tests/testthat/test-qc.R

In MIC: Analysis of Antimicrobial Minimum Inhibitory Concentration Data

test_that("test qc_in_range", {
  expect_true(qc_in_range(AMR::as.mic(0.5), 25922, AMR::as.ab("GEN")))
  expect_true(qc_in_range(AMR::as.mic(0.25), 25922, AMR::as.ab("GEN")))
  expect_true(qc_in_range(AMR::as.mic(1.0), 25922, AMR::as.ab("AMK")))
  expect_true(qc_in_range(AMR::as.mic(4.0), 25922, AMR::as.ab("AMK")))

  expect_false(qc_in_range(AMR::as.mic("<0.25"), 25922, AMR::as.ab("GEN")))
  expect_false(qc_in_range(AMR::as.mic(8.0), 25922, AMR::as.ab("AMK")))
  expect_false(qc_in_range(AMR::as.mic(">4.0"), 25922, AMR::as.ab("AMK")))
  expect_false(qc_in_range(AMR::as.mic(0.25), 25922, AMR::as.ab("AMK")))

  expect_true(qc_in_range(NA, 25922, "GEN"))
  expect_true(qc_in_range(AMR::as.mic(8.0), NA, "GEN"))

  expect_false(qc_in_range(AMR::as.mic("<0.0625"), 25922, "CIP"))
})

test_that("test qc_on_target", {
  expect_true(qc_on_target(AMR::as.mic(0.5), 25922, AMR::as.ab("GEN")))
  expect_true(qc_on_target(AMR::as.mic(1), 25922, AMR::as.ab("AMK")))
  expect_true(qc_on_target(AMR::as.mic(2), 25922, AMR::as.ab("AMK")))

  expect_false(qc_on_target(AMR::as.mic("<0.5"), 25922, AMR::as.ab("GEN")))
  expect_false(qc_on_target(AMR::as.mic(4), 25922, AMR::as.ab("AMK")))

  expect_true(qc_on_target(NA, 25922, AMR::as.ab("AMK")))
  expect_true(qc_on_target(AMR::as.mic("<0.5"), 25922, NA))
})

test_that("test standardise_mic", {
  expect_warning(
    standardise_mic(AMR::as.mic(8.0),
                    AMR::as.mic(2),
                    25922,
                    AMR::as.ab("GEN"))
    )

  expect_equal(standardise_mic(AMR::as.mic(8.0),
                               AMR::as.mic(1),
                               25922, AMR::as.ab("GEN")),
               AMR::as.mic(4.0))

  expect_equal(standardise_mic(AMR::as.mic(8.0),
                               AMR::as.mic(2),
                               25922,
                               AMR::as.ab("AMK")),
               AMR::as.mic(8.0))

  expect_equal(standardise_mic(AMR::as.mic(8.0),
                               AMR::as.mic(1),
                               25922,
                               AMR::as.ab("AMK")),
               AMR::as.mic(8.0))

  expect_equal(standardise_mic(AMR::as.mic(8.0),
                               AMR::as.mic(0.5),
                               25922,
                               AMR::as.ab("AMK"),
                               prefer_upper = TRUE),
               AMR::as.mic(32.0))

  expect_equal(standardise_mic(AMR::as.mic(8.0),
                               AMR::as.mic(0.5),
                               25922,
                               AMR::as.ab("AMK"),
                               prefer_upper = FALSE),
               AMR::as.mic(16.0))

  expect_equal(standardise_mic(AMR::as.mic(">8.0"),
                               AMR::as.mic(0.5),
                               25922,
                               AMR::as.ab("AMK"),
                               prefer_upper = T),
               AMR::as.mic(">8.0"))

  suppressWarnings(
    expect_equal(standardise_mic(NA,
                                 AMR::as.mic(0.5),
                                 25922,
                                 AMR::as.ab("AMK"),
                                 prefer_upper = T),
                 AMR::NA_mic_)
  )

  expect_equal(standardise_mic(c(AMR::as.mic("4"),
                                 AMR::as.mic("8")),
                               c(AMR::as.mic("1"),
                                 AMR::as.mic("0.5")),
                               25922,
                               AMR::as.ab("GEN")),
               AMR::as.mic(c("2", "8")))
})