2018-12-16 22:45:12 +01:00
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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2019-01-02 23:24:07 +01:00
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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2018-12-16 22:45:12 +01:00
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# #
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# LICENCE #
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2019-01-02 23:24:07 +01:00
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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2018-12-16 22:45:12 +01:00
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# #
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2019-01-02 23:24:07 +01:00
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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2019-04-05 18:47:39 +02:00
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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2018-12-16 22:45:12 +01:00
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# ==================================================================== #
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2019-05-10 16:44:59 +02:00
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context("ab.R")
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test_that("as.ab works", {
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expect_equal(as.character(as.ab(c("J01FA01",
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"J 01 FA 01",
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"Erythromycin",
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"eryt",
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" eryt 123",
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"ERYT",
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"ERY",
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"erytromicine",
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"Erythrocin",
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"Romycin"))),
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rep("ERY", 10))
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expect_identical(class(as.ab("amox")), "ab")
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expect_identical(class(pull(antibiotics, ab)), "ab")
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2019-05-13 10:10:16 +02:00
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expect_true(is.ab(as.ab("amox")))
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expect_output(print(as.ab("amox")))
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expect_output(print(data.frame(a = as.ab("amox"))))
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2019-05-10 16:44:59 +02:00
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expect_warning(as.ab("Z00ZZ00")) # not yet available in data set
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expect_warning(as.ab("UNKNOWN"))
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2019-05-13 14:56:23 +02:00
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expect_warning(as.ab(""))
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2019-05-10 16:44:59 +02:00
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expect_output(print(as.ab("amox")))
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2018-08-29 12:27:37 +02:00
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2019-05-13 14:56:23 +02:00
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expect_identical(class(pull(antibiotics, ab)), "ab")
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2018-08-28 13:51:13 +02:00
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# first 5 chars of official name
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expect_equal(as.character(as.atc(c("nitro", "cipro"))),
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c("J01XE01", "J01MA02"))
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2018-08-25 22:01:14 +02:00
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2019-01-29 00:06:50 +01:00
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# EARS-Net
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expect_equal(as.character(as.atc("AMX")),
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"J01CA04")
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2019-05-13 14:56:23 +02:00
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expect_equal(as.character(as.ab("Phloxapen")),
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"FLC")
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2019-06-07 22:47:37 +02:00
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expect_equal(suppressWarnings(as.character(as.ab(c("Bacteria", "Bacterial")))),
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c(NA, "TMP"))
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2018-08-25 22:01:14 +02:00
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})
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