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# ==================================================================== #
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2023-07-08 17:30:05 +02:00
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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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2024-07-16 14:51:57 +02:00
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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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vctr_disk <- as.disk(c(20:25))
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vctr_mic <- as.mic(2^c(0:5))
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vctr_sir <- as.sir(c("S", "S", "I", "I", "R", "R"))
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expect_identical(
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mean_amr_distance(vctr_disk),
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(as.double(vctr_disk) - mean(as.double(vctr_disk))) / sd(as.double(vctr_disk))
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)
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expect_identical(
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mean_amr_distance(vctr_mic),
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(log2(vctr_mic) - mean(log2(vctr_mic))) / sd(log2(vctr_mic))
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)
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expect_identical(
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mean_amr_distance(vctr_sir, combine_SI = FALSE),
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(c(1, 1, 2, 2, 3, 3) - mean(c(1, 1, 2, 2, 3, 3))) / sd(c(1, 1, 2, 2, 3, 3))
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)
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expect_identical(
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mean_amr_distance(vctr_sir, combine_SI = TRUE),
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(c(1, 1, 1, 1, 3, 3) - mean(c(1, 1, 1, 1, 3, 3))) / sd(c(1, 1, 1, 1, 3, 3))
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)
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expect_equal(
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mean_amr_distance(data.frame(AMX = vctr_mic, GEN = vctr_sir, TOB = vctr_disk)),
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c(-1.10603655, -0.74968823, -0.39333990, -0.03699158, 0.96485397, 1.32120229),
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tolerance = 0.00001
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)
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expect_equal(
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mean_amr_distance(data.frame(AMX = vctr_mic, GEN = vctr_sir, TOB = vctr_disk), 2:3),
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c(-0.9909017, -0.7236405, -0.4563792, -0.1891180, 1.0463891, 1.3136503),
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tolerance = 0.00001
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)
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