tests/testthat/test-derive_last_dose.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_last_dose works as expected", {

  expected_output <- mutate(
    input_ae,
    LDOSEDTM = as.POSIXct(
      c("2020-01-01", "2020-08-29", "2020-09-02", NA, "2020-01-20", NA, NA), tz = "UTC"
    )
  )

  res <- derive_last_dose(
    input_ae,
    input_ex,
    filter_ex = (EXDOSE > 0) | (EXDOSE == 0 & EXTRT == "placebo"),
    by_vars = vars(STUDYID, USUBJID),
    dose_start = EXSTDTC,
    dose_end = EXENDTC,
    analysis_date = AESTDTC,
    dataset_seq_var = AESEQ,
    new_var = LDOSEDTM,
    output_datetime = TRUE,
    check_dates_only = FALSE,
    traceability_vars = NULL
  )

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

})

test_that("derive_last_dose works as expected with dates only", {

  expected_output <- mutate(
    input_ae,
    LDOSEDTM = as.Date(
      c("2020-01-01", "2020-08-29", "2020-09-02", NA, "2020-01-20", NA, NA)
    )
  )

  res <- derive_last_dose(
    input_ae,
    input_ex,
    filter_ex = (EXDOSE > 0) | (EXDOSE == 0 & EXTRT == "placebo"),
    by_vars = vars(STUDYID, USUBJID),
    dose_start = EXSTDTC,
    dose_end = EXENDTC,
    analysis_date = AESTDTC,
    dataset_seq_var = AESEQ,
    new_var = LDOSEDTM,
    output_datetime = FALSE,
    check_dates_only = FALSE,
    traceability_vars = NULL
  )

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

})

test_that("derive_last_dose checks validity of start and end dose inputs", {

  input_ex_wrong <- dplyr::bind_rows(
    input_ex,
    tibble::tribble(
      ~STUDYID,   ~USUBJID,   ~EXSTDTC,              ~EXENDTC,        ~EXSEQ, ~EXDOSE, ~EXTRT,
      "my_study", "subject4", as.Date("2020-11-05"), as.Date("2020-11-06"), 1, 10, "treatment")
  )

  expect_error(
    derive_last_dose(
      input_ae,
      input_ex_wrong,
      filter_ex = (EXDOSE > 0) |
        (EXDOSE == 0 & EXTRT == "placebo"),
      by_vars = vars(STUDYID, USUBJID),
      dose_start = EXSTDTC,
      dose_end = EXENDTC,
      analysis_date = AESTDTC,
      dataset_seq_var = AESEQ,
      new_var = LDOSEDTM,
      output_datetime = FALSE,
      check_dates_only = FALSE,
      traceability_vars = NULL
    ),
    regexp = "Specified single_dose_condition is not satisfied."
  )

})

test_that(paste("derive_last_dose checks validity of start and end dose inputs",
                "- time component (check_dates_only = FALSE)"), {

  input_ex_wrong <- dplyr::bind_rows(
    mutate_at(input_ex, c("EXSTDTC", "EXENDTC"), as.POSIXct),
    tibble::tribble(
      ~STUDYID,   ~USUBJID,   ~EXSTDTC, ~EXENDTC, ~EXSEQ, ~EXDOSE, ~EXTRT,
      "my_study", "subject4", as.POSIXct("2020-11-06 00:00:00"),
      as.POSIXct("2020-11-06 00:00:01"), 1, 10, "treatment")
  )

  expect_error(
    derive_last_dose(
      input_ae,
      input_ex_wrong,
      filter_ex = (EXDOSE > 0) |
        (EXDOSE == 0 & EXTRT == "placebo"),
      by_vars = vars(STUDYID, USUBJID),
      dose_start = EXSTDTC,
      dose_end = EXENDTC,
      analysis_date = AESTDTC,
      dataset_seq_var = AESEQ,
      new_var = LDOSEDTM,
      output_datetime = FALSE,
      check_dates_only = FALSE,
      traceability_vars = NULL
    ),
    regexp = "Specified single_dose_condition is not satisfied."
  )
})

test_that(
  paste("derive_last_dose checks validity of start and end dose inputs",
        "- time component (check_dates_only = TRUE)"), {

  input_ex_wrong <- dplyr::bind_rows(
    mutate_at(input_ex, c("EXSTDTC", "EXENDTC"), as.POSIXct),
    tibble::tribble(
      ~STUDYID,   ~USUBJID,   ~EXSTDTC, ~EXENDTC, ~EXSEQ, ~EXDOSE, ~EXTRT,
      "my_study", "subject4", as.POSIXct("2020-11-06 00:00:00"),
      as.POSIXct("2020-11-06 00:00:01"), 1, 10, "treatment")
  )

  expected_output <- expected_output <- mutate(
    input_ae,
    LDOSEDTM = as.Date(
      c("2020-01-01", "2020-08-29", "2020-09-02", NA, "2020-01-20", NA, NA)
    )
  )

  res <- derive_last_dose(
    input_ae,
    input_ex_wrong,
    filter_ex = (EXDOSE > 0) | (EXDOSE == 0 & EXTRT == "placebo"),
    by_vars = vars(STUDYID, USUBJID),
    dose_start = EXSTDTC,
    dose_end = EXENDTC,
    analysis_date = AESTDTC,
    dataset_seq_var = AESEQ,
    new_var = LDOSEDTM,
    output_datetime = FALSE,
    check_dates_only = TRUE,
    traceability_vars = NULL
  )

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

})

test_that("derive_last_dose returns traceability vars", {

  expected_output <- mutate(
    input_ae,
    LDOSEDOM = c("EX", "EX", "EX", NA, "EX", NA, NA),
    LDOSESEQ = c(1, 2, 3, NA, 2, NA, NA),
    LDOSEVAR = c("EXSTDTC", "EXSTDTC", "EXSTDTC", NA, "EXSTDTC", NA, NA),
    LDOSEDTM = as.Date(
      c("2020-01-01", "2020-08-29", "2020-09-02", NA, "2020-01-20", NA, NA)
    )
  )

  res <- derive_last_dose(
    input_ae,
    input_ex,
    filter_ex = (EXDOSE > 0) | (EXDOSE == 0 & EXTRT == "placebo"),
    by_vars = vars(STUDYID, USUBJID),
    dose_start = EXSTDTC,
    dose_end = EXENDTC,
    analysis_date = AESTDTC,
    dataset_seq_var = AESEQ,
    new_var = LDOSEDTM,
    output_datetime = FALSE,
    check_dates_only = FALSE,
    traceability_vars = dplyr::vars(
      LDOSEDOM = "EX",
      LDOSESEQ = EXSEQ,
      LDOSEVAR = "EXSTDTC"
    )
  )

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

})