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(v2.1.1.9186) replace antibiotics
with antimicrobials
!
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@ -27,14 +27,16 @@
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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expect_equal(length(key_antimicrobials(example_isolates, antifungal = NULL)), nrow(example_isolates))
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expect_false(all(is.na(key_antimicrobials(example_isolates, antifungal = NULL))))
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expect_true(antimicrobials_equal("SSS", "SSS", type = "points"))
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expect_false(antimicrobials_equal("SSS", "SRS", type = "keyantimicrobials"))
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expect_true(antimicrobials_equal("SSS", "SRS", type = "points"))
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expect_true(antimicrobials_equal("SSS", "SIS", ignore_I = TRUE, type = "keyantimicrobials"))
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expect_false(antimicrobials_equal("SSS", "SIS", ignore_I = FALSE, type = "keyantimicrobials"))
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expect_true(antimicrobials_equal(".SS", "SI.", ignore_I = TRUE, type = "keyantimicrobials"))
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expect_false(antimicrobials_equal(".SS", "SI.", ignore_I = FALSE, type = "keyantimicrobials"))
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test_that("key_antimicrobials works", {
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expect_equal(length(key_antimicrobials(example_isolates, antifungal = NULL)), nrow(example_isolates))
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expect_false(all(is.na(key_antimicrobials(example_isolates, antifungal = NULL))))
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expect_true(antimicrobials_equal("SSS", "SSS", type = "points"))
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expect_false(antimicrobials_equal("SSS", "SRS", type = "keyantimicrobials"))
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expect_true(antimicrobials_equal("SSS", "SRS", type = "points"))
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expect_true(antimicrobials_equal("SSS", "SIS", ignore_I = TRUE, type = "keyantimicrobials"))
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expect_false(antimicrobials_equal("SSS", "SIS", ignore_I = FALSE, type = "keyantimicrobials"))
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expect_true(antimicrobials_equal(".SS", "SI.", ignore_I = TRUE, type = "keyantimicrobials"))
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expect_false(antimicrobials_equal(".SS", "SI.", ignore_I = FALSE, type = "keyantimicrobials"))
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# expect_warning(key_antimicrobials(example_isolates[rep(1, 10), , drop = FALSE]))
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# expect_warning(key_antimicrobials(example_isolates[rep(1, 10), , drop = FALSE]))
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})
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