mirror of
https://github.com/msberends/AMR.git
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(v1.8.0) prerelease 1.8.0
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# https://github.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# https://github.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# https://github.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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Package: AMR
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Package: AMR
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Version: 1.7.1.9077
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Version: 1.8.0
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Date: 2021-12-23
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Date: 2022-01-03
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Title: Antimicrobial Resistance Data Analysis
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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data analysis and to work with microbial and antimicrobial properties by
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data analysis and to work with microbial and antimicrobial properties by
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NEWS.md
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NEWS.md
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# `AMR` 1.7.1.9077
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# `AMR` 1.8.0
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## <small>Last updated: 23 December 2021</small>
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All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.
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All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.
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# https://github.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# https://github.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# https://github.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# https://github.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# https://github.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# https://github.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# https://github.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# https://github.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# https://github.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# https://github.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# https://github.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# https://github.com/msberends/AMR #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# https://github.com/msberends/AMR #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# https://github.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# https://github.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# https://github.com/msberends/AMR #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# https://github.com/msberends/AMR #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# https://github.com/msberends/AMR #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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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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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# https://github.com/msberends/AMR #
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# #
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# #
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# LICENCE #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
2
R/like.R
2
R/like.R
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
2
R/mdro.R
2
R/mdro.R
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
2
R/mic.R
2
R/mic.R
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
2
R/mo.R
2
R/mo.R
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
2
R/pca.R
2
R/pca.R
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
2
R/plot.R
2
R/plot.R
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
2
R/rsi.R
2
R/rsi.R
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
2
R/zzz.R
2
R/zzz.R
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
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|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
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|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
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|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
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|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
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|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
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|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -6,7 +6,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -43,7 +43,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
|
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9071</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -17,7 +17,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9071</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -44,7 +44,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9068</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -191,7 +191,7 @@
|
|||||||
<h1 data-toc-skip>How to conduct AMR data analysis</h1>
|
<h1 data-toc-skip>How to conduct AMR data analysis</h1>
|
||||||
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
|
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
|
||||||
|
|
||||||
<h4 data-toc-skip class="date">12 December 2021</h4>
|
<h4 data-toc-skip class="date">23 December 2021</h4>
|
||||||
|
|
||||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
|
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
|
||||||
<div class="hidden name"><code>AMR.Rmd</code></div>
|
<div class="hidden name"><code>AMR.Rmd</code></div>
|
||||||
@ -200,7 +200,7 @@
|
|||||||
|
|
||||||
|
|
||||||
|
|
||||||
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 12 December 2021.</p>
|
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 23 December 2021.</p>
|
||||||
<div class="section level1">
|
<div class="section level1">
|
||||||
<h1 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
|
<h1 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
|
||||||
</h1>
|
</h1>
|
||||||
@ -231,21 +231,21 @@
|
|||||||
</tr></thead>
|
</tr></thead>
|
||||||
<tbody>
|
<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">2021-12-12</td>
|
<td align="center">2021-12-23</td>
|
||||||
<td align="center">abcd</td>
|
<td align="center">abcd</td>
|
||||||
<td align="center">Escherichia coli</td>
|
<td align="center">Escherichia coli</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">2021-12-12</td>
|
<td align="center">2021-12-23</td>
|
||||||
<td align="center">abcd</td>
|
<td align="center">abcd</td>
|
||||||
<td align="center">Escherichia coli</td>
|
<td align="center">Escherichia coli</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">2021-12-12</td>
|
<td align="center">2021-12-23</td>
|
||||||
<td align="center">efgh</td>
|
<td align="center">efgh</td>
|
||||||
<td align="center">Escherichia coli</td>
|
<td align="center">Escherichia coli</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
@ -342,71 +342,71 @@
|
|||||||
</tr></thead>
|
</tr></thead>
|
||||||
<tbody>
|
<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">2014-11-21</td>
|
<td align="center">2010-03-07</td>
|
||||||
<td align="center">L5</td>
|
<td align="center">U8</td>
|
||||||
<td align="center">Hospital C</td>
|
|
||||||
<td align="center">Escherichia coli</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">M</td>
|
|
||||||
</tr>
|
|
||||||
<tr class="even">
|
|
||||||
<td align="center">2015-03-18</td>
|
|
||||||
<td align="center">G9</td>
|
|
||||||
<td align="center">Hospital D</td>
|
|
||||||
<td align="center">Staphylococcus aureus</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">M</td>
|
|
||||||
</tr>
|
|
||||||
<tr class="odd">
|
|
||||||
<td align="center">2011-10-31</td>
|
|
||||||
<td align="center">Z3</td>
|
|
||||||
<td align="center">Hospital A</td>
|
|
||||||
<td align="center">Escherichia coli</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">F</td>
|
|
||||||
</tr>
|
|
||||||
<tr class="even">
|
|
||||||
<td align="center">2017-05-24</td>
|
|
||||||
<td align="center">A3</td>
|
|
||||||
<td align="center">Hospital A</td>
|
|
||||||
<td align="center">Staphylococcus aureus</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">I</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">M</td>
|
|
||||||
</tr>
|
|
||||||
<tr class="odd">
|
|
||||||
<td align="center">2013-01-31</td>
|
|
||||||
<td align="center">Y10</td>
|
|
||||||
<td align="center">Hospital C</td>
|
|
||||||
<td align="center">Escherichia coli</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">F</td>
|
|
||||||
</tr>
|
|
||||||
<tr class="even">
|
|
||||||
<td align="center">2013-04-13</td>
|
|
||||||
<td align="center">L6</td>
|
|
||||||
<td align="center">Hospital B</td>
|
<td align="center">Hospital B</td>
|
||||||
|
<td align="center">Escherichia coli</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">F</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td align="center">2015-08-15</td>
|
||||||
|
<td align="center">A4</td>
|
||||||
|
<td align="center">Hospital C</td>
|
||||||
|
<td align="center">Escherichia coli</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">M</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td align="center">2012-02-22</td>
|
||||||
|
<td align="center">T7</td>
|
||||||
|
<td align="center">Hospital A</td>
|
||||||
|
<td align="center">Staphylococcus aureus</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">F</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td align="center">2017-04-28</td>
|
||||||
|
<td align="center">J10</td>
|
||||||
|
<td align="center">Hospital A</td>
|
||||||
<td align="center">Klebsiella pneumoniae</td>
|
<td align="center">Klebsiella pneumoniae</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">I</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">M</td>
|
<td align="center">M</td>
|
||||||
</tr>
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td align="center">2013-05-14</td>
|
||||||
|
<td align="center">X5</td>
|
||||||
|
<td align="center">Hospital A</td>
|
||||||
|
<td align="center">Escherichia coli</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">I</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">F</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td align="center">2011-09-09</td>
|
||||||
|
<td align="center">Z1</td>
|
||||||
|
<td align="center">Hospital A</td>
|
||||||
|
<td align="center">Escherichia coli</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">F</td>
|
||||||
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
<p>Now, let’s start the cleaning and the analysis!</p>
|
<p>Now, let’s start the cleaning and the analysis!</p>
|
||||||
@ -439,16 +439,16 @@ Longest: 1</p>
|
|||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">1</td>
|
<td align="left">1</td>
|
||||||
<td align="left">M</td>
|
<td align="left">M</td>
|
||||||
<td align="right">10,451</td>
|
<td align="right">10,513</td>
|
||||||
<td align="right">52.26%</td>
|
<td align="right">52.56%</td>
|
||||||
<td align="right">10,451</td>
|
<td align="right">10,513</td>
|
||||||
<td align="right">52.26%</td>
|
<td align="right">52.56%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">2</td>
|
<td align="left">2</td>
|
||||||
<td align="left">F</td>
|
<td align="left">F</td>
|
||||||
<td align="right">9,549</td>
|
<td align="right">9,487</td>
|
||||||
<td align="right">47.75%</td>
|
<td align="right">47.44%</td>
|
||||||
<td align="right">20,000</td>
|
<td align="right">20,000</td>
|
||||||
<td align="right">100.00%</td>
|
<td align="right">100.00%</td>
|
||||||
</tr>
|
</tr>
|
||||||
@ -502,7 +502,7 @@ Longest: 1</p>
|
|||||||
<span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span>
|
<span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span>
|
||||||
<span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span>
|
<span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span>
|
||||||
<span class="co"># 2</span>
|
<span class="co"># 2</span>
|
||||||
<span class="co"># => Found 10,684 'phenotype-based' first isolates (53.4% of total where a</span>
|
<span class="co"># => Found 10,677 'phenotype-based' first isolates (53.4% of total where a</span>
|
||||||
<span class="co"># microbial ID was available)</span></code></pre></div>
|
<span class="co"># microbial ID was available)</span></code></pre></div>
|
||||||
<p>So only 53.4% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
|
<p>So only 53.4% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
|
||||||
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
|
||||||
@ -512,10 +512,10 @@ Longest: 1</p>
|
|||||||
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||||
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
|
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
|
||||||
<p>So we end up with 10,684 isolates for analysis. Now our data looks like:</p>
|
<p>So we end up with 10,677 isolates for analysis. Now our data looks like:</p>
|
||||||
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></code></pre></div>
|
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></code></pre></div>
|
||||||
<table style="width:100%;" class="table">
|
<table class="table">
|
||||||
<colgroup>
|
<colgroup>
|
||||||
<col width="2%">
|
<col width="2%">
|
||||||
<col width="9%">
|
<col width="9%">
|
||||||
@ -528,7 +528,7 @@ Longest: 1</p>
|
|||||||
<col width="3%">
|
<col width="3%">
|
||||||
<col width="6%">
|
<col width="6%">
|
||||||
<col width="11%">
|
<col width="11%">
|
||||||
<col width="12%">
|
<col width="10%">
|
||||||
<col width="9%">
|
<col width="9%">
|
||||||
<col width="5%">
|
<col width="5%">
|
||||||
</colgroup>
|
</colgroup>
|
||||||
@ -550,46 +550,14 @@ Longest: 1</p>
|
|||||||
</tr></thead>
|
</tr></thead>
|
||||||
<tbody>
|
<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">2</td>
|
<td align="left">1</td>
|
||||||
<td align="center">2015-03-18</td>
|
<td align="center">2010-03-07</td>
|
||||||
<td align="center">G9</td>
|
<td align="center">U8</td>
|
||||||
<td align="center">Hospital D</td>
|
<td align="center">Hospital B</td>
|
||||||
<td align="center">B_STPHY_AURS</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">M</td>
|
|
||||||
<td align="center">Gram-positive</td>
|
|
||||||
<td align="center">Staphylococcus</td>
|
|
||||||
<td align="center">aureus</td>
|
|
||||||
<td align="center">TRUE</td>
|
|
||||||
</tr>
|
|
||||||
<tr class="even">
|
|
||||||
<td align="left">4</td>
|
|
||||||
<td align="center">2017-05-24</td>
|
|
||||||
<td align="center">A3</td>
|
|
||||||
<td align="center">Hospital A</td>
|
|
||||||
<td align="center">B_STPHY_AURS</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">M</td>
|
|
||||||
<td align="center">Gram-positive</td>
|
|
||||||
<td align="center">Staphylococcus</td>
|
|
||||||
<td align="center">aureus</td>
|
|
||||||
<td align="center">TRUE</td>
|
|
||||||
</tr>
|
|
||||||
<tr class="odd">
|
|
||||||
<td align="left">5</td>
|
|
||||||
<td align="center">2013-01-31</td>
|
|
||||||
<td align="center">Y10</td>
|
|
||||||
<td align="center">Hospital C</td>
|
|
||||||
<td align="center">B_ESCHR_COLI</td>
|
<td align="center">B_ESCHR_COLI</td>
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">F</td>
|
<td align="center">F</td>
|
||||||
<td align="center">Gram-negative</td>
|
<td align="center">Gram-negative</td>
|
||||||
@ -598,29 +566,13 @@ Longest: 1</p>
|
|||||||
<td align="center">TRUE</td>
|
<td align="center">TRUE</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">10</td>
|
<td align="left">2</td>
|
||||||
<td align="center">2014-07-29</td>
|
<td align="center">2015-08-15</td>
|
||||||
<td align="center">G3</td>
|
<td align="center">A4</td>
|
||||||
<td align="center">Hospital D</td>
|
<td align="center">Hospital C</td>
|
||||||
<td align="center">B_STRPT_PNMN</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">M</td>
|
|
||||||
<td align="center">Gram-positive</td>
|
|
||||||
<td align="center">Streptococcus</td>
|
|
||||||
<td align="center">pneumoniae</td>
|
|
||||||
<td align="center">TRUE</td>
|
|
||||||
</tr>
|
|
||||||
<tr class="odd">
|
|
||||||
<td align="left">11</td>
|
|
||||||
<td align="center">2010-12-28</td>
|
|
||||||
<td align="center">G5</td>
|
|
||||||
<td align="center">Hospital B</td>
|
|
||||||
<td align="center">B_ESCHR_COLI</td>
|
<td align="center">B_ESCHR_COLI</td>
|
||||||
<td align="center">R</td>
|
<td align="center">S</td>
|
||||||
<td align="center">R</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">M</td>
|
<td align="center">M</td>
|
||||||
@ -629,20 +581,68 @@ Longest: 1</p>
|
|||||||
<td align="center">coli</td>
|
<td align="center">coli</td>
|
||||||
<td align="center">TRUE</td>
|
<td align="center">TRUE</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="odd">
|
||||||
<td align="left">14</td>
|
<td align="left">4</td>
|
||||||
<td align="center">2015-01-05</td>
|
<td align="center">2017-04-28</td>
|
||||||
<td align="center">A8</td>
|
<td align="center">J10</td>
|
||||||
<td align="center">Hospital A</td>
|
<td align="center">Hospital A</td>
|
||||||
<td align="center">B_STPHY_AURS</td>
|
<td align="center">B_KLBSL_PNMN</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">M</td>
|
<td align="center">M</td>
|
||||||
<td align="center">Gram-positive</td>
|
<td align="center">Gram-negative</td>
|
||||||
<td align="center">Staphylococcus</td>
|
<td align="center">Klebsiella</td>
|
||||||
<td align="center">aureus</td>
|
<td align="center">pneumoniae</td>
|
||||||
|
<td align="center">TRUE</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td align="left">6</td>
|
||||||
|
<td align="center">2011-09-09</td>
|
||||||
|
<td align="center">Z1</td>
|
||||||
|
<td align="center">Hospital A</td>
|
||||||
|
<td align="center">B_ESCHR_COLI</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">F</td>
|
||||||
|
<td align="center">Gram-negative</td>
|
||||||
|
<td align="center">Escherichia</td>
|
||||||
|
<td align="center">coli</td>
|
||||||
|
<td align="center">TRUE</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td align="left">7</td>
|
||||||
|
<td align="center">2017-04-11</td>
|
||||||
|
<td align="center">I3</td>
|
||||||
|
<td align="center">Hospital B</td>
|
||||||
|
<td align="center">B_ESCHR_COLI</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">M</td>
|
||||||
|
<td align="center">Gram-negative</td>
|
||||||
|
<td align="center">Escherichia</td>
|
||||||
|
<td align="center">coli</td>
|
||||||
|
<td align="center">TRUE</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td align="left">10</td>
|
||||||
|
<td align="center">2011-06-22</td>
|
||||||
|
<td align="center">D10</td>
|
||||||
|
<td align="center">Hospital B</td>
|
||||||
|
<td align="center">B_KLBSL_PNMN</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">M</td>
|
||||||
|
<td align="center">Gram-negative</td>
|
||||||
|
<td align="center">Klebsiella</td>
|
||||||
|
<td align="center">pneumoniae</td>
|
||||||
<td align="center">TRUE</td>
|
<td align="center">TRUE</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
@ -666,8 +666,8 @@ Longest: 1</p>
|
|||||||
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></code></pre></div>
|
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></code></pre></div>
|
||||||
<p><strong>Frequency table</strong></p>
|
<p><strong>Frequency table</strong></p>
|
||||||
<p>Class: character<br>
|
<p>Class: character<br>
|
||||||
Length: 10,684<br>
|
Length: 10,677<br>
|
||||||
Available: 10,684 (100.0%, NA: 0 = 0.0%)<br>
|
Available: 10,677 (100.0%, NA: 0 = 0.0%)<br>
|
||||||
Unique: 4</p>
|
Unique: 4</p>
|
||||||
<p>Shortest: 16<br>
|
<p>Shortest: 16<br>
|
||||||
Longest: 24</p>
|
Longest: 24</p>
|
||||||
@ -684,33 +684,33 @@ Longest: 24</p>
|
|||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">1</td>
|
<td align="left">1</td>
|
||||||
<td align="left">Escherichia coli</td>
|
<td align="left">Escherichia coli</td>
|
||||||
<td align="right">4,660</td>
|
<td align="right">4,609</td>
|
||||||
<td align="right">43.62%</td>
|
<td align="right">43.17%</td>
|
||||||
<td align="right">4,660</td>
|
<td align="right">4,609</td>
|
||||||
<td align="right">43.62%</td>
|
<td align="right">43.17%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">2</td>
|
<td align="left">2</td>
|
||||||
<td align="left">Staphylococcus aureus</td>
|
<td align="left">Staphylococcus aureus</td>
|
||||||
<td align="right">2,727</td>
|
<td align="right">2,773</td>
|
||||||
<td align="right">25.52%</td>
|
<td align="right">25.97%</td>
|
||||||
<td align="right">7,387</td>
|
<td align="right">7,382</td>
|
||||||
<td align="right">69.14%</td>
|
<td align="right">69.14%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">3</td>
|
<td align="left">3</td>
|
||||||
<td align="left">Streptococcus pneumoniae</td>
|
<td align="left">Streptococcus pneumoniae</td>
|
||||||
<td align="right">2,106</td>
|
<td align="right">2,087</td>
|
||||||
<td align="right">19.71%</td>
|
<td align="right">19.55%</td>
|
||||||
<td align="right">9,493</td>
|
<td align="right">9,469</td>
|
||||||
<td align="right">88.85%</td>
|
<td align="right">88.69%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">4</td>
|
<td align="left">4</td>
|
||||||
<td align="left">Klebsiella pneumoniae</td>
|
<td align="left">Klebsiella pneumoniae</td>
|
||||||
<td align="right">1,191</td>
|
<td align="right">1,208</td>
|
||||||
<td align="right">11.15%</td>
|
<td align="right">11.31%</td>
|
||||||
<td align="right">10,684</td>
|
<td align="right">10,677</td>
|
||||||
<td align="right">100.00%</td>
|
<td align="right">100.00%</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
@ -757,53 +757,23 @@ Longest: 24</p>
|
|||||||
</tr></thead>
|
</tr></thead>
|
||||||
<tbody>
|
<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">2017-05-24</td>
|
<td align="center">2017-04-11</td>
|
||||||
<td align="center">A3</td>
|
<td align="center">I3</td>
|
||||||
<td align="center">Hospital A</td>
|
<td align="center">Hospital B</td>
|
||||||
<td align="center">B_STPHY_AURS</td>
|
<td align="center">B_ESCHR_COLI</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
<td align="center">M</td>
|
<td align="center">M</td>
|
||||||
<td align="center">Gram-positive</td>
|
<td align="center">Gram-negative</td>
|
||||||
<td align="center">Staphylococcus</td>
|
<td align="center">Escherichia</td>
|
||||||
<td align="center">aureus</td>
|
<td align="center">coli</td>
|
||||||
<td align="center">TRUE</td>
|
<td align="center">TRUE</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">2014-07-29</td>
|
<td align="center">2013-07-04</td>
|
||||||
<td align="center">G3</td>
|
<td align="center">C4</td>
|
||||||
<td align="center">Hospital D</td>
|
|
||||||
<td align="center">B_STRPT_PNMN</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">M</td>
|
|
||||||
<td align="center">Gram-positive</td>
|
|
||||||
<td align="center">Streptococcus</td>
|
|
||||||
<td align="center">pneumoniae</td>
|
|
||||||
<td align="center">TRUE</td>
|
|
||||||
</tr>
|
|
||||||
<tr class="odd">
|
|
||||||
<td align="center">2014-10-24</td>
|
|
||||||
<td align="center">S9</td>
|
|
||||||
<td align="center">Hospital A</td>
|
|
||||||
<td align="center">B_STRPT_PNMN</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">F</td>
|
|
||||||
<td align="center">Gram-positive</td>
|
|
||||||
<td align="center">Streptococcus</td>
|
|
||||||
<td align="center">pneumoniae</td>
|
|
||||||
<td align="center">TRUE</td>
|
|
||||||
</tr>
|
|
||||||
<tr class="even">
|
|
||||||
<td align="center">2012-08-31</td>
|
|
||||||
<td align="center">A1</td>
|
|
||||||
<td align="center">Hospital B</td>
|
<td align="center">Hospital B</td>
|
||||||
<td align="center">B_STRPT_PNMN</td>
|
<td align="center">B_STRPT_PNMN</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
@ -817,27 +787,12 @@ Longest: 24</p>
|
|||||||
<td align="center">TRUE</td>
|
<td align="center">TRUE</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">2016-04-25</td>
|
<td align="center">2010-11-18</td>
|
||||||
<td align="center">Z10</td>
|
<td align="center">F8</td>
|
||||||
<td align="center">Hospital C</td>
|
<td align="center">Hospital B</td>
|
||||||
<td align="center">B_KLBSL_PNMN</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">F</td>
|
|
||||||
<td align="center">Gram-negative</td>
|
|
||||||
<td align="center">Klebsiella</td>
|
|
||||||
<td align="center">pneumoniae</td>
|
|
||||||
<td align="center">TRUE</td>
|
|
||||||
</tr>
|
|
||||||
<tr class="even">
|
|
||||||
<td align="center">2011-04-30</td>
|
|
||||||
<td align="center">J10</td>
|
|
||||||
<td align="center">Hospital D</td>
|
|
||||||
<td align="center">B_STPHY_AURS</td>
|
<td align="center">B_STPHY_AURS</td>
|
||||||
<td align="center">S</td>
|
<td align="center">R</td>
|
||||||
<td align="center">S</td>
|
<td align="center">R</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
<td align="center">M</td>
|
<td align="center">M</td>
|
||||||
@ -846,6 +801,51 @@ Longest: 24</p>
|
|||||||
<td align="center">aureus</td>
|
<td align="center">aureus</td>
|
||||||
<td align="center">TRUE</td>
|
<td align="center">TRUE</td>
|
||||||
</tr>
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td align="center">2017-06-06</td>
|
||||||
|
<td align="center">H4</td>
|
||||||
|
<td align="center">Hospital D</td>
|
||||||
|
<td align="center">B_ESCHR_COLI</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">M</td>
|
||||||
|
<td align="center">Gram-negative</td>
|
||||||
|
<td align="center">Escherichia</td>
|
||||||
|
<td align="center">coli</td>
|
||||||
|
<td align="center">TRUE</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td align="center">2014-02-16</td>
|
||||||
|
<td align="center">V2</td>
|
||||||
|
<td align="center">Hospital C</td>
|
||||||
|
<td align="center">B_STRPT_PNMN</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">F</td>
|
||||||
|
<td align="center">Gram-positive</td>
|
||||||
|
<td align="center">Streptococcus</td>
|
||||||
|
<td align="center">pneumoniae</td>
|
||||||
|
<td align="center">TRUE</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td align="center">2013-02-16</td>
|
||||||
|
<td align="center">M1</td>
|
||||||
|
<td align="center">Hospital D</td>
|
||||||
|
<td align="center">B_STRPT_PNMN</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">M</td>
|
||||||
|
<td align="center">Gram-positive</td>
|
||||||
|
<td align="center">Streptococcus</td>
|
||||||
|
<td align="center">pneumoniae</td>
|
||||||
|
<td align="center">TRUE</td>
|
||||||
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
<p>If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> function:</p>
|
<p>If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> function:</p>
|
||||||
@ -867,50 +867,50 @@ Longest: 24</p>
|
|||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">E. coli</td>
|
<td align="center">E. coli</td>
|
||||||
<td align="center">AMX</td>
|
<td align="center">AMX</td>
|
||||||
<td align="center">2148</td>
|
<td align="center">2190</td>
|
||||||
<td align="center">144</td>
|
<td align="center">112</td>
|
||||||
<td align="center">2368</td>
|
<td align="center">2307</td>
|
||||||
<td align="center">4660</td>
|
<td align="center">4609</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">E. coli</td>
|
<td align="center">E. coli</td>
|
||||||
<td align="center">AMC</td>
|
<td align="center">AMC</td>
|
||||||
<td align="center">3418</td>
|
<td align="center">3359</td>
|
||||||
<td align="center">162</td>
|
<td align="center">170</td>
|
||||||
<td align="center">1080</td>
|
<td align="center">1080</td>
|
||||||
<td align="center">4660</td>
|
<td align="center">4609</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">E. coli</td>
|
<td align="center">E. coli</td>
|
||||||
<td align="center">CIP</td>
|
<td align="center">CIP</td>
|
||||||
<td align="center">3376</td>
|
<td align="center">3366</td>
|
||||||
<td align="center">0</td>
|
<td align="center">0</td>
|
||||||
<td align="center">1284</td>
|
<td align="center">1243</td>
|
||||||
<td align="center">4660</td>
|
<td align="center">4609</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">E. coli</td>
|
<td align="center">E. coli</td>
|
||||||
<td align="center">GEN</td>
|
<td align="center">GEN</td>
|
||||||
<td align="center">4068</td>
|
<td align="center">4002</td>
|
||||||
<td align="center">0</td>
|
<td align="center">0</td>
|
||||||
<td align="center">592</td>
|
<td align="center">607</td>
|
||||||
<td align="center">4660</td>
|
<td align="center">4609</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">K. pneumoniae</td>
|
<td align="center">K. pneumoniae</td>
|
||||||
<td align="center">AMX</td>
|
<td align="center">AMX</td>
|
||||||
<td align="center">0</td>
|
<td align="center">0</td>
|
||||||
<td align="center">0</td>
|
<td align="center">0</td>
|
||||||
<td align="center">1191</td>
|
<td align="center">1208</td>
|
||||||
<td align="center">1191</td>
|
<td align="center">1208</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">K. pneumoniae</td>
|
<td align="center">K. pneumoniae</td>
|
||||||
<td align="center">AMC</td>
|
<td align="center">AMC</td>
|
||||||
<td align="center">947</td>
|
<td align="center">951</td>
|
||||||
<td align="center">46</td>
|
<td align="center">35</td>
|
||||||
<td align="center">198</td>
|
<td align="center">222</td>
|
||||||
<td align="center">1191</td>
|
<td align="center">1208</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
@ -933,34 +933,34 @@ Longest: 24</p>
|
|||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">E. coli</td>
|
<td align="center">E. coli</td>
|
||||||
<td align="center">GEN</td>
|
<td align="center">GEN</td>
|
||||||
<td align="center">4068</td>
|
<td align="center">4002</td>
|
||||||
<td align="center">0</td>
|
<td align="center">0</td>
|
||||||
<td align="center">592</td>
|
<td align="center">607</td>
|
||||||
<td align="center">4660</td>
|
<td align="center">4609</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">K. pneumoniae</td>
|
<td align="center">K. pneumoniae</td>
|
||||||
<td align="center">GEN</td>
|
<td align="center">GEN</td>
|
||||||
<td align="center">1062</td>
|
<td align="center">1063</td>
|
||||||
<td align="center">0</td>
|
<td align="center">0</td>
|
||||||
<td align="center">129</td>
|
<td align="center">145</td>
|
||||||
<td align="center">1191</td>
|
<td align="center">1208</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">S. aureus</td>
|
<td align="center">S. aureus</td>
|
||||||
<td align="center">GEN</td>
|
<td align="center">GEN</td>
|
||||||
<td align="center">2401</td>
|
<td align="center">2446</td>
|
||||||
<td align="center">0</td>
|
<td align="center">0</td>
|
||||||
<td align="center">326</td>
|
<td align="center">327</td>
|
||||||
<td align="center">2727</td>
|
<td align="center">2773</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">S. pneumoniae</td>
|
<td align="center">S. pneumoniae</td>
|
||||||
<td align="center">GEN</td>
|
<td align="center">GEN</td>
|
||||||
<td align="center">0</td>
|
<td align="center">0</td>
|
||||||
<td align="center">0</td>
|
<td align="center">0</td>
|
||||||
<td align="center">2106</td>
|
<td align="center">2087</td>
|
||||||
<td align="center">2106</td>
|
<td align="center">2087</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
@ -974,7 +974,7 @@ Longest: 24</p>
|
|||||||
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
|
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
|
||||||
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>
|
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>
|
||||||
<span class="co"># [1] 0.5497005</span></code></pre></div>
|
<span class="co"># [1] 0.544254</span></code></pre></div>
|
||||||
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
|
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
|
||||||
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||||
@ -988,19 +988,19 @@ Longest: 24</p>
|
|||||||
<tbody>
|
<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">Hospital A</td>
|
<td align="center">Hospital A</td>
|
||||||
<td align="center">0.5528455</td>
|
<td align="center">0.5349716</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">Hospital B</td>
|
<td align="center">Hospital B</td>
|
||||||
<td align="center">0.5463890</td>
|
<td align="center">0.5482514</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">Hospital C</td>
|
<td align="center">Hospital C</td>
|
||||||
<td align="center">0.5533333</td>
|
<td align="center">0.5800508</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">Hospital D</td>
|
<td align="center">Hospital D</td>
|
||||||
<td align="center">0.5482679</td>
|
<td align="center">0.5244591</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
@ -1019,23 +1019,23 @@ Longest: 24</p>
|
|||||||
<tbody>
|
<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">Hospital A</td>
|
<td align="center">Hospital A</td>
|
||||||
<td align="center">0.5528455</td>
|
<td align="center">0.5349716</td>
|
||||||
<td align="center">3075</td>
|
<td align="center">3174</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">Hospital B</td>
|
<td align="center">Hospital B</td>
|
||||||
<td align="center">0.5463890</td>
|
<td align="center">0.5482514</td>
|
||||||
<td align="center">3794</td>
|
<td align="center">3803</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">Hospital C</td>
|
<td align="center">Hospital C</td>
|
||||||
<td align="center">0.5533333</td>
|
<td align="center">0.5800508</td>
|
||||||
<td align="center">1650</td>
|
<td align="center">1574</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">Hospital D</td>
|
<td align="center">Hospital D</td>
|
||||||
<td align="center">0.5482679</td>
|
<td align="center">0.5244591</td>
|
||||||
<td align="center">2165</td>
|
<td align="center">2126</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
@ -1056,27 +1056,27 @@ Longest: 24</p>
|
|||||||
<tbody>
|
<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">Escherichia</td>
|
<td align="center">Escherichia</td>
|
||||||
<td align="center">0.7682403</td>
|
<td align="center">0.7656759</td>
|
||||||
<td align="center">0.8729614</td>
|
<td align="center">0.8683011</td>
|
||||||
<td align="center">0.9766094</td>
|
<td align="center">0.9709264</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">Klebsiella</td>
|
<td align="center">Klebsiella</td>
|
||||||
<td align="center">0.8337531</td>
|
<td align="center">0.8162252</td>
|
||||||
<td align="center">0.8916877</td>
|
<td align="center">0.8799669</td>
|
||||||
<td align="center">0.9806885</td>
|
<td align="center">0.9726821</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">Staphylococcus</td>
|
<td align="center">Staphylococcus</td>
|
||||||
<td align="center">0.7887789</td>
|
<td align="center">0.7991345</td>
|
||||||
<td align="center">0.8804547</td>
|
<td align="center">0.8820772</td>
|
||||||
<td align="center">0.9790979</td>
|
<td align="center">0.9772809</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">Streptococcus</td>
|
<td align="center">Streptococcus</td>
|
||||||
<td align="center">0.5318139</td>
|
<td align="center">0.5462386</td>
|
||||||
<td align="center">0.0000000</td>
|
<td align="center">0.0000000</td>
|
||||||
<td align="center">0.5318139</td>
|
<td align="center">0.5462386</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
@ -1101,23 +1101,23 @@ Longest: 24</p>
|
|||||||
<tbody>
|
<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">Hospital A</td>
|
<td align="left">Hospital A</td>
|
||||||
<td align="right">55.3%</td>
|
<td align="right">53.5%</td>
|
||||||
<td align="right">26.3%</td>
|
<td align="right">26.0%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">Hospital B</td>
|
<td align="left">Hospital B</td>
|
||||||
<td align="right">54.6%</td>
|
<td align="right">54.8%</td>
|
||||||
<td align="right">27.2%</td>
|
<td align="right">26.1%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">Hospital C</td>
|
<td align="left">Hospital C</td>
|
||||||
<td align="right">55.3%</td>
|
<td align="right">58.0%</td>
|
||||||
<td align="right">25.7%</td>
|
<td align="right">28.5%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">Hospital D</td>
|
<td align="left">Hospital D</td>
|
||||||
<td align="right">54.8%</td>
|
<td align="right">52.4%</td>
|
||||||
<td align="right">26.5%</td>
|
<td align="right">25.4%</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
@ -1201,16 +1201,16 @@ Longest: 24</p>
|
|||||||
<code class="sourceCode R"><span class="va">mic_values</span> <span class="op"><-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
|
<code class="sourceCode R"><span class="va">mic_values</span> <span class="op"><-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
|
||||||
<span class="va">mic_values</span>
|
<span class="va">mic_values</span>
|
||||||
<span class="co"># Class <mic></span>
|
<span class="co"># Class <mic></span>
|
||||||
<span class="co"># [1] 0.0625 0.002 0.002 0.001 4 1 0.0625 32 0.5 0.5 </span>
|
<span class="co"># [1] 0.5 1 0.002 0.125 0.025 2 8 0.125 0.125 4 </span>
|
||||||
<span class="co"># [11] 0.25 0.025 0.001 64 0.5 0.5 2 0.005 16 0.5 </span>
|
<span class="co"># [11] 0.0625 0.001 0.025 0.001 8 64 0.025 32 0.001 64 </span>
|
||||||
<span class="co"># [21] 0.25 64 4 0.002 128 0.01 64 0.25 0.01 0.005 </span>
|
<span class="co"># [21] 8 0.001 16 0.5 0.0625 0.002 128 8 0.125 4 </span>
|
||||||
<span class="co"># [31] 32 32 16 0.25 0.002 1 128 128 0.25 0.001 </span>
|
<span class="co"># [31] 0.125 64 32 0.001 0.0625 0.005 2 4 0.125 32 </span>
|
||||||
<span class="co"># [41] 0.0625 0.125 0.001 128 0.0625 0.001 1 0.25 2 0.001 </span>
|
<span class="co"># [41] 0.125 0.5 0.0625 128 0.125 0.125 0.01 0.25 0.5 0.002 </span>
|
||||||
<span class="co"># [51] 0.005 4 8 2 0.125 0.0625 16 0.25 64 8 </span>
|
<span class="co"># [51] 8 8 0.002 0.002 0.25 256 1 8 2 2 </span>
|
||||||
<span class="co"># [61] 0.005 32 0.0625 0.01 0.002 32 8 64 16 2 </span>
|
<span class="co"># [61] 0.0625 0.005 0.005 16 0.5 0.025 16 8 8 0.0625</span>
|
||||||
<span class="co"># [71] 1 2 32 2 8 0.001 0.25 8 8 64 </span>
|
<span class="co"># [71] 0.002 0.125 0.025 0.025 1 32 0.25 16 128 8 </span>
|
||||||
<span class="co"># [81] 128 0.01 0.0625 0.125 0.002 8 0.025 0.0625 0.0625 8 </span>
|
<span class="co"># [81] 0.0625 0.025 64 0.001 0.5 4 8 4 16 32 </span>
|
||||||
<span class="co"># [91] 0.005 16 4 8 0.25 0.025 8 0.002 0.25 0.25</span></code></pre></div>
|
<span class="co"># [91] 0.005 8 0.125 256 64 0.001 1 32 0.005 0.025</span></code></pre></div>
|
||||||
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R"><span class="co"># base R:</span>
|
<code class="sourceCode R"><span class="co"># base R:</span>
|
||||||
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></code></pre></div>
|
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></code></pre></div>
|
||||||
@ -1236,13 +1236,13 @@ Longest: 24</p>
|
|||||||
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R"><span class="va">disk_values</span> <span class="op"><-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span>
|
<code class="sourceCode R"><span class="va">disk_values</span> <span class="op"><-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span>
|
||||||
<span class="co"># ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
<span class="co"># ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||||
<span class="co"># coli). Run `mo_uncertainties()` to review this uncertainty.</span>
|
<span class="co"># coli). Run `mo_uncertainties()` to review this.</span>
|
||||||
<span class="va">disk_values</span>
|
<span class="va">disk_values</span>
|
||||||
<span class="co"># Class <disk></span>
|
<span class="co"># Class <disk></span>
|
||||||
<span class="co"># [1] 22 25 27 18 21 30 29 21 21 24 26 18 23 28 22 24 18 20 19 18 27 23 25 23 21</span>
|
<span class="co"># [1] 29 17 17 18 17 29 28 25 21 24 30 29 20 26 21 28 22 21 28 25 25 22 29 29 27</span>
|
||||||
<span class="co"># [26] 24 22 22 23 27 23 19 22 20 17 19 30 19 23 19 23 21 24 30 30 26 25 27 17 29</span>
|
<span class="co"># [26] 19 30 19 25 28 27 26 19 16 29 20 19 25 16 27 25 19 30 23 20 20 25 23 25 17</span>
|
||||||
<span class="co"># [51] 25 30 31 26 17 18 30 24 18 25 21 19 31 24 20 24 18 25 26 24 19 30 27 21 26</span>
|
<span class="co"># [51] 19 21 20 25 19 25 22 16 29 25 25 21 29 29 28 24 30 23 22 22 31 26 20 19 30</span>
|
||||||
<span class="co"># [76] 20 17 31 28 31 26 27 30 17 27 19 26 26 31 17 30 23 20 17 30 19 19 20 21 19</span></code></pre></div>
|
<span class="co"># [76] 30 28 26 25 26 27 16 25 27 21 29 17 31 16 27 22 19 26 20 21 19 27 21 24 27</span></code></pre></div>
|
||||||
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R"><span class="co"># base R:</span>
|
<code class="sourceCode R"><span class="co"># base R:</span>
|
||||||
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></code></pre></div>
|
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></code></pre></div>
|
||||||
|
|||||||
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|
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@ -44,7 +44,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9068</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -44,7 +44,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9068</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -358,18 +358,18 @@ Unique: 2</p>
|
|||||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
|
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
|
||||||
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
|
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
|
||||||
<span class="co"># 1 R R I S I I</span>
|
<span class="co"># 1 I R I S R S</span>
|
||||||
<span class="co"># 2 I I I I R S</span>
|
<span class="co"># 2 I S R R S R</span>
|
||||||
<span class="co"># 3 I R S I R S</span>
|
<span class="co"># 3 R I S I R S</span>
|
||||||
<span class="co"># 4 R S I I I R</span>
|
<span class="co"># 4 S S I R I S</span>
|
||||||
<span class="co"># 5 S S R I I S</span>
|
<span class="co"># 5 S R S S S I</span>
|
||||||
<span class="co"># 6 R R R I S R</span>
|
<span class="co"># 6 S R R S R I</span>
|
||||||
<span class="co"># kanamycin</span>
|
<span class="co"># kanamycin</span>
|
||||||
<span class="co"># 1 I</span>
|
<span class="co"># 1 S</span>
|
||||||
<span class="co"># 2 R</span>
|
<span class="co"># 2 I</span>
|
||||||
<span class="co"># 3 S</span>
|
<span class="co"># 3 R</span>
|
||||||
<span class="co"># 4 R</span>
|
<span class="co"># 4 R</span>
|
||||||
<span class="co"># 5 R</span>
|
<span class="co"># 5 I</span>
|
||||||
<span class="co"># 6 R</span></code></pre></div>
|
<span class="co"># 6 R</span></code></pre></div>
|
||||||
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
|
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
|
||||||
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
|
||||||
@ -413,40 +413,40 @@ Unique: 5</p>
|
|||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">1</td>
|
<td align="left">1</td>
|
||||||
<td align="left">Mono-resistant</td>
|
<td align="left">Mono-resistant</td>
|
||||||
<td align="right">3246</td>
|
<td align="right">3250</td>
|
||||||
<td align="right">64.92%</td>
|
<td align="right">65.00%</td>
|
||||||
<td align="right">3246</td>
|
<td align="right">3250</td>
|
||||||
<td align="right">64.92%</td>
|
<td align="right">65.00%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">2</td>
|
<td align="left">2</td>
|
||||||
<td align="left">Negative</td>
|
<td align="left">Negative</td>
|
||||||
<td align="right">999</td>
|
<td align="right">975</td>
|
||||||
<td align="right">19.98%</td>
|
<td align="right">19.50%</td>
|
||||||
<td align="right">4245</td>
|
<td align="right">4225</td>
|
||||||
<td align="right">84.90%</td>
|
<td align="right">84.50%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">3</td>
|
<td align="left">3</td>
|
||||||
<td align="left">Multi-drug-resistant</td>
|
<td align="left">Multi-drug-resistant</td>
|
||||||
<td align="right">437</td>
|
<td align="right">474</td>
|
||||||
<td align="right">8.74%</td>
|
<td align="right">9.48%</td>
|
||||||
<td align="right">4682</td>
|
<td align="right">4699</td>
|
||||||
<td align="right">93.64%</td>
|
<td align="right">93.98%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">4</td>
|
<td align="left">4</td>
|
||||||
<td align="left">Poly-resistant</td>
|
<td align="left">Poly-resistant</td>
|
||||||
<td align="right">218</td>
|
<td align="right">203</td>
|
||||||
<td align="right">4.36%</td>
|
<td align="right">4.06%</td>
|
||||||
<td align="right">4900</td>
|
<td align="right">4902</td>
|
||||||
<td align="right">98.00%</td>
|
<td align="right">98.04%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">5</td>
|
<td align="left">5</td>
|
||||||
<td align="left">Extensively drug-resistant</td>
|
<td align="left">Extensively drug-resistant</td>
|
||||||
<td align="right">100</td>
|
<td align="right">98</td>
|
||||||
<td align="right">2.00%</td>
|
<td align="right">1.96%</td>
|
||||||
<td align="right">5000</td>
|
<td align="right">5000</td>
|
||||||
<td align="right">100.00%</td>
|
<td align="right">100.00%</td>
|
||||||
</tr>
|
</tr>
|
||||||
|
|||||||
@ -44,7 +44,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9068</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -44,7 +44,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9074</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -191,7 +191,7 @@
|
|||||||
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
|
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
|
||||||
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
|
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
|
||||||
|
|
||||||
<h4 data-toc-skip class="date">14 December 2021</h4>
|
<h4 data-toc-skip class="date">23 December 2021</h4>
|
||||||
|
|
||||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
|
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
|
||||||
<div class="hidden name"><code>SPSS.Rmd</code></div>
|
<div class="hidden name"><code>SPSS.Rmd</code></div>
|
||||||
@ -226,7 +226,7 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<p><strong>R has a huge community.</strong></p>
|
<p><strong>R has a huge community.</strong></p>
|
||||||
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">429,535 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
|
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">430,288 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<p><strong>R understands any data type, including SPSS/SAS/Stata.</strong></p>
|
<p><strong>R understands any data type, including SPSS/SAS/Stata.</strong></p>
|
||||||
|
|||||||
@ -44,7 +44,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9068</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -44,7 +44,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9073</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -222,23 +222,23 @@
|
|||||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>, <span class="co"># Methicillin Resistant S. aureus</span>
|
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>, <span class="co"># Methicillin Resistant S. aureus</span>
|
||||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span>, <span class="co"># Vancomycin Intermediate S. aureus</span>
|
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span>, <span class="co"># Vancomycin Intermediate S. aureus</span>
|
||||||
times <span class="op">=</span> <span class="fl">25</span><span class="op">)</span>
|
times <span class="op">=</span> <span class="fl">25</span><span class="op">)</span>
|
||||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
|
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
|
||||||
<span class="co"># Unit: milliseconds</span>
|
<span class="co"># Unit: milliseconds</span>
|
||||||
<span class="co"># expr min lq mean median uq max neval</span>
|
<span class="co"># expr min lq mean median uq max neval</span>
|
||||||
<span class="co"># as.mo("sau") 12.0 12.0 17.0 14.0 15.0 56 25</span>
|
<span class="co"># as.mo("sau") 10.0 12.0 20.0 12.0 15.0 53 25</span>
|
||||||
<span class="co"># as.mo("stau") 51.0 60.0 81.0 87.0 98.0 120 25</span>
|
<span class="co"># as.mo("stau") 49.0 54.0 72.0 58.0 91.0 97 25</span>
|
||||||
<span class="co"># as.mo("STAU") 51.0 64.0 83.0 90.0 98.0 130 25</span>
|
<span class="co"># as.mo("STAU") 50.0 54.0 71.0 57.0 90.0 110 25</span>
|
||||||
<span class="co"># as.mo("staaur") 9.7 12.0 15.0 15.0 15.0 46 25</span>
|
<span class="co"># as.mo("staaur") 10.0 12.0 17.0 12.0 14.0 51 25</span>
|
||||||
<span class="co"># as.mo("STAAUR") 11.0 14.0 17.0 15.0 16.0 45 25</span>
|
<span class="co"># as.mo("STAAUR") 10.0 12.0 17.0 12.0 14.0 54 25</span>
|
||||||
<span class="co"># as.mo("S. aureus") 24.0 31.0 43.0 33.0 63.0 77 25</span>
|
<span class="co"># as.mo("S. aureus") 26.0 27.0 40.0 31.0 56.0 74 25</span>
|
||||||
<span class="co"># as.mo("S aureus") 26.0 28.0 45.0 34.0 62.0 76 25</span>
|
<span class="co"># as.mo("S aureus") 26.0 27.0 39.0 29.0 58.0 68 25</span>
|
||||||
<span class="co"># as.mo("Staphylococcus aureus") 3.0 3.7 5.4 3.8 4.6 37 25</span>
|
<span class="co"># as.mo("Staphylococcus aureus") 3.5 3.9 6.6 4.1 4.8 38 25</span>
|
||||||
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 240.0 250.0 270.0 260.0 270.0 310 25</span>
|
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 230.0 240.0 250.0 240.0 250.0 280 25</span>
|
||||||
<span class="co"># as.mo("Sthafilokkockus aaureuz") 180.0 190.0 210.0 200.0 220.0 260 25</span>
|
<span class="co"># as.mo("Sthafilokkockus aaureuz") 180.0 190.0 200.0 190.0 200.0 290 25</span>
|
||||||
<span class="co"># as.mo("MRSA") 10.0 13.0 20.0 15.0 17.0 73 25</span>
|
<span class="co"># as.mo("MRSA") 11.0 12.0 19.0 13.0 14.0 50 25</span>
|
||||||
<span class="co"># as.mo("VISA") 20.0 23.0 38.0 26.0 49.0 150 25</span></code></pre></div>
|
<span class="co"># as.mo("VISA") 21.0 22.0 32.0 25.0 50.0 60 25</span></code></pre></div>
|
||||||
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="750"></p>
|
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="750"></p>
|
||||||
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 69 times slower to determine.</p>
|
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 47 times slower to determine.</p>
|
||||||
<p>To improve performance, we implemented two important algorithms to save unnecessary calculations: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
|
<p>To improve performance, we implemented two important algorithms to save unnecessary calculations: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
|
||||||
<div class="section level3">
|
<div class="section level3">
|
||||||
<h3 id="repetitive-results">Repetitive results<a class="anchor" aria-label="anchor" href="#repetitive-results"></a>
|
<h3 id="repetitive-results">Repetitive results<a class="anchor" aria-label="anchor" href="#repetitive-results"></a>
|
||||||
@ -258,8 +258,8 @@
|
|||||||
<span class="co"># what do these values look like? They are of class <mo>:</span>
|
<span class="co"># what do these values look like? They are of class <mo>:</span>
|
||||||
<span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
|
<span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
|
||||||
<span class="co"># Class <mo></span>
|
<span class="co"># Class <mo></span>
|
||||||
<span class="co"># [1] B_STRPT_PNMN B_ESCHR_COLI B_STPHY_AURS B_STPHY_CONS B_ENTRC </span>
|
<span class="co"># [1] B_STPHY_AURS B_STRPT_EQNS B_KLBSL_PNMN B_STPHY_EPDR B_STPHY_AURS</span>
|
||||||
<span class="co"># [6] B_STPHY_HMNS</span>
|
<span class="co"># [6] B_CRYNB_STRT</span>
|
||||||
|
|
||||||
<span class="co"># as the example_isolates data set has 2,000 rows, we should have 2 million items</span>
|
<span class="co"># as the example_isolates data set has 2,000 rows, we should have 2 million items</span>
|
||||||
<span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
|
<span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
|
||||||
@ -272,11 +272,11 @@
|
|||||||
<span class="co"># now let's see:</span>
|
<span class="co"># now let's see:</span>
|
||||||
<span class="va">run_it</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>,
|
<span class="va">run_it</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>,
|
||||||
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
||||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||||
<span class="co"># Unit: milliseconds</span>
|
<span class="co"># Unit: milliseconds</span>
|
||||||
<span class="co"># expr min lq mean median uq max neval</span>
|
<span class="co"># expr min lq mean median uq max neval</span>
|
||||||
<span class="co"># mo_name(x) 205 234 315 310 393 447 10</span></code></pre></div>
|
<span class="co"># mo_name(x) 196 209 274 223 364 388 10</span></code></pre></div>
|
||||||
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.31 seconds. That is 155 nanoseconds on average. You only lose time on your unique input values.</p>
|
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.223 seconds. That is 112 nanoseconds on average. You only lose time on your unique input values.</p>
|
||||||
</div>
|
</div>
|
||||||
<div class="section level3">
|
<div class="section level3">
|
||||||
<h3 id="precalculated-results">Precalculated results<a class="anchor" aria-label="anchor" href="#precalculated-results"></a>
|
<h3 id="precalculated-results">Precalculated results<a class="anchor" aria-label="anchor" href="#precalculated-results"></a>
|
||||||
@ -287,12 +287,12 @@
|
|||||||
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>,
|
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>,
|
||||||
C <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span>,
|
C <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span>,
|
||||||
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
||||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||||
<span class="co"># Unit: milliseconds</span>
|
<span class="co"># Unit: milliseconds</span>
|
||||||
<span class="co"># expr min lq mean median uq max neval</span>
|
<span class="co"># expr min lq mean median uq max neval</span>
|
||||||
<span class="co"># A 7.89 8.95 14.80 9.21 10.50 64.60 10</span>
|
<span class="co"># A 8.00 9.16 9.19 9.28 9.46 9.73 10</span>
|
||||||
<span class="co"># B 22.60 26.10 33.80 26.90 29.80 89.20 10</span>
|
<span class="co"># B 23.40 27.20 32.60 27.90 28.10 80.20 10</span>
|
||||||
<span class="co"># C 1.76 2.04 2.44 2.49 2.73 3.37 10</span></code></pre></div>
|
<span class="co"># C 1.85 2.25 2.40 2.47 2.62 2.90 10</span></code></pre></div>
|
||||||
<p>So going from <code>mo_name("Staphylococcus aureus")</code> to <code>"Staphylococcus aureus"</code> takes 0.0025 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
|
<p>So going from <code>mo_name("Staphylococcus aureus")</code> to <code>"Staphylococcus aureus"</code> takes 0.0025 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
|
||||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R"><span class="va">run_it</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
|
<code class="sourceCode R"><span class="va">run_it</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
|
||||||
@ -304,17 +304,17 @@
|
|||||||
G <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_phylum</a></span><span class="op">(</span><span class="st">"Firmicutes"</span><span class="op">)</span>,
|
G <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_phylum</a></span><span class="op">(</span><span class="st">"Firmicutes"</span><span class="op">)</span>,
|
||||||
H <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span><span class="op">(</span><span class="st">"Bacteria"</span><span class="op">)</span>,
|
H <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span><span class="op">(</span><span class="st">"Bacteria"</span><span class="op">)</span>,
|
||||||
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
||||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||||
<span class="co"># Unit: milliseconds</span>
|
<span class="co"># Unit: milliseconds</span>
|
||||||
<span class="co"># expr min lq mean median uq max neval</span>
|
<span class="co"># expr min lq mean median uq max neval</span>
|
||||||
<span class="co"># A 1.62 1.67 1.81 1.71 1.75 2.45 10</span>
|
<span class="co"># A 1.76 1.80 2.07 1.95 2.26 2.90 10</span>
|
||||||
<span class="co"># B 1.59 1.62 1.94 1.75 2.15 3.08 10</span>
|
<span class="co"># B 1.69 1.73 1.90 1.81 2.03 2.48 10</span>
|
||||||
<span class="co"># C 1.61 1.64 1.74 1.70 1.73 2.09 10</span>
|
<span class="co"># C 1.71 1.77 1.92 1.91 2.05 2.17 10</span>
|
||||||
<span class="co"># D 1.58 1.66 1.87 1.69 2.07 2.63 10</span>
|
<span class="co"># D 1.68 1.71 1.76 1.76 1.82 1.88 10</span>
|
||||||
<span class="co"># E 1.59 1.61 1.70 1.64 1.72 2.15 10</span>
|
<span class="co"># E 1.68 1.70 1.89 1.89 2.04 2.26 10</span>
|
||||||
<span class="co"># F 1.57 1.60 1.69 1.66 1.71 2.07 10</span>
|
<span class="co"># F 1.67 1.75 1.93 1.89 2.11 2.35 10</span>
|
||||||
<span class="co"># G 1.56 1.60 1.75 1.67 1.73 2.21 10</span>
|
<span class="co"># G 1.70 1.76 1.97 1.88 2.12 2.43 10</span>
|
||||||
<span class="co"># H 1.60 1.62 1.67 1.64 1.70 1.81 10</span></code></pre></div>
|
<span class="co"># H 1.67 1.71 1.83 1.75 1.98 2.14 10</span></code></pre></div>
|
||||||
<p>Of course, when running <code>mo_phylum("Firmicutes")</code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package contains all phyla of all known bacteria, it can just return the initial value immediately.</p>
|
<p>Of course, when running <code>mo_phylum("Firmicutes")</code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package contains all phyla of all known bacteria, it can just return the initial value immediately.</p>
|
||||||
</div>
|
</div>
|
||||||
<div class="section level3">
|
<div class="section level3">
|
||||||
@ -347,19 +347,19 @@
|
|||||||
ru <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"ru"</span><span class="op">)</span>,
|
ru <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"ru"</span><span class="op">)</span>,
|
||||||
sv <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"sv"</span><span class="op">)</span>,
|
sv <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"sv"</span><span class="op">)</span>,
|
||||||
times <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
|
times <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
|
||||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
|
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
|
||||||
<span class="co"># Unit: milliseconds</span>
|
<span class="co"># Unit: milliseconds</span>
|
||||||
<span class="co"># expr min lq mean median uq max neval</span>
|
<span class="co"># expr min lq mean median uq max neval</span>
|
||||||
<span class="co"># da 1.9160 2.012 2.308 2.213 2.445 4.040 100</span>
|
<span class="co"># da 1.9470 2.0220 2.190 2.0720 2.358 3.234 100</span>
|
||||||
<span class="co"># de 1.9130 2.057 3.165 2.358 2.495 44.140 100</span>
|
<span class="co"># de 1.9560 2.0330 3.649 2.1610 2.401 50.670 100</span>
|
||||||
<span class="co"># en 0.8684 0.910 1.076 1.004 1.137 2.173 100</span>
|
<span class="co"># en 0.8937 0.9124 1.022 0.9776 1.120 1.748 100</span>
|
||||||
<span class="co"># es 1.9060 2.066 3.304 2.335 2.595 60.500 100</span>
|
<span class="co"># es 1.9710 2.0290 2.216 2.1000 2.391 3.109 100</span>
|
||||||
<span class="co"># fr 1.7950 1.888 2.169 2.104 2.338 3.366 100</span>
|
<span class="co"># fr 1.8280 1.8960 3.214 1.9420 2.237 71.550 100</span>
|
||||||
<span class="co"># it 1.8830 2.025 2.809 2.342 2.536 45.730 100</span>
|
<span class="co"># it 1.9370 1.9970 2.163 2.0610 2.339 3.210 100</span>
|
||||||
<span class="co"># nl 1.9370 2.034 3.482 2.316 2.626 60.780 100</span>
|
<span class="co"># nl 1.9710 2.0280 2.698 2.1110 2.421 49.340 100</span>
|
||||||
<span class="co"># pt 1.8450 1.983 3.125 2.293 2.447 43.830 100</span>
|
<span class="co"># pt 1.8920 1.9600 2.119 2.0200 2.261 3.265 100</span>
|
||||||
<span class="co"># ru 1.8260 1.932 3.454 2.018 2.413 87.210 100</span>
|
<span class="co"># ru 1.8630 1.9420 2.779 2.0270 2.335 66.660 100</span>
|
||||||
<span class="co"># sv 1.8260 1.930 3.428 2.207 2.441 72.080 100</span></code></pre></div>
|
<span class="co"># sv 1.8680 1.9190 4.062 1.9890 2.263 78.870 100</span></code></pre></div>
|
||||||
<p>Currently supported languages are Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish.</p>
|
<p>Currently supported languages are Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish.</p>
|
||||||
</div>
|
</div>
|
||||||
</div>
|
</div>
|
||||||
|
|||||||
Binary file not shown.
|
Before Width: | Height: | Size: 82 KiB After Width: | Height: | Size: 81 KiB |
@ -44,7 +44,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9077</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -17,7 +17,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9075</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -44,7 +44,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9068</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -44,7 +44,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9070</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -17,7 +17,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9071</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
# https://github.com/msberends/AMR #
|
# https://github.com/msberends/AMR #
|
||||||
# #
|
# #
|
||||||
# LICENCE #
|
# LICENCE #
|
||||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||||
# Developed at the University of Groningen, the Netherlands, in #
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
# collaboration with non-profit organisations Certe Medical #
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
|||||||
@ -47,7 +47,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9071</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in New Issue
Block a user