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(v2.1.1.9186) replace antibiotics with antimicrobials!

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dr. M.S. (Matthijs) Berends
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
140 changed files with 4870 additions and 4702 deletions
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22
tests/testthat/test-key_antimicrobials.R
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@ -27,14 +27,16 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
expect_equal(length(key_antimicrobials(example_isolates, antifungal = NULL)), nrow(example_isolates))
expect_false(all(is.na(key_antimicrobials(example_isolates, antifungal = NULL))))
expect_true(antimicrobials_equal("SSS", "SSS", type = "points"))
expect_false(antimicrobials_equal("SSS", "SRS", type = "keyantimicrobials"))
expect_true(antimicrobials_equal("SSS", "SRS", type = "points"))
expect_true(antimicrobials_equal("SSS", "SIS", ignore_I = TRUE, type = "keyantimicrobials"))
expect_false(antimicrobials_equal("SSS", "SIS", ignore_I = FALSE, type = "keyantimicrobials"))
expect_true(antimicrobials_equal(".SS", "SI.", ignore_I = TRUE, type = "keyantimicrobials"))
expect_false(antimicrobials_equal(".SS", "SI.", ignore_I = FALSE, type = "keyantimicrobials"))
test_that("key_antimicrobials works", {
expect_equal(length(key_antimicrobials(example_isolates, antifungal = NULL)), nrow(example_isolates))
expect_false(all(is.na(key_antimicrobials(example_isolates, antifungal = NULL))))
expect_true(antimicrobials_equal("SSS", "SSS", type = "points"))
expect_false(antimicrobials_equal("SSS", "SRS", type = "keyantimicrobials"))
expect_true(antimicrobials_equal("SSS", "SRS", type = "points"))
expect_true(antimicrobials_equal("SSS", "SIS", ignore_I = TRUE, type = "keyantimicrobials"))
expect_false(antimicrobials_equal("SSS", "SIS", ignore_I = FALSE, type = "keyantimicrobials"))
expect_true(antimicrobials_equal(".SS", "SI.", ignore_I = TRUE, type = "keyantimicrobials"))
expect_false(antimicrobials_equal(".SS", "SI.", ignore_I = FALSE, type = "keyantimicrobials"))
# expect_warning(key_antimicrobials(example_isolates[rep(1, 10), , drop = FALSE]))
# expect_warning(key_antimicrobials(example_isolates[rep(1, 10), , drop = FALSE]))
})