tests/testthat/test-derive_vars_transposed.R

In admiral: ADaM in R Asset Library

dataset <- tibble::tribble(
  ~USUBJID, ~VAR1,
  "P01",    3,
  "P02",    31,
  "P03",    42
)
dataset_merge <- tibble::tribble(
  ~USUBJID, ~TESTCD, ~VALUE,
  "P01",    "T01",   31,
  "P01",    "T02",   5,
  "P02",    "T01",   3,
  "P03",    "T02",   9
)

test_that("the merge dataset is transposed and merged correctly", {
  expected_output <- tibble::tribble(
    ~USUBJID, ~VAR1, ~T01, ~T02,
    "P01", 3, 31, 5,
    "P02", 31, 3, NA,
    "P03", 42, NA, 9
  )
  actual_output <- derive_vars_transposed(
    dataset,
    dataset_merge,
    by_vars = exprs(USUBJID),
    key_var = TESTCD,
    value_var = VALUE
  )

  expect_dfs_equal(expected_output, actual_output, keys = "USUBJID")
})


test_that("filtering the merge dataset works", {
  expected_output <- tibble::tribble(
    ~USUBJID, ~VAR1, ~T01,
    "P01", 3, 31,
    "P02", 31, 3,
    "P03", 42, NA
  )
  actual_output <- derive_vars_transposed(
    dataset,
    dataset_merge,
    by_vars = exprs(USUBJID),
    key_var = TESTCD,
    value_var = VALUE,
    filter = TESTCD == "T01"
  )

  expect_dfs_equal(expected_output, actual_output, keys = "USUBJID")
})

test_that("ATC variables are merged properly", {
  cm <- tibble::tribble(
    ~USUBJID, ~CMGRPID, ~CMREFID, ~CMDECOD,
    "BP40257-1001", "14", "1192056", "PARACETAMOL",
    "BP40257-1001", "18", "2007001", "SOLUMEDROL",
    "BP40257-1002", "19", "2791596", "SPIRONOLACTONE"
  )
  facm <- tibble::tribble(
    ~USUBJID, ~FAGRPID, ~FAREFID, ~FATESTCD, ~FASTRESC,
    "BP40257-1001", "1", "1192056", "CMATC1CD", "N",
    "BP40257-1001", "1", "1192056", "CMATC2CD", "N02",
    "BP40257-1001", "1", "1192056", "CMATC3CD", "N02B",
    "BP40257-1001", "1", "1192056", "CMATC4CD", "N02BE",
    "BP40257-1001", "1", "2007001", "CMATC1CD", "D",
    "BP40257-1001", "1", "2007001", "CMATC2CD", "D10",
    "BP40257-1001", "1", "2007001", "CMATC3CD", "D10A",
    "BP40257-1001", "1", "2007001", "CMATC4CD", "D10AA",
    "BP40257-1001", "2", "2007001", "CMATC1CD", "D",
    "BP40257-1001", "2", "2007001", "CMATC2CD", "D07",
    "BP40257-1001", "2", "2007001", "CMATC3CD", "D07A",
    "BP40257-1001", "2", "2007001", "CMATC4CD", "D07AA",
    "BP40257-1001", "3", "2007001", "CMATC1CD", "H",
    "BP40257-1001", "3", "2007001", "CMATC2CD", "H02",
    "BP40257-1001", "3", "2007001", "CMATC3CD", "H02A",
    "BP40257-1001", "3", "2007001", "CMATC4CD", "H02AB",
    "BP40257-1002", "1", "2791596", "CMATC1CD", "C",
    "BP40257-1002", "1", "2791596", "CMATC2CD", "C03",
    "BP40257-1002", "1", "2791596", "CMATC3CD", "C03D",
    "BP40257-1002", "1", "2791596", "CMATC4CD", "C03DA"
  )
  # nolint start
  expected_output <- tibble::tribble(
    ~USUBJID, ~CMGRPID, ~CMREFID, ~CMDECOD, ~ATC1CD, ~ATC2CD, ~ATC3CD, ~ATC4CD,
    "BP40257-1001", "14", "1192056", "PARACETAMOL", "N", "N02", "N02B", "N02BE",
    "BP40257-1001", "18", "2007001", "SOLUMEDROL", "D", "D07", "D07A", "D07AA",
    "BP40257-1001", "18", "2007001", "SOLUMEDROL", "D", "D10", "D10A", "D10AA",
    "BP40257-1001", "18", "2007001", "SOLUMEDROL", "H", "H02", "H02A", "H02AB",
    "BP40257-1002", "19", "2791596", "SPIRONOLACTONE", "C", "C03", "C03D", "C03DA"
  )
  # nolint end
  actual_output <- derive_vars_atc(cm, facm)

  expect_dfs_equal(expected_output, actual_output, keys = c("USUBJID", "CMDECOD", "ATC4CD"))
})