AMR/tests/testthat/test-mdro.R

context("mdro.R")


test_that("MDRO works", {
  library(dplyr)

  outcome <- suppressWarnings(MDRO(septic_patients, "EUCAST", info = TRUE))
  outcome <- suppressWarnings(EUCAST_exceptional_phenotypes(septic_patients, info = TRUE))
  # check class
  expect_equal(outcome %>% class(), c('ordered', 'factor'))

  outcome <- suppressWarnings(MDRO(septic_patients, "nl", info = TRUE))
  # check class
  expect_equal(outcome %>% class(), c('ordered', 'factor'))

  # septic_patients should have these finding using Dutch guidelines
  expect_equal(outcome %>% freq() %>% pull(count),
               c(2, 14)) # 2 unconfirmed, 14 positive

  expect_equal(BRMO(septic_patients, info = FALSE), MDRO(septic_patients, "nl", info = FALSE))

  # still working on German guidelines
  expect_error(suppressWarnings(MRGN(septic_patients, info = TRUE)))

})