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
  septic_ptns <- septic_patients
  expect_equal(sum(first_isolate(tbl = septic_ptns,
                                 col_date = "date",
                                 col_patient_id = "patient_id",
                                 col_bactid = "bactid",
                                 info = FALSE)), 1960)

  # septic_patients contains 1962 out of 2000 first weighted isolates
  septic_ptns$keyab <- suppressWarnings(key_antibiotics(septic_ptns))
  expect_equal(
    suppressWarnings(sum(
      first_isolate(tbl = septic_ptns,
                    col_date = "date",
                    col_patient_id = "patient_id",
                    col_bactid = "bactid",
                    col_keyantibiotics = "keyab",
                    type = "keyantibiotics",
                    info = TRUE))),
    1962)
})