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New mo algorithm, prepare for 2.0
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@ -1,12 +1,16 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# CITE 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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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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@ -1,12 +1,16 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# CITE 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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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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@ -31,11 +35,15 @@ expect_equal(AMR:::percentage(0.1234), "12.3%")
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expect_equal(AMR:::percentage(0.0054), "0.5%")
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expect_equal(AMR:::percentage(0.0055), "0.6%")
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expect_equal(AMR:::strrep("A", 5), "AAAAA")
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expect_equal(AMR:::strrep(c("A", "B"), c(5, 2)), c("AAAAA", "BB"))
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expect_equal(AMR:::trimws(" test "), "test")
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expect_equal(AMR:::trimws(" test ", "l"), "test ")
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expect_equal(AMR:::trimws(" test ", "r"), " test")
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# test functions on all R versions - R < 3.3 did not contain these
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expect_equal(strrep("A", 5), "AAAAA")
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expect_equal(strrep(c("A", "B"), c(5, 2)), c("AAAAA", "BB"))
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expect_equal(trimws(" test "), "test")
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expect_equal(trimws(" test ", "l"), "test ")
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expect_equal(trimws(" test ", "r"), " test")
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expect_equal(AMR:::trimws2(" test "), "test")
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expect_equal(AMR:::trimws2(" test ", "l"), "test ")
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expect_equal(AMR:::trimws2(" test ", "r"), " test")
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expect_warning(AMR:::generate_warning_abs_missing(c("AMP", "AMX")))
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expect_warning(AMR:::generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
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@ -1,12 +1,16 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# CITE 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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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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@ -1,12 +1,16 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# CITE 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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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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@ -1,12 +1,16 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# CITE 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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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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@ -1,12 +1,16 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# CITE 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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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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@ -1,12 +1,16 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# CITE 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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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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@ -1,12 +1,16 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# CITE 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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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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@ -1,12 +1,16 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# CITE 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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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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@ -1,12 +1,16 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# CITE 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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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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@ -1,12 +1,16 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# CITE 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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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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@ -1,12 +1,16 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# CITE 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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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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@ -23,8 +27,6 @@
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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expect_true(AMR:::check_dataset_integrity()) # in misc.R
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# IDs should always be unique
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expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
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expect_identical(class(microorganisms$mo), c("mo", "character"))
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@ -66,26 +68,14 @@ df <- AMR:::MO_lookup
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expect_true(nrow(df[which(df$prevalence == 1), , drop = FALSE]) < nrow(df[which(df$prevalence == 2), , drop = FALSE]))
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expect_true(nrow(df[which(df$prevalence == 2), , drop = FALSE]) < nrow(df[which(df$prevalence == 3), , drop = FALSE]))
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expect_true(all(c(
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"mo", "fullname",
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"kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies",
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"rank", "ref", "species_id", "source", "prevalence", "snomed",
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"kingdom_index", "fullname_lower", "g_species"
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"mo", "fullname", "status", "kingdom", "phylum", "class", "order",
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"family", "genus", "species", "subspecies", "rank", "ref", "source",
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"lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence",
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"snomed", "kingdom_index", "fullname_lower", "full_first", "species_first"
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) %in% colnames(df)))
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expect_true(all(c(
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"fullname", "fullname_new", "ref", "prevalence",
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"fullname_lower", "g_species"
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) %in% colnames(AMR:::MO.old_lookup)))
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expect_inherits(AMR:::MO_CONS, "mo")
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expect_identical(
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class(catalogue_of_life_version()),
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c("catalogue_of_life_version", "list")
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)
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expect_stdout(print(catalogue_of_life_version()))
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uncategorised <- subset(
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microorganisms,
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genus == "Staphylococcus" &
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@ -97,7 +87,8 @@ expect_true(NROW(uncategorised) == 0,
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"All staphylococcal species categorised as CoNS/CoPS.",
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paste0(
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"Staphylococcal species not categorised as CoNS/CoPS: S. ",
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uncategorised$species, " (", uncategorised$mo, ")"
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uncategorised$species, " (", uncategorised$mo, ")",
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collapse = "\n"
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)
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)
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)
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# CITE 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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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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@ -42,11 +46,11 @@ pdf(NULL) # prevent Rplots.pdf being created
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expect_silent(barplot(as.disk(c(10, 20, 40))))
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expect_silent(plot(as.disk(c(10, 20, 40))))
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expect_silent(plot(as.disk(c(10, 20, 40)), expand = FALSE))
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expect_silent(plot(as.disk(c(10, 20, 40)), mo = "esco", ab = "cipr"))
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expect_silent(plot(as.disk(c(10, 20, 40)), mo = "Escherichia coli", ab = "cipr"))
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if (AMR:::pkg_is_available("ggplot2")) {
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expect_inherits(autoplot(as.disk(c(10, 20, 40))), "gg")
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expect_inherits(autoplot(as.disk(c(10, 20, 40)), expand = FALSE), "gg")
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expect_inherits(autoplot(as.disk(c(10, 20, 40)), mo = "esco", ab = "cipr"), "gg")
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expect_inherits(autoplot(as.disk(c(10, 20, 40)), mo = "Escherichia coli", ab = "cipr"), "gg")
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}
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expect_stdout(print(as.disk(12)))
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# CITE 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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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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@ -1,12 +1,16 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# CITE 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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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
@ -36,8 +40,8 @@ expect_equal(
|
||||
)
|
||||
)
|
||||
MOs_mentioned <- unique(AMR:::EUCAST_RULES_DF$this_value)
|
||||
MOs_mentioned <- sort(AMR:::trimws(unlist(strsplit(MOs_mentioned[!AMR:::is_valid_regex(MOs_mentioned)], ",", fixed = TRUE))))
|
||||
MOs_test <- suppressWarnings(suppressMessages(mo_name(MOs_mentioned)))
|
||||
MOs_mentioned <- sort(trimws(unlist(strsplit(MOs_mentioned[!AMR:::is_valid_regex(MOs_mentioned)], ",", fixed = TRUE))))
|
||||
MOs_test <- suppressWarnings(suppressMessages(mo_name(MOs_mentioned, keep_synonyms = TRUE, language = NULL)))
|
||||
expect_true(length(MOs_mentioned[MOs_test != MOs_mentioned]) == 0)
|
||||
|
||||
expect_error(suppressWarnings(eucast_rules(example_isolates, col_mo = "Non-existing")))
|
||||
|
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
@ -57,11 +61,11 @@ pdf(NULL) # prevent Rplots.pdf being created
|
||||
expect_silent(barplot(as.mic(c(1, 2, 4, 8))))
|
||||
expect_silent(plot(as.mic(c(1, 2, 4, 8))))
|
||||
expect_silent(plot(as.mic(c(1, 2, 4, 8)), expand = FALSE))
|
||||
expect_silent(plot(as.mic(c(1, 2, 4, 8)), mo = "esco", ab = "cipr"))
|
||||
expect_silent(plot(as.mic(c(1, 2, 4, 8)), mo = "Escherichia coli", ab = "cipr"))
|
||||
if (AMR:::pkg_is_available("ggplot2")) {
|
||||
expect_inherits(autoplot(as.mic(c(1, 2, 4, 8))), "gg")
|
||||
expect_inherits(autoplot(as.mic(c(1, 2, 4, 8)), expand = FALSE), "gg")
|
||||
expect_inherits(autoplot(as.mic(c(1, 2, 4, 8, 32)), mo = "esco", ab = "cipr"), "gg")
|
||||
expect_inherits(autoplot(as.mic(c(1, 2, 4, 8, 32)), mo = "Escherichia coli", ab = "cipr"), "gg")
|
||||
}
|
||||
expect_stdout(print(as.mic(c(1, 2, 4, 8))))
|
||||
|
||||
|
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
@ -27,7 +31,7 @@ MOs <- subset(microorganisms, !is.na(mo) & nchar(mo) > 3)
|
||||
expect_identical(as.character(MOs$mo), as.character(as.mo(MOs$mo)))
|
||||
|
||||
expect_identical(
|
||||
as.character(as.mo(c("E. coli", "H. influenzae"))),
|
||||
as.character(as.mo(c("E. coli", "H. influenzae"), keep_synonyms = FALSE)),
|
||||
c("B_ESCHR_COLI", "B_HMPHL_INFL")
|
||||
)
|
||||
|
||||
@ -36,12 +40,12 @@ expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI")
|
||||
expect_equal(as.character(as.mo(112283007)), "B_ESCHR_COLI")
|
||||
expect_equal(as.character(as.mo("Escherichia species")), "B_ESCHR")
|
||||
expect_equal(as.character(as.mo("Escherichia")), "B_ESCHR")
|
||||
expect_equal(as.character(as.mo("Esch spp.")), "B_ESCHR")
|
||||
expect_equal(as.character(as.mo("Eschr spp.")), "B_ESCHR")
|
||||
expect_equal(as.character(as.mo(" B_ESCHR_COLI ")), "B_ESCHR_COLI")
|
||||
expect_equal(as.character(as.mo("e coli")), "B_ESCHR_COLI") # not Campylobacter
|
||||
expect_equal(as.character(as.mo("klpn")), "B_KLBSL_PNMN")
|
||||
expect_equal(as.character(as.mo("Klebsiella")), "B_KLBSL")
|
||||
expect_equal(as.character(as.mo("K. pneu rhino")), "B_KLBSL_PNMN_RHNS") # K. pneumoniae subspp. rhinoscleromatis
|
||||
expect_equal(as.character(as.mo("K. pneumo rhino")), "B_KLBSL_PNMN_RHNS") # K. pneumoniae subspp. rhinoscleromatis
|
||||
expect_equal(as.character(as.mo("Bartonella")), "B_BRTNL")
|
||||
expect_equal(as.character(as.mo("C. difficile")), "B_CRDDS_DFFC")
|
||||
expect_equal(as.character(as.mo("L. pneumophila")), "B_LGNLL_PNMP")
|
||||
@ -49,9 +53,8 @@ expect_equal(as.character(as.mo("Strepto")), "B_STRPT")
|
||||
expect_equal(as.character(as.mo("Streptococcus")), "B_STRPT") # not Peptostreptoccus
|
||||
expect_equal(as.character(as.mo("Estreptococos grupo B")), "B_STRPT_GRPB")
|
||||
expect_equal(as.character(as.mo("Group B Streptococci")), "B_STRPT_GRPB")
|
||||
expect_equal(as.character(as.mo(c("mycobacterie", "mycobakterium"))), c("B_MYCBC", "B_MYCBC"))
|
||||
|
||||
expect_equal(as.character(as.mo(c("GAS", "GBS", "a MGS", "haemoly strep"))), c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_MILL", "B_STRPT_HAEM"))
|
||||
expect_equal(as.character(as.mo(c("GAS", "GBS", "haemoly strep"))), c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_HAEM"))
|
||||
|
||||
|
||||
expect_equal(as.character(as.mo("S. pyo")), "B_STRPT_PYGN") # not Actinomyces pyogenes
|
||||
@ -86,14 +89,13 @@ expect_identical(
|
||||
"staaur",
|
||||
"S. aureus",
|
||||
"S aureus",
|
||||
"Sthafilokkockus aureeuzz",
|
||||
"Sthafilokkockus aureus",
|
||||
"Staphylococcus aureus",
|
||||
"MRSA",
|
||||
"VISA",
|
||||
"meth.-resis. S. aureus (MRSA)"
|
||||
))
|
||||
"VISA"
|
||||
), minimum_matching_score = 0)
|
||||
)),
|
||||
rep("B_STPHY_AURS", 10)
|
||||
rep("B_STPHY_AURS", 9)
|
||||
)
|
||||
expect_identical(
|
||||
as.character(
|
||||
@ -144,8 +146,8 @@ expect_identical(as.character(as.mo("STCPYO", Lancefield = TRUE)), "B_STRPT_GRPA
|
||||
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = FALSE)), "B_STRPT_AGLC")
|
||||
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = TRUE)), "B_STRPT_GRPB") # group B
|
||||
expect_identical(as.character(suppressWarnings(as.mo("estreptococos grupo B"))), "B_STRPT_GRPB")
|
||||
expect_identical(as.character(as.mo("S. equisimilis", Lancefield = FALSE)), "B_STRPT_DYSG_EQSM")
|
||||
expect_identical(as.character(as.mo("S. equisimilis", Lancefield = TRUE)), "B_STRPT_GRPC") # group C
|
||||
expect_identical(as.character(as.mo("S. equi", Lancefield = FALSE)), "B_STRPT_EQUI")
|
||||
expect_identical(as.character(as.mo("S. equi", Lancefield = TRUE)), "B_STRPT_GRPC") # group C
|
||||
# Enterococci must only be influenced if Lancefield = "all"
|
||||
expect_identical(as.character(as.mo("E. faecium", Lancefield = FALSE)), "B_ENTRC_FACM")
|
||||
expect_identical(as.character(as.mo("E. faecium", Lancefield = TRUE)), "B_ENTRC_FACM")
|
||||
@ -209,34 +211,23 @@ expect_equal(
|
||||
|
||||
# check empty values
|
||||
expect_equal(
|
||||
as.character(suppressWarnings(as.mo(""))),
|
||||
as.character(as.mo("")),
|
||||
NA_character_
|
||||
)
|
||||
|
||||
# check less prevalent MOs
|
||||
expect_equal(as.character(as.mo("Gomphosphaeria aponina delicatula")), "B_GMPHS_APNN_DLCT")
|
||||
expect_equal(as.character(as.mo("Gomphosphaeria apo del")), "B_GMPHS_APNN_DLCT")
|
||||
expect_equal(as.character(as.mo("G apo deli")), "B_GMPHS_APNN_DLCT")
|
||||
expect_equal(as.character(as.mo("Gomphosphaeria aponina")), "B_GMPHS_APNN")
|
||||
expect_equal(as.character(as.mo("Gomphosphaeria species")), "B_GMPHS")
|
||||
expect_equal(as.character(as.mo("Gomphosphaeria")), "B_GMPHS")
|
||||
expect_equal(as.character(as.mo(" B_GMPHS_APNN ")), "B_GMPHS_APNN")
|
||||
expect_equal(as.character(as.mo("g aponina")), "B_GMPHS_APNN")
|
||||
expect_equal(as.character(as.mo("Actinosynnema pretiosum auranticum")), "B_ANNMA_PRTS_ARNT")
|
||||
expect_equal(as.character(as.mo("Actinosynnema preti aura")), "B_ANNMA_PRTS_ARNT")
|
||||
expect_equal(as.character(as.mo("A pre aur")), "B_ANNMA_PRTS_ARNT")
|
||||
expect_equal(as.character(as.mo("Actinosynnema pretiosum")), "B_ANNMA_PRTS")
|
||||
expect_equal(as.character(as.mo("Actinosynnema")), "B_ANNMA")
|
||||
expect_equal(as.character(as.mo(" B_ANNMA_PRTS ")), "B_ANNMA_PRTS")
|
||||
|
||||
# check old names
|
||||
expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLTT")
|
||||
print(mo_renamed())
|
||||
expect_equal(suppressMessages(as.character(as.mo(c("E. coli", "Chlamydo psittaci")))), c("B_ESCHR_COLI", "B_CHLMY_PSTT"))
|
||||
expect_equal(suppressMessages(mo_name("eubcom")), "Clostridium combesii")
|
||||
|
||||
# check uncertain names
|
||||
expect_equal(suppressMessages(as.character(as.mo("staaur extratest", allow_uncertain = TRUE))), "B_STPHY_AURS")
|
||||
expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = FALSE))), "UNKNOWN")
|
||||
expect_message(as.mo("e coli extra_text", allow_uncertain = TRUE))
|
||||
expect_equal(suppressMessages(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AURS")
|
||||
expect_equal(suppressMessages(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY_COPS")
|
||||
expect_equal(suppressMessages(as.character(as.mo(c("s aure THISISATEST", "Staphylococcus aureus unexisting"), allow_uncertain = 3))), c("B_STPHY_AURS_AURS", "B_STPHY_AURS_AURS"))
|
||||
|
||||
# predefined reference_df
|
||||
expect_equal(
|
||||
as.character(as.mo("TestingOwnID",
|
||||
@ -255,7 +246,7 @@ expect_error(as.mo("E. coli", reference_df = data.frame(mycol = "TestingOwnID"))
|
||||
|
||||
# combination of existing mo and other code
|
||||
expect_identical(
|
||||
as.character(as.mo(c("B_ESCHR_COL", "ESCCOL"))),
|
||||
suppressWarnings(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL")))),
|
||||
c("B_ESCHR_COLI", "B_ESCHR_COLI")
|
||||
)
|
||||
|
||||
@ -279,18 +270,18 @@ expect_equal(
|
||||
c("B_MCRBC_PRXY", "B_STRPT_SUIS", "B_RLTLL_TRRG")
|
||||
)
|
||||
expect_stdout(print(mo_uncertainties()))
|
||||
x <- as.mo("S. aur")
|
||||
x <- as.mo("Sta. aur")
|
||||
# many hits
|
||||
expect_stdout(print(mo_uncertainties()))
|
||||
|
||||
# Salmonella (City) are all actually Salmonella enterica spp (City)
|
||||
expect_equal(
|
||||
suppressMessages(as.mo(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"))),
|
||||
suppressMessages(as.mo(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"), keep_synonyms = FALSE)),
|
||||
as.mo(c("Salmonella enterica", "Salmonella enterica", "Salmonella"))
|
||||
)
|
||||
|
||||
# no viruses
|
||||
expect_equal(as.character(as.mo("Virus")), NA_character_)
|
||||
expect_equal(as.mo("Virus"), as.mo("UNKNOWN"))
|
||||
|
||||
# summary
|
||||
expect_equal(length(summary(example_isolates$mo)), 6)
|
||||
@ -308,13 +299,6 @@ expect_equal(
|
||||
rep("UNKNOWN", 3)
|
||||
)
|
||||
|
||||
expect_null(mo_failures())
|
||||
|
||||
expect_error(translate_allow_uncertain(5))
|
||||
|
||||
# debug mode
|
||||
expect_stdout(print(suppressMessages(suppressWarnings(as.mo("kshgcjkhsdgkshjdfsfvsdfv", debug = TRUE, allow_uncertain = 3)))))
|
||||
|
||||
# ..coccus
|
||||
expect_equal(
|
||||
as.character(as.mo(c("meningococ", "gonococ", "pneumococ"))),
|
||||
|
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
@ -25,7 +29,7 @@
|
||||
|
||||
expect_equal(mo_kingdom("Escherichia coli"), "Bacteria")
|
||||
expect_equal(mo_kingdom("Escherichia coli"), mo_domain("Escherichia coli"))
|
||||
expect_equal(mo_phylum("Escherichia coli"), "Proteobacteria")
|
||||
expect_equal(mo_phylum("Escherichia coli"), "Pseudomonadota")
|
||||
expect_equal(mo_class("Escherichia coli"), "Gammaproteobacteria")
|
||||
expect_equal(mo_order("Escherichia coli"), "Enterobacterales")
|
||||
expect_equal(mo_family("Escherichia coli"), "Enterobacteriaceae")
|
||||
@ -55,7 +59,7 @@ expect_inherits(mo_synonyms(c("Candida albicans", "Escherichia coli")), "list")
|
||||
expect_equal(names(mo_info("Escherichia coli")), c(
|
||||
"kingdom", "phylum", "class", "order",
|
||||
"family", "genus", "species", "subspecies",
|
||||
"synonyms", "gramstain", "url", "ref",
|
||||
"status", "synonyms", "gramstain", "url", "ref",
|
||||
"snomed"
|
||||
))
|
||||
expect_inherits(mo_info(c("Escherichia coli", "Staphylococcus aureus")), "list")
|
||||
@ -64,31 +68,29 @@ expect_equal(mo_ref("Escherichia coli"), "Castellani et al., 1919")
|
||||
expect_equal(mo_authors("Escherichia coli"), "Castellani et al.")
|
||||
expect_equal(mo_year("Escherichia coli"), 1919)
|
||||
|
||||
expect_true(mo_url("Candida albicans") %like% "catalogueoflife.org")
|
||||
expect_true(mo_url("Candida albicans") %like% "gbif.org")
|
||||
expect_true(mo_url("Escherichia coli") %like% "lpsn.dsmz.de")
|
||||
|
||||
# test integrity
|
||||
MOs <- microorganisms
|
||||
expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en"))
|
||||
expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en", keep_synonyms = TRUE))
|
||||
|
||||
# check languages
|
||||
expect_equal(mo_type("Escherichia coli", language = "de"), "Bakterien")
|
||||
expect_equal(mo_gramstain("Escherichia coli", language = "nl"), "Gram-negatief")
|
||||
|
||||
expect_stdout(print(mo_gramstain("Escherichia coli", language = "en")))
|
||||
expect_stdout(print(mo_gramstain("Escherichia coli", language = "de")))
|
||||
expect_stdout(print(mo_gramstain("Escherichia coli", language = "nl")))
|
||||
expect_stdout(print(mo_gramstain("Escherichia coli", language = "es")))
|
||||
expect_stdout(print(mo_gramstain("Escherichia coli", language = "pt")))
|
||||
expect_stdout(print(mo_gramstain("Escherichia coli", language = "it")))
|
||||
expect_stdout(print(mo_gramstain("Escherichia coli", language = "fr")))
|
||||
gr <- mo_gramstain("Escherichia coli", language = NULL)
|
||||
for (l in AMR:::LANGUAGES_SUPPORTED[-1]) {
|
||||
expect_false(mo_gramstain("Escherichia coli", language = l) == gr, info = paste("Gram-stain in language", l))
|
||||
}
|
||||
|
||||
expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN"))
|
||||
dutch <- mo_name(microorganisms$fullname, language = "nl") # should be transformable to English again
|
||||
expect_identical(mo_name(dutch, language = NULL), microorganisms$fullname) # gigantic test - will run ALL names
|
||||
dutch <- mo_name(microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase|Fungi")], language = "nl", keep_synonyms = TRUE) # should be transformable to English again
|
||||
expect_identical(mo_name(dutch, language = NULL, keep_synonyms = TRUE),
|
||||
microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase|Fungi")]) # gigantic test - will run ALL names
|
||||
|
||||
# manual property function
|
||||
expect_error(mo_property("Escherichia coli", property = c("tsn", "fullname")))
|
||||
expect_error(mo_property("Escherichia coli", property = c("genus", "fullname")))
|
||||
expect_error(mo_property("Escherichia coli", property = "UNKNOWN"))
|
||||
expect_identical(
|
||||
mo_property("Escherichia coli", property = "fullname"),
|
||||
@ -103,12 +105,16 @@ expect_identical(
|
||||
mo_species("Escherichia coli")
|
||||
)
|
||||
expect_identical(
|
||||
mo_property("Escherichia coli", property = "species_id"),
|
||||
mo_property("Escherichia coli", property = "lpsn"),
|
||||
mo_lpsn("Escherichia coli")
|
||||
)
|
||||
expect_identical(
|
||||
mo_property("Escherichia coli", property = "gbif"),
|
||||
mo_gbif("Escherichia coli")
|
||||
)
|
||||
|
||||
expect_identical(suppressWarnings(mo_ref("Chlamydia psittaci")), "Page, 1968")
|
||||
expect_identical(mo_ref("Chlamydophila psittaci"), "Everett et al., 1999")
|
||||
expect_identical(mo_ref("Chlamydia psittaci"), "Garcia-Lopez et al., 2019")
|
||||
expect_identical(mo_ref("Chlamydophila psittaci", keep_synonyms = TRUE), "Everett et al., 1999")
|
||||
|
||||
expect_true(112283007 %in% mo_snomed("Escherichia coli"))
|
||||
# old codes must throw a warning in mo_* family
|
||||
|
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
@ -28,7 +32,9 @@
|
||||
|
||||
# functions used by import_fn()
|
||||
import_functions <- c(
|
||||
"%chin%" = "data.table",
|
||||
"anti_join" = "dplyr",
|
||||
"chmatch" = "data.table",
|
||||
"cur_column" = "dplyr",
|
||||
"full_join" = "dplyr",
|
||||
"has_internet" = "curl",
|
||||
|
Reference in New Issue
Block a user