tests/testthat/test-derive_var_basetype.R

In epijim/admiral: ADaM in R Asset Library

test_that("records are duplicated across different `BASETYPE` values", {
  input <- tibble::tribble(
    ~USUBJID, ~EPOCH,         ~PARAMCD,  ~ASEQ, ~AVAL,
    "P01",    "RUN-IN",       "PARAM01", 1,     10,
    "P01",    "RUN-IN",       "PARAM01", 2,      9.8,
    "P01",    "DOUBLE-BLIND", "PARAM01", 3,      9.2,
    "P01",    "DOUBLE-BLIND", "PARAM01", 4,     10.1,
    "P01",    "OPEN-LABEL",   "PARAM01", 5,     10.4,
    "P01",    "OPEN-LABEL",   "PARAM01", 6,      9.9,
    "P02",    "RUN-IN",       "PARAM01", 1,     12.1,
    "P02",    "DOUBLE-BLIND", "PARAM01", 2,     10.2,
    "P02",    "DOUBLE-BLIND", "PARAM01", 3,     10.8,
    "P02",    "OPEN-LABEL",   "PARAM01", 4,     11.4,
    "P02",    "OPEN-LABEL",   "PARAM01", 5,     10.8
  )
  expect_output <- tibble::tribble(
    ~USUBJID, ~EPOCH,         ~PARAMCD,  ~ASEQ, ~AVAL, ~BASETYPE,
    "P01",    "RUN-IN",       "PARAM01", 1,     10,    "RUN-IN",
    "P01",    "RUN-IN",       "PARAM01", 2,      9.8,  "RUN-IN",
    "P01",    "DOUBLE-BLIND", "PARAM01", 3,      9.2,  "RUN-IN",
    "P01",    "DOUBLE-BLIND", "PARAM01", 4,     10.1,  "RUN-IN",
    "P01",    "OPEN-LABEL",   "PARAM01", 5,     10.4,  "RUN-IN",
    "P01",    "OPEN-LABEL",   "PARAM01", 6,      9.9,  "RUN-IN",
    "P01",    "DOUBLE-BLIND", "PARAM01", 3,      9.2,  "DOUBLE-BLIND",
    "P01",    "DOUBLE-BLIND", "PARAM01", 4,     10.1,  "DOUBLE-BLIND",
    "P01",    "OPEN-LABEL",   "PARAM01", 5,     10.4,  "DOUBLE-BLIND",
    "P01",    "OPEN-LABEL",   "PARAM01", 6,      9.9,  "DOUBLE-BLIND",
    "P01",    "OPEN-LABEL",   "PARAM01", 5,     10.4,  "OPEN-LABEL",
    "P01",    "OPEN-LABEL",   "PARAM01", 6,      9.9,  "OPEN-LABEL",
    "P02",    "RUN-IN",       "PARAM01", 1,     12.1,  "RUN-IN",
    "P02",    "DOUBLE-BLIND", "PARAM01", 2,     10.2,  "RUN-IN",
    "P02",    "DOUBLE-BLIND", "PARAM01", 3,     10.8,  "RUN-IN",
    "P02",    "OPEN-LABEL",   "PARAM01", 4,     11.4,  "RUN-IN",
    "P02",    "OPEN-LABEL",   "PARAM01", 5,     10.8,  "RUN-IN",
    "P02",    "DOUBLE-BLIND", "PARAM01", 2,     10.2,  "DOUBLE-BLIND",
    "P02",    "DOUBLE-BLIND", "PARAM01", 3,     10.8,  "DOUBLE-BLIND",
    "P02",    "OPEN-LABEL",   "PARAM01", 4,     11.4,  "DOUBLE-BLIND",
    "P02",    "OPEN-LABEL",   "PARAM01", 5,     10.8,  "DOUBLE-BLIND",
    "P02",    "OPEN-LABEL",   "PARAM01", 4,     11.4,  "OPEN-LABEL",
    "P02",    "OPEN-LABEL",   "PARAM01", 5,     10.8,  "OPEN-LABEL",
  )
  actual_output <- derive_var_basetype(
    dataset = input,
    basetypes = exprs(
      "RUN-IN" = EPOCH %in% c("RUN-IN", "STABILIZATION", "DOUBLE-BLIND", "OPEN-LABEL"),
      "DOUBLE-BLIND" = EPOCH %in% c("DOUBLE-BLIND", "OPEN-LABEL"),
      "OPEN-LABEL" = EPOCH == "OPEN-LABEL"
    )
  )

  expect_dfs_equal(actual_output, expect_output, keys = c("USUBJID", "BASETYPE", "PARAMCD", "ASEQ"))
})

test_that("records that do not match any condition are kept", {
  input <- tibble::tribble(
    ~USUBJID, ~EPOCH,         ~PARAMCD,  ~ASEQ, ~AVAL,
    "P01",    "SCREENING",    "PARAM01", 1,     10.2,
    "P01",    "RUN-IN",       "PARAM01", 2,     10,
    "P01",    "RUN-IN",       "PARAM01", 3,      9.8,
    "P01",    "DOUBLE-BLIND", "PARAM01", 4,      9.2,
    "P01",    "DOUBLE-BLIND", "PARAM01", 5,     10.1,
    "P01",    "OPEN-LABEL",   "PARAM01", 6,     10.4,
    "P01",    "OPEN-LABEL",   "PARAM01", 7,      9.9,
    "P02",    "SCREENING",    "PARAM01", 1,     12.2,
    "P02",    "RUN-IN",       "PARAM01", 2,     12.1,
    "P02",    "DOUBLE-BLIND", "PARAM01", 3,     10.2,
    "P02",    "DOUBLE-BLIND", "PARAM01", 4,     10.8,
    "P02",    "OPEN-LABEL",   "PARAM01", 5,     11.4,
    "P02",    "OPEN-LABEL",   "PARAM01", 6,     10.8
  )
  expect_output <- tibble::tribble(
    ~USUBJID, ~EPOCH,         ~PARAMCD,  ~ASEQ, ~AVAL, ~BASETYPE,
    "P01",    "SCREENING",    "PARAM01", 1,     10.2,  NA,
    "P01",    "RUN-IN",       "PARAM01", 2,     10,    "RUN-IN",
    "P01",    "RUN-IN",       "PARAM01", 3,      9.8,  "RUN-IN",
    "P01",    "DOUBLE-BLIND", "PARAM01", 4,      9.2,  "RUN-IN",
    "P01",    "DOUBLE-BLIND", "PARAM01", 5,     10.1,  "RUN-IN",
    "P01",    "OPEN-LABEL",   "PARAM01", 6,     10.4,  "RUN-IN",
    "P01",    "OPEN-LABEL",   "PARAM01", 7,      9.9,  "RUN-IN",
    "P01",    "DOUBLE-BLIND", "PARAM01", 4,      9.2,  "DOUBLE-BLIND",
    "P01",    "DOUBLE-BLIND", "PARAM01", 5,     10.1,  "DOUBLE-BLIND",
    "P01",    "OPEN-LABEL",   "PARAM01", 6,     10.4,  "DOUBLE-BLIND",
    "P01",    "OPEN-LABEL",   "PARAM01", 7,      9.9,  "DOUBLE-BLIND",
    "P01",    "OPEN-LABEL",   "PARAM01", 6,     10.4,  "OPEN-LABEL",
    "P01",    "OPEN-LABEL",   "PARAM01", 7,      9.9,  "OPEN-LABEL",
    "P02",    "SCREENING",    "PARAM01", 1,     12.2,  NA,
    "P02",    "RUN-IN",       "PARAM01", 2,     12.1,  "RUN-IN",
    "P02",    "DOUBLE-BLIND", "PARAM01", 3,     10.2,  "RUN-IN",
    "P02",    "DOUBLE-BLIND", "PARAM01", 4,     10.8,  "RUN-IN",
    "P02",    "OPEN-LABEL",   "PARAM01", 5,     11.4,  "RUN-IN",
    "P02",    "OPEN-LABEL",   "PARAM01", 6,     10.8,  "RUN-IN",
    "P02",    "DOUBLE-BLIND", "PARAM01", 3,     10.2,  "DOUBLE-BLIND",
    "P02",    "DOUBLE-BLIND", "PARAM01", 4,     10.8,  "DOUBLE-BLIND",
    "P02",    "OPEN-LABEL",   "PARAM01", 5,     11.4,  "DOUBLE-BLIND",
    "P02",    "OPEN-LABEL",   "PARAM01", 6,     10.8,  "DOUBLE-BLIND",
    "P02",    "OPEN-LABEL",   "PARAM01", 5,     11.4,  "OPEN-LABEL",
    "P02",    "OPEN-LABEL",   "PARAM01", 6,     10.8,  "OPEN-LABEL",
  )
  actual_output <- derive_var_basetype(
    dataset = input,
    basetypes = exprs(
      "RUN-IN" = EPOCH %in% c("RUN-IN", "STABILIZATION", "DOUBLE-BLIND", "OPEN-LABEL"),
      "DOUBLE-BLIND" = EPOCH %in% c("DOUBLE-BLIND", "OPEN-LABEL"),
      "OPEN-LABEL" = EPOCH == "OPEN-LABEL"
    )
  )

  expect_dfs_equal(actual_output, expect_output, keys = c("USUBJID", "BASETYPE", "PARAMCD", "ASEQ"))
})