mirror of https://github.com/msberends/AMR.git
102 lines
3.9 KiB
R
Executable File
102 lines
3.9 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, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. 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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expect_equal(
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as.character(as.ab(c(
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"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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))),
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rep("ERY", 10)
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)
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expect_identical(class(as.ab("amox")), c("ab", "character"))
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expect_identical(class(antibiotics$ab), c("ab", "character"))
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expect_true(is.ab(as.ab("amox")))
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expect_stdout(print(as.ab("amox")))
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expect_stdout(print(data.frame(a = as.ab("amox"))))
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# expect_warning(as.ab("J00AA00")) # ATC not yet available in data set
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# expect_warning(as.ab("UNKNOWN"))
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expect_stdout(print(as.ab("amox")))
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expect_equal(
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as.character(as.ab("Phloxapen")),
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"FLC"
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)
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expect_equal(
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suppressWarnings(as.character(as.ab(c("Bacteria", "Bacterial")))),
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c(NA, "TMP")
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)
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expect_equal(
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as.character(as.ab("Amoxy + clavulaanzuur")),
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"AMC"
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)
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expect_equal(
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as.character(as.ab(c("mreopenem", "co-maoxiclav"))),
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c("MEM", "AMC")
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)
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# expect_warning(as.ab("cipro mero"))
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# based on Levenshtein distance
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expect_identical(ab_name("ceftazidim/avibactam", language = NULL), "Ceftazidime/avibactam")
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expect_identical(as.character(as.ab(c("gentamicine High Level",
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"gentamicine High",
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"gentamicine (High Level)",
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"gentamicine (High)",
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"gentamicine HL",
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"gentamicine H-L",
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"gentamicine (HL)",
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"gentamicine (H-L)"))),
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rep("GEH", 8))
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# assigning and subsetting
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x <- antibiotics$ab
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expect_inherits(x[1], "ab")
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expect_inherits(x[[1]], "ab")
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expect_inherits(c(x[1], x[9]), "ab")
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expect_inherits(unique(x[1], x[9]), "ab")
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expect_inherits(rep(x[1], 2), "ab")
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# expect_warning(x[1] <- "invalid code")
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# expect_warning(x[[1]] <- "invalid code")
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# expect_warning(c(x[1], "test"))
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