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54 lines
2.8 KiB
R
Executable File
54 lines
2.8 KiB
R
Executable File
# ==================================================================== #
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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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# extra tests for {vctrs} pkg support
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if (AMR:::pkg_is_available("tibble")) {
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test <- tibble::tibble(ab = as.ab("CIP"),
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mo = as.mo("Escherichia coli"),
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mic = as.mic(2),
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disk = as.disk(20),
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sir = as.sir("S"))
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check1 <- lapply(test, class)
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test[1, "ab"] <- "GEN"
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test[1, "mo"] <- "B_KLBSL_PNMN"
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test[1, "mic"] <- ">=32"
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test[1, "mic"] <- 32
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test[1, "disk"] <- "35"
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test[1, "disk"] <- 25
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test[1, "disk"] <- 26L
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test[1, "sir"] <- "R"
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check2 <- lapply(test, class)
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expect_identical(check1, check2)
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test <- tibble::tibble(cipro = as.sir("S"),
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variable = "test")
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expect_equal(nrow(test[quinolones() == "S", ]), 1)
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expect_equal(nrow(test[quinolones() == "R", ]), 0)
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}
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