input <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~PARAMCD,  ~AVISIT,    ~ADT,                 ~AVAL,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-27"), 15.0,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0,
    "TEST01", "PAT01",  "PARAM01", "WEEK 1",   as.Date("2021-04-27"), 10.0,
    "TEST01", "PAT01",  "PARAM01", "WEEK 2",   as.Date("2021-04-30"), 12.0,

    "TEST01", "PAT02",  "PARAM01", "SCREEN",   as.Date("2021-04-27"), 15.0,
    "TEST01", "PAT02",  "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0,
    "TEST01", "PAT02",  "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0,
    "TEST01", "PAT02",  "PARAM01", "WEEK 1",   as.Date("2021-04-27"), 10.0,
    "TEST01", "PAT02",  "PARAM01", "WEEK 2",   as.Date("2021-04-30"), 12.0,

    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-27"), 15.0,
    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-25"), 14.0,
    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-23"), 15.0,
    "TEST01", "PAT01",  "PARAM02", "BASELINE", as.Date("2021-04-27"), 10.0,
    "TEST01", "PAT01",  "PARAM02", "WEEK 2",   as.Date("2021-04-30"), 12.0,

    "TEST01", "PAT02",  "PARAM02", "SCREEN",   as.Date("2021-04-27"), 15.0,
    "TEST01", "PAT02",  "PARAM02", "BASELINE", as.Date("2021-04-25"), 14.0,
    "TEST01", "PAT02",  "PARAM02", "WEEK 1",   as.Date("2021-04-23"), 15.0,
    "TEST01", "PAT02",  "PARAM02", "WEEK 1",   as.Date("2021-04-27"), 10.0,
    "TEST01", "PAT02",  "PARAM02", "BASELINE", as.Date("2021-04-30"), 12.0

  )
  expected_output <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~PARAMCD,  ~AVISIT,    ~ADT,                 ~AVAL, ~ABLFL,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-27"), 15.0, "Y",
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0, NA,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0, NA,
    "TEST01", "PAT01",  "PARAM01", "WEEK 1",   as.Date("2021-04-27"), 10.0, NA,
    "TEST01", "PAT01",  "PARAM01", "WEEK 2",   as.Date("2021-04-30"), 12.0, NA,

    "TEST01", "PAT02",  "PARAM01", "SCREEN",   as.Date("2021-04-27"), 15.0, NA,
    "TEST01", "PAT02",  "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0, NA,
    "TEST01", "PAT02",  "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0, "Y",
    "TEST01", "PAT02",  "PARAM01", "WEEK 1",   as.Date("2021-04-27"), 10.0, NA,
    "TEST01", "PAT02",  "PARAM01", "WEEK 2",   as.Date("2021-04-30"), 12.0, NA,

    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-27"), 15.0, NA,
    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-25"), 14.0, NA,
    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-23"), 15.0, NA,
    "TEST01", "PAT01",  "PARAM02", "BASELINE", as.Date("2021-04-27"), 10.0, "Y",
    "TEST01", "PAT01",  "PARAM02", "WEEK 2",   as.Date("2021-04-30"), 12.0, NA,

    "TEST01", "PAT02",  "PARAM02", "SCREEN",   as.Date("2021-04-27"), 15.0, NA,
    "TEST01", "PAT02",  "PARAM02", "BASELINE", as.Date("2021-04-25"), 14.0, "Y",
    "TEST01", "PAT02",  "PARAM02", "WEEK 1",   as.Date("2021-04-23"), 15.0, NA,
    "TEST01", "PAT02",  "PARAM02", "WEEK 1",   as.Date("2021-04-27"), 10.0, NA,
    "TEST01", "PAT02",  "PARAM02", "BASELINE", as.Date("2021-04-30"), 12.0, NA
  )

  actual_output <- derive_var_extreme_flag(
    input,
    by_vars = vars(USUBJID, PARAMCD),
    order = vars(AVAL, ADT),
    new_var = ABLFL,
    mode = "last",
    filter = AVISIT == "BASELINE"
  )

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

test_that("ABLFL = Y worst observation = LO within a subset", {
  input <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~PARAMCD,  ~AVISIT,    ~ADT,                 ~AVAL,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-27"), 15.0,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0,
    "TEST01", "PAT01",  "PARAM01", "WEEK 1",   as.Date("2021-04-27"), 10.0,
    "TEST01", "PAT01",  "PARAM01", "WEEK 2",   as.Date("2021-04-30"), 12.0,

    "TEST01", "PAT02",  "PARAM01", "SCREEN",   as.Date("2021-04-27"), 15.0,
    "TEST01", "PAT02",  "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0,
    "TEST01", "PAT02",  "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0,
    "TEST01", "PAT02",  "PARAM01", "WEEK 1",   as.Date("2021-04-27"), 10.0,
    "TEST01", "PAT02",  "PARAM01", "WEEK 2",   as.Date("2021-04-30"), 12.0,

    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-27"), 15.0,
    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-25"), 14.0,
    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-23"), 15.0,
    "TEST01", "PAT01",  "PARAM02", "BASELINE", as.Date("2021-04-27"), 10.0,
    "TEST01", "PAT01",  "PARAM02", "WEEK 2",   as.Date("2021-04-30"), 12.0,

    "TEST01", "PAT02",  "PARAM02", "SCREEN",   as.Date("2021-04-27"), 15.0,
    "TEST01", "PAT02",  "PARAM02", "BASELINE", as.Date("2021-04-25"), 14.0,
    "TEST01", "PAT02",  "PARAM02", "WEEK 1",   as.Date("2021-04-23"), 15.0,
    "TEST01", "PAT02",  "PARAM02", "WEEK 1",   as.Date("2021-04-27"), 10.0,
    "TEST01", "PAT02",  "PARAM02", "BASELINE", as.Date("2021-04-30"), 12.0

  )
  expected_output <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~PARAMCD,  ~AVISIT,    ~ADT,                 ~AVAL, ~ABLFL,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-27"), 15.0, NA,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0, "Y",
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0, NA,
    "TEST01", "PAT01",  "PARAM01", "WEEK 1",   as.Date("2021-04-27"), 10.0, NA,
    "TEST01", "PAT01",  "PARAM01", "WEEK 2",   as.Date("2021-04-30"), 12.0, NA,

    "TEST01", "PAT02",  "PARAM01", "SCREEN",   as.Date("2021-04-27"), 15.0, NA,
    "TEST01", "PAT02",  "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0, "Y",
    "TEST01", "PAT02",  "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0, NA,
    "TEST01", "PAT02",  "PARAM01", "WEEK 1",   as.Date("2021-04-27"), 10.0, NA,
    "TEST01", "PAT02",  "PARAM01", "WEEK 2",   as.Date("2021-04-30"), 12.0, NA,

    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-27"), 15.0, NA,
    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-25"), 14.0, NA,
    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-23"), 15.0, NA,
    "TEST01", "PAT01",  "PARAM02", "BASELINE", as.Date("2021-04-27"), 10.0, "Y",
    "TEST01", "PAT01",  "PARAM02", "WEEK 2",   as.Date("2021-04-30"), 12.0, NA,

    "TEST01", "PAT02",  "PARAM02", "SCREEN",   as.Date("2021-04-27"), 15.0, NA,
    "TEST01", "PAT02",  "PARAM02", "BASELINE", as.Date("2021-04-25"), 14.0, NA,
    "TEST01", "PAT02",  "PARAM02", "WEEK 1",   as.Date("2021-04-23"), 15.0, NA,
    "TEST01", "PAT02",  "PARAM02", "WEEK 1",   as.Date("2021-04-27"), 10.0, NA,
    "TEST01", "PAT02",  "PARAM02", "BASELINE", as.Date("2021-04-30"), 12.0, "Y"
  )

  actual_output <- derive_var_extreme_flag(
    input,
    by_vars = vars(USUBJID, PARAMCD),
    order = vars(desc(AVAL), ADT),
    new_var = ABLFL,
    mode = "last",
    filter = AVISIT == "BASELINE"
  )

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

test_that("ABLFL = Y average records within a subset", {
  input <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~PARAMCD,  ~AVISIT,    ~ADT,                 ~AVAL, ~DTYPE,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-27"), 15.0, NA,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0, NA,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0, "AVERAGE",
    "TEST01", "PAT01",  "PARAM01", "WEEK 1",   as.Date("2021-04-27"), 10.0, "AVERAGE",
    "TEST01", "PAT01",  "PARAM01", "WEEK 2",   as.Date("2021-04-30"), 12.0, NA,

    "TEST01", "PAT02",  "PARAM01", "SCREEN",   as.Date("2021-04-27"), 15.0, "AVERAGE",
    "TEST01", "PAT02",  "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0, "AVERAGE",
    "TEST01", "PAT02",  "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0, "AVERAGE",
    "TEST01", "PAT02",  "PARAM01", "WEEK 1",   as.Date("2021-04-27"), 10.0, "AVERAGE",
    "TEST01", "PAT02",  "PARAM01", "WEEK 2",   as.Date("2021-04-30"), 12.0, "AVERAGE",

    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-27"), 15.0, "AVERAGE",
    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-25"), 14.0, "AVERAGE",
    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-23"), 15.0, NA,
    "TEST01", "PAT01",  "PARAM02", "BASELINE", as.Date("2021-04-27"), 10.0, "AVERAGE",
    "TEST01", "PAT01",  "PARAM02", "WEEK 2",   as.Date("2021-04-30"), 12.0, NA,

    "TEST01", "PAT02",  "PARAM02", "SCREEN",   as.Date("2021-04-27"), 15.0, NA,
    "TEST01", "PAT02",  "PARAM02", "BASELINE", as.Date("2021-04-25"), 14.0, NA,
    "TEST01", "PAT02",  "PARAM02", "WEEK 1",   as.Date("2021-04-23"), 15.0, NA,
    "TEST01", "PAT02",  "PARAM02", "WEEK 1",   as.Date("2021-04-27"), 10.0, NA,
    "TEST01", "PAT02",  "PARAM02", "BASELINE", as.Date("2021-04-30"), 12.0, NA

  )
  expected_output <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~PARAMCD,  ~AVISIT,    ~ADT,                 ~AVAL, ~DTYPE,    ~ABLFL,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-27"), 15.0, NA,        NA,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0, NA,        NA,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0, "AVERAGE", "Y",
    "TEST01", "PAT01",  "PARAM01", "WEEK 1",   as.Date("2021-04-27"), 10.0, "AVERAGE", NA,
    "TEST01", "PAT01",  "PARAM01", "WEEK 2",   as.Date("2021-04-30"), 12.0, NA,        NA,

    "TEST01", "PAT02",  "PARAM01", "SCREEN",   as.Date("2021-04-27"), 15.0, "AVERAGE", NA,
    "TEST01", "PAT02",  "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0, "AVERAGE", "Y",
    "TEST01", "PAT02",  "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0, "AVERAGE", NA,
    "TEST01", "PAT02",  "PARAM01", "WEEK 1",   as.Date("2021-04-27"), 10.0, "AVERAGE", NA,
    "TEST01", "PAT02",  "PARAM01", "WEEK 2",   as.Date("2021-04-30"), 12.0, "AVERAGE", NA,

    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-27"), 15.0, "AVERAGE", NA,
    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-25"), 14.0, "AVERAGE", NA,
    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-23"), 15.0, NA,        NA,
    "TEST01", "PAT01",  "PARAM02", "BASELINE", as.Date("2021-04-27"), 10.0, "AVERAGE", "Y",
    "TEST01", "PAT01",  "PARAM02", "WEEK 2",   as.Date("2021-04-30"), 12.0, NA,        NA,

    "TEST01", "PAT02",  "PARAM02", "SCREEN",   as.Date("2021-04-27"), 15.0, NA,        NA,
    "TEST01", "PAT02",  "PARAM02", "BASELINE", as.Date("2021-04-25"), 14.0, NA,        NA,
    "TEST01", "PAT02",  "PARAM02", "WEEK 1",   as.Date("2021-04-23"), 15.0, NA,        NA,
    "TEST01", "PAT02",  "PARAM02", "WEEK 1",   as.Date("2021-04-27"), 10.0, NA,        NA,
    "TEST01", "PAT02",  "PARAM02", "BASELINE", as.Date("2021-04-30"), 12.0, NA,        NA
  )

  actual_output <- derive_var_extreme_flag(
    input,
    by_vars = vars(USUBJID, PARAMCD),
    order = vars(ADT, desc(AVAL)),
    new_var = ABLFL,
    mode = "last",
    filter = AVISIT == "BASELINE" & DTYPE == "AVERAGE"
  )

  expect_dfs_equal(
    expected_output,
    actual_output,
    keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT", "ADT", "AVAL")
  )
})

test_that("ABLFL = Y using last observation within a subset and multiple baselines
          possible", {
  input <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~PARAMCD,  ~AVISIT,    ~ADT,                 ~AVAL,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-27"), 15.0,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0,
    "TEST01", "PAT01",  "PARAM01", "WEEK 1",   as.Date("2021-04-27"), 10.0,
    "TEST01", "PAT01",  "PARAM01", "WEEK 2",   as.Date("2021-04-30"), 12.0,

    "TEST01", "PAT02",  "PARAM01", "SCREEN",   as.Date("2021-04-27"), 15.0,
    "TEST01", "PAT02",  "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0,
    "TEST01", "PAT02",  "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0,
    "TEST01", "PAT02",  "PARAM01", "WEEK 1",   as.Date("2021-04-27"), 10.0,
    "TEST01", "PAT02",  "PARAM01", "WEEK 2",   as.Date("2021-04-30"), 12.0,

    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-27"), 15.0,
    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-25"), 14.0,
    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-23"), 15.0,
    "TEST01", "PAT01",  "PARAM02", "BASELINE", as.Date("2021-04-27"), 10.0,
    "TEST01", "PAT01",  "PARAM02", "WEEK 2",   as.Date("2021-04-30"), 12.0,

    "TEST01", "PAT02",  "PARAM02", "SCREEN",   as.Date("2021-04-27"), 15.0,
    "TEST01", "PAT02",  "PARAM02", "BASELINE", as.Date("2021-04-25"), 14.0,
    "TEST01", "PAT02",  "PARAM02", "WEEK 1",   as.Date("2021-04-23"), 15.0,
    "TEST01", "PAT02",  "PARAM02", "WEEK 1",   as.Date("2021-04-27"), 10.0,
    "TEST01", "PAT02",  "PARAM02", "BASELINE", as.Date("2021-04-30"), 12.0
  )

  expected_output <- tibble::tribble(
    ~STUDYID, ~USUBJID, ~PARAMCD,  ~AVISIT,    ~ADT,                 ~AVAL, ~ABLFL,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-27"), 15.0, "Y",
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0, NA,
    "TEST01", "PAT01",  "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0, NA,
    "TEST01", "PAT01",  "PARAM01", "WEEK 1",   as.Date("2021-04-27"), 10.0, "Y",
    "TEST01", "PAT01",  "PARAM01", "WEEK 2",   as.Date("2021-04-30"), 12.0, NA,

    "TEST01", "PAT02",  "PARAM01", "SCREEN",   as.Date("2021-04-27"), 15.0, NA,
    "TEST01", "PAT02",  "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0, "Y",
    "TEST01", "PAT02",  "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0, NA,
    "TEST01", "PAT02",  "PARAM01", "WEEK 1",   as.Date("2021-04-27"), 10.0, "Y",
    "TEST01", "PAT02",  "PARAM01", "WEEK 2",   as.Date("2021-04-30"), 12.0, NA,

    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-27"), 15.0, NA,
    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-25"), 14.0, NA,
    "TEST01", "PAT01",  "PARAM02", "SCREEN",   as.Date("2021-04-23"), 15.0, NA,
    "TEST01", "PAT01",  "PARAM02", "BASELINE", as.Date("2021-04-27"), 10.0, "Y",
    "TEST01", "PAT01",  "PARAM02", "WEEK 2",   as.Date("2021-04-30"), 12.0, NA,

    "TEST01", "PAT02",  "PARAM02", "SCREEN",   as.Date("2021-04-27"), 15.0, NA,
    "TEST01", "PAT02",  "PARAM02", "BASELINE", as.Date("2021-04-25"), 14.0, NA,
    "TEST01", "PAT02",  "PARAM02", "WEEK 1",   as.Date("2021-04-23"), 15.0, NA,
    "TEST01", "PAT02",  "PARAM02", "WEEK 1",   as.Date("2021-04-27"), 10.0, "Y",
    "TEST01", "PAT02",  "PARAM02", "BASELINE", as.Date("2021-04-30"), 12.0, "Y"
  )

  actual_output <- derive_var_extreme_flag(
    input,
    by_vars = vars(USUBJID, PARAMCD, AVISIT),
    order = vars(ADT),
    new_var = ABLFL,
    mode = "last",
    filter = AVISIT %in% c("BASELINE", "WEEK 1")
  )

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

test_that("Derive worst flag works correctly", {

  expected_output <- input_worst_flag %>%
    mutate(WORSTFL = c("Y", NA, NA, "Y", "Y", "Y", NA, "Y", "Y", "Y", NA,
                       "Y", NA, "Y", "Y", "Y", NA, NA, "Y", "Y", "Y", "Y",
                       "Y", NA, NA))

  actual_output <- derive_var_worst_flag(
    input_worst_flag,
    by_vars = vars(USUBJID, PARAMCD, AVISIT),
    order = vars(desc(ADT)),
    new_var = WORSTFL,
    param_var = PARAMCD,
    analysis_var = AVAL,
    worst_high = c("PARAM01", "PARAM03"),
    worst_low = "PARAM02"
  )

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

test_that("Derive worst flag works correctly with no worst_high option", {

  expected_output <- input_worst_flag %>%
    mutate(WORSTFL = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
                       "Y", NA, "Y", "Y", "Y", NA, NA, "Y", "Y", NA, NA,
                       NA, NA, NA))

  actual_output <- derive_var_worst_flag(
    input_worst_flag,
    by_vars = vars(USUBJID, PARAMCD, AVISIT),
    order = vars(ADT),
    new_var = WORSTFL,
    param_var = PARAMCD,
    analysis_var = AVAL,
    worst_high = character(0),
    worst_low = "PARAM02"
  )

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

test_that("Derive worst flag catches invalid parameters", {

  expect_error(
    derive_var_worst_flag(
      input_worst_flag,
      by_vars = vars(USUBJID, PARAMCD, AVISIT),
      order = vars(ADT),
      new_var = WORSTFL,
      param_var = PARAMCD,
      analysis_var = AVAL,
      worst_high = character(0),
      worst_low = c("A", "B")
    ),
    regexp = paste(
      "^The following parameter\\(-s\\) in `worst_low`",
      "are not available in column PARAMCD: A, B$"
    )
  )

  expect_error(
    derive_var_worst_flag(
      input_worst_flag,
      new_var = WORSTFL,
      by_vars = vars(USUBJID, PARAMCD, AVISIT),
      order = vars(ADT),
      param_var = PARAMCD,
      analysis_var = AVAL,
      worst_high = "A",
      worst_low = character(0)
    ),
    regexp = paste(
      "^The following parameter\\(-s\\) in `worst_high`",
      "are not available in column PARAMCD: A$"
    )
  )

  expect_error(
    derive_var_worst_flag(
      input_worst_flag,
      by_vars = vars(USUBJID, PARAMCD, AVISIT),
      order = vars(ADT),
      new_var = WORSTFL,
      param_var = PARAMCD,
      analysis_var = AVAL,
      worst_high = c("A", "B", "C"),
      worst_low = c("B", "C", "D")
    ),
    regexp = paste(
      "^The following parameter\\(-s\\) are both assigned to `worst_high` and `worst_low`",
      "flags: B, C$"
    )
  )

})