tests/testthat/test-derive_var_last_dose_date.R

In epijim/admiral: ADaM in R Asset Library

input_ae <- tibble::tribble(
  ~STUDYID, ~USUBJID, ~AESEQ, ~AESTDTC,
  "my_study", "subject1", 1, "2020-01-02",
  "my_study", "subject1", 2, "2020-08-31",
  "my_study", "subject1", 3, "2020-10-10",
  "my_study", "subject2", 1, "2019-05-15",
  "my_study", "subject2", 2, "2020-02-20",
  "my_study", "subject3", 1, "2020-03-02",
  "my_study", "subject4", 1, "2020-11-02"
)

input_ex <- tibble::tribble(
  ~STUDYID,   ~USUBJID,   ~EXSTDTC,     ~EXENDTC,    ~EXSEQ, ~EXDOSE, ~EXTRT,
  "my_study", "subject1", "2020-01-01", "2020-01-01", 1,     10,      "treatment",
  "my_study", "subject1", "2020-08-29", "2020-08-29", 2,     10,      "treatment",
  "my_study", "subject1", "2020-09-02", "2020-09-02", 3,     10,      "treatment",
  "my_study", "subject1", "2020-10-20", "2020-10-20", 4,     10,      "treatment",
  "my_study", "subject2", "2019-05-25", "2019-05-25", 1,      0,      "placebo",
  "my_study", "subject2", "2020-01-20", "2020-01-20", 2,      0,      "placebo",
  "my_study", "subject3", "2020-03-15", "2020-03-15", 1,     10,      "treatment"
) %>%
  mutate(EXSTDTC = as.Date(EXSTDTC), EXENDTC = as.Date(EXENDTC))


test_that("derive_var_last_dose_date works as expected output_datetime = FALSE", {

  expected_output <-  tibble::tribble(
  ~STUDYID,        ~USUBJID,  ~AESEQ,    ~AESTDTC,      ~LDOSEDTM,
    "my_study",   "subject1",  1,        "2020-01-02",   "2020-01-01",
    "my_study",   "subject1",  2,        "2020-08-31",   "2020-08-29",
    "my_study",   "subject1",  3,        "2020-10-10",   "2020-09-02",
    "my_study",   "subject2",  1,        "2019-05-15",   NA_character_,
    "my_study",   "subject2",  2,        "2020-02-20",   "2020-01-20",
    "my_study",   "subject3",  1,        "2020-03-02",   NA_character_,
    "my_study",   "subject4",  1,        "2020-11-02",   NA_character_) %>%
    mutate(LDOSEDTM = as.Date(LDOSEDTM))

  res <- derive_var_last_dose_date(
    input_ae,
    input_ex,
    filter_ex = (EXDOSE > 0) | (EXDOSE == 0 & EXTRT == "placebo"),
    by_vars = vars(STUDYID, USUBJID),
    dose_date = EXENDTC,
    analysis_date = AESTDTC,
    new_var = LDOSEDTM,
    single_dose_condition = (EXSTDTC == EXENDTC),
    output_datetime = FALSE,
    traceability_vars = NULL
  )

  expect_dfs_equal(expected_output, res, keys = c("STUDYID", "USUBJID", "AESEQ", "AESTDTC"))

})

test_that("derive_var_last_dose_date works as expected with output_datetime = TRUE", {

  expected_output <-  tibble::tribble(
    ~STUDYID,        ~USUBJID,  ~AESEQ,    ~AESTDTC,      ~LDOSEDTM,
    "my_study",   "subject1",  1,        "2020-01-02",   "2020-01-01 00:00:00",
    "my_study",   "subject1",  2,        "2020-08-31",   "2020-08-29 00:00:00",
    "my_study",   "subject1",  3,        "2020-10-10",   "2020-09-02 00:00:00",
    "my_study",   "subject2",  1,        "2019-05-15",   NA_character_,
    "my_study",   "subject2",  2,        "2020-02-20",   "2020-01-20 00:00:00",
    "my_study",   "subject3",  1,        "2020-03-02",   NA_character_,
    "my_study",   "subject4",  1,        "2020-11-02",   NA_character_) %>%
    mutate(LDOSEDTM = as.POSIXct(as.character(LDOSEDTM), tz = "UTC"))

  res <- derive_var_last_dose_date(
    input_ae,
    input_ex,
    filter_ex = (EXDOSE > 0) | (EXDOSE == 0 & EXTRT == "placebo"),
    by_vars = vars(STUDYID, USUBJID),
    dose_date = EXENDTC,
    analysis_date = AESTDTC,
    new_var = LDOSEDTM,
    output_datetime = TRUE,
    single_dose_condition = (EXSTDTC == EXENDTC),
    traceability_vars = NULL
  )

  expect_dfs_equal(expected_output, res, keys = c("STUDYID", "USUBJID", "AESEQ", "AESTDTC"))

})

test_that("derive_var_last_dose_date returns traceability vars", {

  expected_output <-  tibble::tribble(
    ~STUDYID,    ~USUBJID,   ~AESEQ,  ~AESTDTC,      ~LDOSEDTM,
    "my_study",  "subject1",  1,      "2020-01-02",  "2020-01-01 00:00:00",
    "my_study",  "subject1",  2,      "2020-08-31",  "2020-08-29 00:00:00",
    "my_study",  "subject1",  3,      "2020-10-10",  "2020-09-02 00:00:00",
    "my_study",  "subject2",  1,      "2019-05-15",  NA_character_,
    "my_study",  "subject2",  2,      "2020-02-20",  "2020-01-20 00:00:00",
    "my_study",  "subject3",  1,      "2020-03-02",  NA_character_,
    "my_study",  "subject4",  1,      "2020-11-02",  NA_character_) %>%
    mutate(LDOSEDTM = as.POSIXct(as.character(LDOSEDTM), tz = "UTC"),
          LDOSEDOM = c("EX", "EX", "EX", NA, "EX", NA, NA),
          LDOSESEQ = c(1, 2, 3, NA, 2, NA, NA),
          LDOSEVAR = c("EXENDTC", "EXENDTC", "EXENDTC", NA, "EXENDTC", NA, NA))

  res <- derive_var_last_dose_date(
    input_ae,
    input_ex,
    filter_ex = (EXDOSE > 0) | (EXDOSE == 0 & EXTRT == "placebo"),
    by_vars = vars(STUDYID, USUBJID),
    dose_date = EXENDTC,
    analysis_date = AESTDTC,
    new_var = LDOSEDTM,
    single_dose_condition = (EXSTDTC == EXENDTC),
    output_datetime = TRUE,
    traceability_vars = dplyr::vars(LDOSEDOM = "EX", LDOSESEQ = EXSEQ, LDOSEVAR = "EXENDTC"))

  expect_dfs_equal(expected_output, res, keys = c("STUDYID", "USUBJID", "AESEQ", "AESTDTC"))

})