tests/testthat/test-derive_var_last_dose_grp.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", 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,     1,      "treatment",
  "my_study", "subject1", "2020-08-29", "2020-08-29", 2,     3,      "treatment",
  "my_study", "subject1", "2020-09-02", "2020-09-02", 3,     4,      "treatment",
  "my_study", "subject1", "2020-10-20", "2020-10-20", 4,     4,      "treatment",
  "my_study", "subject2", "2019-05-25", "2019-05-25", 1,     6,      "placebo",
  "my_study", "subject3", "2020-01-20", "2020-01-20", 2,     7,      "placebo",
  "my_study", "subject4", "2020-03-15", "2020-03-15", 1,     13,     "treatment"
) %>%
  mutate(EXSTDTC = as.Date(EXSTDTC), EXENDTC = as.Date(EXENDTC))


test_that("derive_last_dose_date works as expected", {

  expected_output <- tibble::tribble(
  ~STUDYID, ~USUBJID,  ~AESEQ, ~AESTDTC, ~LDGRP,
  "my_study", "subject1",     1, "2020-01-02", "G1",
  "my_study", "subject1",     2, "2020-08-31", "G1",
  "my_study", "subject1",     3, "2020-10-10", "G1",
  "my_study", "subject2",     2, "2020-02-20", "G2",
  "my_study", "subject3",     1, "2020-03-02", "G2",
  "my_study", "subject4",     1, "2020-11-02", "G3")


  res <- derive_var_last_dose_grp(input_ae,
                     input_ex,
                     filter_ex = (EXDOSE > 0) | (EXDOSE == 0 & EXTRT == "placebo"),
                     by_vars = vars(STUDYID, USUBJID),
                     dose_date = EXENDTC,
                     new_var = LDGRP,
                     grp_brks = c(1, 5, 10, 15),
                     grp_lbls = c("G1", "G2", "G3"),
                     dose_var = EXDOSE,
                     analysis_date = AESTDTC,
                     single_dose_condition = (EXSTDTC == EXENDTC),
                     traceability_vars = NULL)

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

  })