mirror of
https://github.com/msberends/AMR.git
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44 lines
2.7 KiB
R
44 lines
2.7 KiB
R
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# ==================================================================== #
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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://msberends.github.io/AMR/ #
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# ==================================================================== #
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out1 <- top_n_microorganisms(example_isolates, n = 3)
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out2 <- top_n_microorganisms(example_isolates, n = 5, property = "genus")
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out3 <- top_n_microorganisms(example_isolates, n = 5, property = "genus", n_for_each = 3)
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expect_equal(NROW(out1), 1015, tolerance = 0.5)
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expect_equal(NROW(out2), 1742, tolerance = 0.5)
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expect_equal(NROW(out3), 1497, tolerance = 0.5)
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expect_equal(length(table(out1$mo)), 3, tolerance = 0.5)
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expect_equal(length(table(out2$mo)), 39, tolerance = 0.5)
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expect_equal(length(table(out3$mo)), 13, tolerance = 0.5)
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expect_equal(length(unique(mo_genus(out2$mo))), 5, tolerance = 0.5)
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expect_equal(length(unique(mo_genus(out3$mo))), 5, tolerance = 0.5)
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