context("first_isolates.R")

test_that("keyantibiotics work", {
  expect_equal(length(key_antibiotics(septic_patients, info = FALSE)), nrow(septic_patients))
  expect_true(key_antibiotics_equal("SSS", "SSS"))
  expect_true(key_antibiotics_equal("SSS", "SIS", ignore_I = TRUE))
  expect_false(key_antibiotics_equal("SSS", "SIS", ignore_I = FALSE))
})


test_that("guess_bactid works", {
  expect_equal(guess_bactid("E. coli"), "ESCCOL")
  expect_equal(guess_bactid("Escherichia coli"), "ESCCOL")
})

test_that("first isolates work", {
  # septic_patients contains 1960 out of 2000 first isolates
  expect_equal(sum(first_isolate(septic_patients,
                             "date",
                             "patient_id",
                             "bactid",
                             info = FALSE)), 1960)
})