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62 lines
3.5 KiB
R
62 lines
3.5 KiB
R
# ==================================================================== #
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# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
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# AMR: An R Package for Working with Antimicrobial Resistance Data. #
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# Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in the Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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# #
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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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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://amr-for-r.org #
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# ==================================================================== #
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test_that("test-random.R", {
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skip_on_cran()
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expect_inherits(random_mic(100), "mic")
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expect_inherits(random_mic(100, mo = "Klebsiella pneumoniae"), "mic")
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expect_inherits(random_mic(100, mo = "Klebsiella pneumoniae", ab = "meropenem"), "mic")
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expect_inherits(random_mic(100, ab = "meropenem"), "mic")
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# no normal factors of 2
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expect_inherits(random_mic(100, "Haemophilus influenzae", "ceftaroline"), "mic")
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expect_inherits(random_disk(100), "disk")
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expect_inherits(random_disk(100, mo = "Klebsiella pneumoniae"), "disk")
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expect_inherits(random_disk(100, mo = "Klebsiella pneumoniae", ab = "meropenem"), "disk")
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expect_inherits(random_disk(100, ab = "meropenem"), "disk")
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expect_inherits(random_sir(100), "sir")
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# guideline: without a year the latest version is used, and the AMR_guideline option is the default
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latest_clsi <- max(AMR::clinical_breakpoints$guideline[AMR::clinical_breakpoints$guideline %like% "CLSI"])
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set.seed(1)
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x1 <- random_disk(100, "Klebsiella pneumoniae", "ampicillin", guideline = "CLSI")
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set.seed(1)
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x2 <- random_disk(100, "Klebsiella pneumoniae", "ampicillin", guideline = latest_clsi)
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old_opt <- options(AMR_guideline = "CLSI")
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set.seed(1)
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x3 <- random_disk(100, "Klebsiella pneumoniae", "ampicillin")
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options(old_opt)
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set.seed(1)
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x4 <- random_disk(100, "Klebsiella pneumoniae", "ampicillin", guideline = "EUCAST")
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expect_identical(x1, x2)
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expect_identical(x1, x3)
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expect_false(identical(x1, x4))
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expect_error(random_mic(10, guideline = "EUCAST 1999"))
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})
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