tests/testthat/test-derive_vars_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_vars_last_dose works as expected", {

  expected_output <- mutate(
    input_ae,
    EXSTDTC = as.Date(c("2020-01-01", "2020-08-29", "2020-09-02", NA, "2020-01-20", NA, NA)),
    EXENDTC = as.Date(c("2020-01-01", "2020-08-29", "2020-09-02", NA, "2020-01-20", NA, NA)),
    EXSEQ = c(1, 2, 3, NA, 2, NA, NA),
    EXDOSE = c(10, 10, 10, NA, 0, NA, NA),
    EXTRT = c("treatment", "treatment", "treatment", NA, "placebo", NA, NA)
  )

  res <- derive_vars_last_dose(
    input_ae,
    input_ex,
    filter_ex = (EXDOSE > 0) | (EXDOSE == 0 & EXTRT == "placebo"),
    by_vars = vars(STUDYID, USUBJID),
    dose_date = EXENDTC,
    new_vars = vars(EXDOSE, EXTRT, EXSEQ, EXENDTC, EXSTDTC),
    analysis_date = AESTDTC,
    single_dose_condition = (EXSTDTC == EXENDTC),
    traceability_vars = NULL
  )

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

})


test_that("derive_vars_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_vars_last_dose(
      input_ae,
      input_ex_wrong,
      filter_ex = (EXDOSE > 0) | (EXDOSE == 0 & EXTRT == "placebo"),
      by_vars = vars(STUDYID, USUBJID),
      dose_date = EXENDTC,
      analysis_date = AESTDTC,
      single_dose_condition = (EXSTDTC == EXENDTC),
      traceability_vars = NULL
    ),
    regexp = "Specified single_dose_condition is not satisfied."
  )

})


test_that("derive_vars_last_dose returns traceability vars", {

  expected_output <- mutate(
    input_ae,
    EXSTDTC = as.Date(c("2020-01-01", "2020-08-29", "2020-09-02", NA, "2020-01-20", NA, NA)),
    EXENDTC = as.Date(c("2020-01-01", "2020-08-29", "2020-09-02", NA, "2020-01-20", NA, NA)),
    EXSEQ = c(1, 2, 3, NA, 2, NA, NA),
    EXDOSE = c(10, 10, 10, NA, 0, NA, NA),
    EXTRT = c("treatment", "treatment", "treatment", NA, "placebo", NA, NA),
    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)
    )

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

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

})


test_that("derive_vars_last_dose when multiple doses on same date - error", {
  input_ex_dup <- dplyr::bind_rows(
    input_ex,
    tibble::tribble(
      ~STUDYID,   ~USUBJID,   ~EXSTDTC,              ~EXENDTC,        ~EXSEQ, ~EXDOSE, ~EXTRT,
      "my_study", "subject2", as.Date("2020-01-20"), as.Date("2020-01-20"), 3, 0, "placebo")
  )

  expected_output <- mutate(
    input_ae,
    EXSTDTC = as.Date(c("2020-01-01", "2020-08-29", "2020-09-02", NA, "2020-01-20", NA, NA)),
    EXENDTC = as.Date(c("2020-01-01", "2020-08-29", "2020-09-02", NA, "2020-01-20", NA, NA)),
    EXSEQ = c(1, 2, 3, NA, 3, NA, NA),
    EXDOSE = c(10, 10, 10, NA, 0, NA, NA),
    EXTRT = c("treatment", "treatment", "treatment", NA, "placebo", NA, NA)
  )

  expect_error(
    derive_vars_last_dose(
      input_ae,
      input_ex_dup,
      filter_ex = (EXDOSE > 0) | (EXDOSE == 0 & EXTRT == "placebo"),
      by_vars = vars(STUDYID, USUBJID),
      dose_date = EXENDTC,
      analysis_date = AESTDTC,
      single_dose_condition = (EXSTDTC == EXENDTC),
      traceability_vars = NULL
    ),
    regexp = "Multiple doses exist for the same dose_date. Update dose_id to identify unique doses."
  )

})


test_that("derive_vars_last_dose when multiple doses on same date - dose_id supplied", {
  input_ex_dup <- dplyr::bind_rows(
    input_ex,
    tibble::tribble(
      ~STUDYID,   ~USUBJID,   ~EXSTDTC,              ~EXENDTC,        ~EXSEQ, ~EXDOSE, ~EXTRT,
      "my_study", "subject2", as.Date("2020-01-20"), as.Date("2020-01-20"), 3, 0, "placebo")
  )

  expected_output <- mutate(
    input_ae,
    EXSTDTC = as.Date(c("2020-01-01", "2020-08-29", "2020-09-02", NA, "2020-01-20", NA, NA)),
    EXENDTC = as.Date(c("2020-01-01", "2020-08-29", "2020-09-02", NA, "2020-01-20", NA, NA)),
    EXSEQ = c(1, 2, 3, NA, 3, NA, NA),
    EXDOSE = c(10, 10, 10, NA, 0, NA, NA),
    EXTRT = c("treatment", "treatment", "treatment", NA, "placebo", NA, NA)
  )

  res <- derive_vars_last_dose(
    input_ae,
    input_ex_dup,
    filter_ex = (EXDOSE > 0) | (EXDOSE == 0 & EXTRT == "placebo"),
    by_vars = vars(STUDYID, USUBJID),
    dose_date = EXENDTC,
    dose_id = vars(EXSEQ),
    new_vars = vars(EXDOSE, EXTRT, EXSEQ, EXSTDTC, EXENDTC),
    analysis_date = AESTDTC,
    single_dose_condition = (EXSTDTC == EXENDTC),
    traceability_vars = NULL
  )

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


})