AMR/tests/testthat/test-first_isolates.R

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2018-03-27 17:43:42 +02:00
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)
})