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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="These functions are so-called 'Deprecated'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one)."><title>Deprecated Functions — AMR-deprecated • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.2/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Deprecated Functions — AMR-deprecated"><meta property="og:description" content="These functions are so-called 'Deprecated'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one)."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@univgroningen"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="These functions are so-called 'Deprecated'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one)."><title>Deprecated Functions — AMR-deprecated • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.2/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Deprecated Functions — AMR-deprecated"><meta property="og:description" content="These functions are so-called 'Deprecated'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one)."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Welcome to the AMR package."><title>The AMR Package — AMR • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.2/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="The AMR Package — AMR"><meta property="og:description" content="Welcome to the AMR package."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@univgroningen"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Welcome to the AMR package.
AMR is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
This work was published in the Journal of Statistical Software (Volume 104(3); doi:10.18637/jss.v104.i03
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
and doi:10.33612/diss.192486375
).
After installing this package, R knows ~49,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.
This package can be used for:
Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF)
Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines
Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records
Determining first isolates to be used for AMR data analysis
Calculating antimicrobial resistance
Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO)
Calculating (empirical) susceptibility of both mono therapy and combination therapies
Predicting future antimicrobial resistance using regression models
Getting properties for any microorganism (such as Gram stain, species, genus or family)
Getting properties for any antibiotic (such as name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name)
Plotting antimicrobial resistance
Applying EUCAST expert rules
Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code
Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code
Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI
Principal component analysis for AMR
"><title>The AMR Package — AMR • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.2/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="The AMR Package — AMR"><meta property="og:description" content="Welcome to the AMR package.
AMR is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
This work was published in the Journal of Statistical Software (Volume 104(3); doi:10.18637/jss.v104.i03
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
and doi:10.33612/diss.192486375
).
After installing this package, R knows ~49,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.
This package can be used for:
Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF)
Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines
Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records
Determining first isolates to be used for AMR data analysis
Calculating antimicrobial resistance
Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO)
Calculating (empirical) susceptibility of both mono therapy and combination therapies
Predicting future antimicrobial resistance using regression models
Getting properties for any microorganism (such as Gram stain, species, genus or family)
Getting properties for any antibiotic (such as name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name)
Plotting antimicrobial resistance
Applying EUCAST expert rules
Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code
Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code
Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI
Principal component analysis for AMR
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@@ -10,7 +62,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -129,15 +181,14 @@
<div class="ref-description section level2">
<p>Welcome to the <code>AMR</code> package.</p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p><code>AMR</code> is a free, open-source and independent <span style="R">R</span> package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
<p>After installing this package, <span style="R">R</span> knows ~71,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p><code>AMR</code> is a free, open-source and independent <span style="R">R</span> package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
<p>This work was published in the Journal of Statistical Software (Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">doi:10.18637/jss.v104.i03</a>
) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">doi:10.33612/diss.177417131</a>
and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">doi:10.33612/diss.192486375</a>
).</p>
<p>After installing this package, <span style="R">R</span> knows ~49,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>This package is fully independent of any other <span style="R">R</span> package and works on Windows, macOS and Linux with all versions of <span style="R">R</span> since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This <span style="R">R</span> package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.</p>
<p>This package can be used for:</p><ul><li><p>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the Catalogue of Life and List of Prokaryotic names with Standing in Nomenclature</p></li>
<p>This package can be used for:</p><ul><li><p>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF)</p></li>
<li><p>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines</p></li>
<li><p>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records</p></li>
<li><p>Determining first isolates to be used for AMR data analysis</p></li>
@@ -154,6 +205,28 @@
<li><p>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI</p></li>
<li><p>Principal component analysis for AMR</p></li>
</ul></div>
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
<p>To cite AMR in publications use:</p>
<p>Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2022). "AMR: An R Package for Working with Antimicrobial Resistance Data." <em>Journal of Statistical Software</em>, <em>104</em>(3), 1-31. <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">doi:10.18637/jss.v104.i03</a>
.</p>
<p>A BibTeX entry for LaTeX users is:</p>
<div class="sourceCode"><pre><code>
@Article{,
title = {{AMR}: An {R} Package for Working with Antimicrobial Resistance Data},
author = {Matthijs S. Berends and Christian F. Luz and Alexander W. Friedrich and Bhanu N. M. Sinha and Casper J. Albers and Corinna Glasner},
journal = {Journal of Statistical Software},
year = {2022},
volume = {104},
number = {3},
pages = {1--31},
doi = {10.18637/jss.v104.i03},
}
</code></pre></div>
</div>
<div class="section level2">
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
@@ -161,21 +234,34 @@
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
</div>
<div class="section level2">
<h2 id="contact-us">Contact Us<a class="anchor" aria-label="anchor" href="#contact-us"></a></h2>
<p>For suggestions, comments or questions, please contact us via:</p>
<p>Dr. Matthijs S. Berends <br>
m.s.berends [at] umcg [dot] nl <br>
University of Groningen
Department of Medical Microbiology and Infection Prevention <br>
University Medical Center Groningen <br>
Post Office Box 30001 <br>
9700 RB Groningen <br>
The Netherlands
<a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR/</a></p>
<p>If you have found a bug, please file a new issue at: <br><a href="https://github.com/msberends/AMR/issues" class="external-link">https://github.com/msberends/AMR/issues</a></p>
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
<div class="dont-index"><p>Useful links:</p><ul><li><p><a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR/</a></p></li>
<li><p><a href="https://github.com/msberends/AMR" class="external-link">https://github.com/msberends/AMR</a></p></li>
<li><p>Report bugs at <a href="https://github.com/msberends/AMR/issues" class="external-link">https://github.com/msberends/AMR/issues</a></p></li>
</ul></div>
</div>
<div class="section level2">
<h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
<p><strong>Maintainer</strong>: Matthijs S. Berends <a href="mailto:m.berends@certe.nl">m.berends@certe.nl</a> (<a href="https://orcid.org/0000-0001-7620-1800" class="external-link">ORCID</a>)</p>
<p>Authors:</p><ul><li><p>Christian F. Luz (<a href="https://orcid.org/0000-0001-5809-5995" class="external-link">ORCID</a>) [contributor]</p></li>
<li><p>Dennis Souverein (<a href="https://orcid.org/0000-0003-0455-0336" class="external-link">ORCID</a>) [contributor]</p></li>
<li><p>Erwin E. A. Hassing [contributor]</p></li>
</ul><p>Other contributors:</p><ul><li><p>Casper J. Albers (<a href="https://orcid.org/0000-0002-9213-6743" class="external-link">ORCID</a>) [thesis advisor]</p></li>
<li><p>Peter Dutey-Magni (<a href="https://orcid.org/0000-0002-8942-9836" class="external-link">ORCID</a>) [contributor]</p></li>
<li><p>Judith M. Fonville [contributor]</p></li>
<li><p>Alex W. Friedrich (<a href="https://orcid.org/0000-0003-4881-038X" class="external-link">ORCID</a>) [thesis advisor]</p></li>
<li><p>Corinna Glasner (<a href="https://orcid.org/0000-0003-1241-1328" class="external-link">ORCID</a>) [thesis advisor]</p></li>
<li><p>Eric H. L. C. M. Hazenberg [contributor]</p></li>
<li><p>Gwen Knight (<a href="https://orcid.org/0000-0002-7263-9896" class="external-link">ORCID</a>) [contributor]</p></li>
<li><p>Annick Lenglet (<a href="https://orcid.org/0000-0003-2013-8405" class="external-link">ORCID</a>) [contributor]</p></li>
<li><p>Bart C. Meijer [contributor]</p></li>
<li><p>Dmytro Mykhailenko [contributor]</p></li>
<li><p>Anton Mymrikov [contributor]</p></li>
<li><p>Sofia Ny (<a href="https://orcid.org/0000-0002-2017-1363" class="external-link">ORCID</a>) [contributor]</p></li>
<li><p>Rogier P. Schade [contributor]</p></li>
<li><p>Bhanu N. M. Sinha (<a href="https://orcid.org/0000-0003-1634-0010" class="external-link">ORCID</a>) [thesis advisor]</p></li>
<li><p>Anthony Underwood (<a href="https://orcid.org/0000-0002-8547-4277" class="external-link">ORCID</a>) [contributor]</p></li>
</ul></div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
</nav></aside></div>
@@ -186,7 +272,7 @@ The Netherlands
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -166,7 +166,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
</div>
<div class="pkgdown-footer-right">
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 200px;"></a></p>
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a></p>
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</footer></div>

6
reference/WHONET.html
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@@ -1,5 +1,5 @@
<!DOCTYPE html>
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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our example_isolates data set. All patient names are created using online surname generators and are only in place for practice purposes."><title>Data Set with 500 Isolates - WHONET Example — WHONET • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.2/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 500 Isolates - WHONET Example — WHONET"><meta property="og:description" content="This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our example_isolates data set. All patient names are created using online surname generators and are only in place for practice purposes."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
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@@ -204,7 +204,7 @@
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6
reference/ab_from_text.html
View File

@@ -1,5 +1,5 @@
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Use this function on e.g. clinical texts from health care records. It returns a list with all antimicrobial drugs, doses and forms of administration found in the texts."><title>Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.2/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text"><meta property="og:description" content="Use this function on e.g. clinical texts from health care records. It returns a list with all antimicrobial drugs, doses and forms of administration found in the texts."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@univgroningen"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
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@@ -288,7 +288,7 @@
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<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 200px;"></a></p>
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6
reference/ab_property.html
View File

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reference/age.html
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@@ -10,7 +10,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</small>
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@@ -190,16 +190,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1950-02-05 72 72.56986 49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1947-04-13 75 75.38630 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1963-10-26 58 58.84932 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1935-04-02 87 87.41644 64</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1954-12-13 67 67.71781 45</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1972-05-21 50 50.28219 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1969-12-18 52 52.70411 30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1932-08-07 90 90.06849 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1963-09-17 58 58.95616 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1937-01-30 85 85.58630 62</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1940-10-14 81 81.97534 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1979-02-05 43 43.66301 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1998-09-03 24 24.08767 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1966-03-09 56 56.57534 33</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1995-04-22 27 27.45479 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-01-30 73 73.67945 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1969-10-25 52 52.94521 30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1997-08-10 25 25.15342 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1958-09-10 64 64.06849 41</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1999-11-01 22 22.92603 0</span>
</code></pre></div>
</div>
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@@ -211,7 +211,7 @@
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reference/antibiotic_class_selectors.html
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reference/antibiotics.html
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reference/as.ab.html
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@@ -1,5 +1,5 @@
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
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@@ -296,7 +296,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
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6
reference/as.disk.html
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<!DOCTYPE html>
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</small>
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@@ -241,7 +241,7 @@
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reference/as.mic.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</small>
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@@ -259,28 +259,20 @@
<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">mic_data</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="as.mic-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">mic_data</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></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> coli). Run `mo_uncertainties()` to review this.</span>
<span class="r-plt img"><img src="as.mic-2.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">mic_data</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></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: ggplot2</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> coli). Run `mo_uncertainties()` to review this.</span>
<span class="r-plt img"><img src="as.mic-3.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span> <span class="co"># Dutch</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> coli). Run `mo_uncertainties()` to review this.</span>
<span class="r-plt img"><img src="as.mic-4.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>, language <span class="op">=</span> <span class="st">"uk"</span><span class="op">)</span> <span class="co"># Ukrainian</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> coli). Run `mo_uncertainties()` to review this.</span>
<span class="r-plt img"><img src="as.mic-5.png" alt="" width="700" height="433"></span>
</code></pre></div>
</div>
@@ -293,7 +285,7 @@
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<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a></p>
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234
reference/as.mo.html
View File

@@ -1,5 +1,5 @@
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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content='Use this function to determine a valid microorganism code (mo). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like "Staphylococcus aureus"), an abbreviated name (such as "S. aureus"), an abbreviation known in the field (such as "MRSA"), or just a genus. See Examples.'><title>Transform Input to a Microorganism Code — as.mo • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.2/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Transform Input to a Microorganism Code — as.mo"><meta property="og:description" content='Use this function to determine a valid microorganism code (mo). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like "Staphylococcus aureus"), an abbreviated name (such as "S. aureus"), an abbreviation known in the field (such as "MRSA"), or just a genus. See Examples.'><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@univgroningen"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content='Use this function to determine a valid microorganism code (mo). Determination is done using intelligent rules and the complete taxonomic kingdoms Animalia, Archaea, Bacteria and Protozoa, and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like "Staphylococcus aureus"), an abbreviated name (such as "S. aureus"), an abbreviation known in the field (such as "MRSA"), or just a genus. See Examples.'><title>Transform Input to a Microorganism Code — as.mo • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.2/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Transform Input to a Microorganism Code — as.mo"><meta property="og:description" content='Use this function to determine a valid microorganism code (mo). Determination is done using intelligent rules and the complete taxonomic kingdoms Animalia, Archaea, Bacteria and Protozoa, and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like "Staphylococcus aureus"), an abbreviated name (such as "S. aureus"), an abbreviation known in the field (such as "MRSA"), or just a genus. See Examples.'><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<![endif]--></head><body>
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -128,7 +128,7 @@
</div>
<div class="ref-description section level2">
<p>Use this function to determine a valid microorganism code (<code>mo</code>). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see <em>Source</em>). The input can be almost anything: a full name (like <code>"Staphylococcus aureus"</code>), an abbreviated name (such as <code>"S. aureus"</code>), an abbreviation known in the field (such as <code>"MRSA"</code>), or just a genus. See <em>Examples</em>.</p>
<p>Use this function to determine a valid microorganism code (<code>mo</code>). Determination is done using intelligent rules and the complete taxonomic kingdoms Animalia, Archaea, Bacteria and Protozoa, and most microbial species from the kingdom Fungi (see <em>Source</em>). The input can be almost anything: a full name (like <code>"Staphylococcus aureus"</code>), an abbreviated name (such as <code>"S. aureus"</code>), an abbreviation known in the field (such as <code>"MRSA"</code>), or just a genus. See <em>Examples</em>.</p>
</div>
<div class="section level2">
@@ -137,9 +137,11 @@
<span> <span class="va">x</span>,</span>
<span> Becker <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> Lancefield <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> allow_uncertain <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> minimum_matching_score <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> reference_df <span class="op">=</span> <span class="fu"><a href="mo_source.html">get_mo_source</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> ignore_pattern <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_ignore_pattern"</span><span class="op">)</span>,</span>
<span> ignore_pattern <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_ignore_pattern"</span>, <span class="cn">NULL</span><span class="op">)</span>,</span>
<span> remove_from_input <span class="op">=</span> <span class="fu">mo_cleaning_regex</span><span class="op">(</span><span class="op">)</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
@@ -147,11 +149,15 @@
<span></span>
<span><span class="fu">is.mo</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_failures</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_uncertainties</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_renamed</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<span><span class="fu">mo_renamed</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_failures</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_reset_session</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_cleaning_regex</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
@@ -161,17 +167,21 @@
<dt>Becker</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether staphylococci should be categorised into coagulase-negative staphylococci ("CoNS") and coagulase-positive staphylococci ("CoPS") instead of their own species, according to Karsten Becker <em>et al.</em> (1,2,3).</p>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether staphylococci should be categorised into coagulase-negative staphylococci ("CoNS") and coagulase-positive staphylococci ("CoPS") instead of their own species, according to Karsten Becker <em>et al.</em> (see Source).</p>
<p>This excludes <em>Staphylococcus aureus</em> at default, use <code>Becker = "all"</code> to also categorise <em>S. aureus</em> as "CoPS".</p></dd>
<dt>Lancefield</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a beta-haemolytic <em>Streptococcus</em> should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (4). These streptococci will be categorised in their first group, e.g. <em>Streptococcus dysgalactiae</em> will be group C, although officially it was also categorised into groups G and L.</p>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a beta-haemolytic <em>Streptococcus</em> should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (see Source). These streptococci will be categorised in their first group, e.g. <em>Streptococcus dysgalactiae</em> will be group C, although officially it was also categorised into groups G and L.</p>
<p>This excludes enterococci at default (who are in group D), use <code>Lancefield = "all"</code> to also categorise all enterococci as group D.</p></dd>
<dt>allow_uncertain</dt>
<dd><p>a number between <code>0</code> (or <code>"none"</code>) and <code>3</code> (or <code>"all"</code>), or <code>TRUE</code> (= <code>2</code>) or <code>FALSE</code> (= <code>0</code>) to indicate whether the input should be checked for less probable results, see <em>Details</em></p></dd>
<dt>minimum_matching_score</dt>
<dd><p>a numeric value to set as the lower limit for the <a href="mo_matching_score.html">MO matching score</a>. When left blank, this will be determined automatically based on the character length of <code>x</code>, its <a href="microorganisms.html">taxonomic kingdom</a> and <a href="mo_matching_score.html">human pathogenicity</a>.</p></dd>
<dt>keep_synonyms</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is <code>FALSE</code>, which will return a note if old taxonomic names were processed. The default can be set with <code>options(AMR_keep_synonyms = TRUE)</code> or <code>options(AMR_keep_synonyms = FALSE)</code>.</p></dd>
<dt>reference_df</dt>
@@ -179,7 +189,11 @@
<dt>ignore_pattern</dt>
<dd><p>a regular expression (case-insensitive) of which all matches in <code>x</code> must return <code>NA</code>. This can be convenient to exclude known non-relevant input and can also be set with the option <code>AMR_ignore_pattern</code>, e.g. <code>options(AMR_ignore_pattern = "(not reported|contaminated flora)")</code>.</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> (case-insensitive) of which all matches in <code>x</code> must return <code>NA</code>. This can be convenient to exclude known non-relevant input and can also be set with the option <code>AMR_ignore_pattern</code>, e.g. <code>options(AMR_ignore_pattern = "(not reported|contaminated flora)")</code>.</p></dd>
<dt>remove_from_input</dt>
<dd><p>a <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> (case-insensitive) to clean the input of <code>x</code>. Everything matched in <code>x</code> will be removed. At default, this is the outcome of <code>mo_cleaning_regex()</code>, which removes texts between brackets and texts such as "species" and "serovar".</p></dd>
<dt>language</dt>
@@ -206,12 +220,7 @@
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<div class="section">
<h3 id="general-info">General Info<a class="anchor" aria-label="anchor" href="#general-info"></a></h3>
<p>A microorganism (MO) code from this package (class: <code>mo</code>) is human readable and typically looks like these examples:</p>
<p>A microorganism (MO) code from this package (class: <code>mo</code>) is human readable and typically looks like these examples:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a> Code Full name</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> <span class="sc">---------------</span> <span class="sc">--------------------------------------</span></span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> B_KLBSL Klebsiella</span>
@@ -219,33 +228,20 @@
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a> B_KLBSL_PNMN_RHNS Klebsiella pneumoniae rhinoscleromatis</span>
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a> <span class="sc">|</span> <span class="er">|</span> <span class="er">|</span> <span class="er">|</span></span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a> <span class="er">|</span> <span class="er">|</span> <span class="er">|</span> <span class="er">|</span></span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a> <span class="er">|</span> <span class="er">|</span> <span class="er">|</span> \<span class="sc">--</span><span class="ot">-&gt;</span> subspecies, a <span class="dv">4-5</span> letter acronym</span>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a> <span class="sc">|</span> <span class="er">|</span> \<span class="sc">---</span><span class="ot">-&gt;</span> species, a <span class="dv">4-5</span> letter acronym</span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a> <span class="sc">|</span> \<span class="sc">---</span><span class="ot">-&gt;</span> genus, a <span class="dv">5-7</span> letter acronym</span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a> <span class="er">|</span> <span class="er">|</span> <span class="er">|</span> \<span class="sc">--</span><span class="ot">-&gt;</span> subspecies, a <span class="dv">3-5</span> letter acronym</span>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a> <span class="sc">|</span> <span class="er">|</span> \<span class="sc">---</span><span class="ot">-&gt;</span> species, a <span class="dv">3-6</span> letter acronym</span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a> <span class="sc">|</span> \<span class="sc">---</span><span class="ot">-&gt;</span> genus, a <span class="dv">4-8</span> letter acronym</span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a> \<span class="sc">---</span><span class="ot">-&gt;</span> taxonomic kingdom<span class="sc">:</span> <span class="fu">A</span> (Archaea), <span class="fu">AN</span> (Animalia), <span class="fu">B</span> (Bacteria),</span>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">C</span> (Chromista), <span class="fu">F</span> (Fungi), <span class="fu">P</span> (Protozoa)</span></code></pre><p></p></div>
<p>Values that cannot be coerced will be considered 'unknown' and will get the MO code <code>UNKNOWN</code>.</p>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">F</span> (Fungi), <span class="fu">PL</span> (Plantae), <span class="fu">P</span> (Protozoa)</span></code></pre><p></p></div>
<p>Values that cannot be coerced will be considered 'unknown' and will be returned as the MO code <code>UNKNOWN</code> with a warning.</p>
<p>Use the <code><a href="mo_property.html">mo_*</a></code> functions to get properties based on the returned code, see <em>Examples</em>.</p>
<p>The algorithm uses data from the Catalogue of Life (see below) and from one other source (see <a href="microorganisms.html">microorganisms</a>).</p>
<p>The <code>as.mo()</code> function uses several coercion rules for fast and logical results. It assesses the input matching criteria in the following order:</p><ol><li><p>Human pathogenic prevalence: the function starts with more prevalent microorganisms, followed by less prevalent ones;</p></li>
<li><p>Taxonomic kingdom: the function starts with determining Bacteria, then Fungi, then Protozoa, then others;</p></li>
<li><p>Breakdown of input values to identify possible matches.</p></li>
</ol><p>This will lead to the effect that e.g. <code>"E. coli"</code> (a microorganism highly prevalent in humans) will return the microbial ID of <em>Escherichia coli</em> and not <em>Entamoeba coli</em> (a microorganism less prevalent in humans), although the latter would alphabetically come first.</p>
</div>
<div class="section">
<p>The <code>as.mo()</code> function uses a novel <a href="mo_matching_score.html">matching score algorithm</a> (see <em>Matching Score for Microorganisms</em> below) to match input against the <a href="microorganisms.html">available microbial taxonomy</a> in this package. This will lead to the effect that e.g. <code>"E. coli"</code> (a microorganism highly prevalent in humans) will return the microbial ID of <em>Escherichia coli</em> and not <em>Entamoeba coli</em> (a microorganism less prevalent in humans), although the latter would alphabetically come first. The algorithm uses data from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF) (see <a href="microorganisms.html">microorganisms</a>).</p><div class="section">
<h3 id="coping-with-uncertain-results">Coping with Uncertain Results<a class="anchor" aria-label="anchor" href="#coping-with-uncertain-results"></a></h3>
<p>In addition, the <code>as.mo()</code> function can differentiate four levels of uncertainty to guess valid results:</p><ul><li><p>Uncertainty level 0: no additional rules are applied;</p></li>
<li><p>Uncertainty level 1: allow previously accepted (but now invalid) taxonomic names and minor spelling errors;</p></li>
<li><p>Uncertainty level 2: allow all of level 1, strip values between brackets, inverse the words of the input, strip off text elements from the end keeping at least two elements;</p></li>
<li><p>Uncertainty level 3: allow all of level 1 and 2, strip off text elements from the end, allow any part of a taxonomic name.</p></li>
</ul><p>The level of uncertainty can be set using the argument <code>allow_uncertain</code>. The default is <code>allow_uncertain = TRUE</code>, which is equal to uncertainty level 2. Using <code>allow_uncertain = FALSE</code> is equal to uncertainty level 0 and will skip all rules. You can also use e.g. <code>as.mo(..., allow_uncertain = 1)</code> to only allow up to level 1 uncertainty.</p>
<p>With the default setting (<code>allow_uncertain = TRUE</code>, level 2), below examples will lead to valid results:</p><ul><li><p><code>"Streptococcus group B (known as S. agalactiae)"</code>. The text between brackets will be removed and a warning will be thrown that the result <em>Streptococcus group B</em> (<code>B_STRPT_GRPB</code>) needs review.</p></li>
<li><p><code>"S. aureus - please mind: MRSA"</code>. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result <em>Staphylococcus aureus</em> (<code>B_STPHY_AURS</code>) needs review.</p></li>
<li><p><code>"Fluoroquinolone-resistant Neisseria gonorrhoeae"</code>. The first word will be stripped, after which the function will try to find a match. A warning will be thrown that the result <em>Neisseria gonorrhoeae</em> (<code>B_NESSR_GNRR</code>) needs review.</p></li>
</ul><p>There are three helper functions that can be run after using the <code>as.mo()</code> function:</p><ul><li><p>Use <code>mo_uncertainties()</code> to get a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> that prints in a pretty format with all taxonomic names that were guessed. The output contains the matching score for all matches (see <em>Matching Score for Microorganisms</em> below).</p></li>
<p>Results of non-exact taxonomic input are based on their <a href="mo_matching_score.html">matching score</a>. The lowest allowed score can be set with the <code>minimum_matching_score</code> argument. At default this will be determined based on the character length of the input, and the <a href="microorganisms.html">taxonomic kingdom</a> and <a href="mo_matching_score.html">human pathogenicity</a> of the taxonomic outcome. If values are matched with uncertainty, a message will be shown to suggest the user to evaluate the results with <code>mo_uncertainties()</code>, which returns a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with all specifications.</p>
<p>To increase the quality of matching, the <code>remove_from_input</code> argument can be used to clean the input (i.e., <code>x</code>). This must be a <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> that matches parts of the input that should be removed before the input is matched against the <a href="microorganisms.html">available microbial taxonomy</a>. It will be matched Perl-compatible and case-insensitive. The default value of <code>remove_from_input</code> is the outcome of the helper function <code>mo_cleaning_regex()</code>.</p>
<p>There are three helper functions that can be run after using the <code>as.mo()</code> function:</p><ul><li><p>Use <code>mo_uncertainties()</code> to get a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> that prints in a pretty format with all taxonomic names that were guessed. The output contains the matching score for all matches (see <em>Matching Score for Microorganisms</em> below).</p></li>
<li><p>Use <code>mo_failures()</code> to get a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> <a href="https://rdrr.io/r/base/vector.html" class="external-link">vector</a> with all values that could not be coerced to a valid value.</p></li>
<li><p>Use <code>mo_renamed()</code> to get a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with all values that could be coerced based on old, previously accepted taxonomic names.</p></li>
</ul></div>
@@ -254,7 +250,7 @@
<h3 id="microbial-prevalence-of-pathogens-in-humans">Microbial Prevalence of Pathogens in Humans<a class="anchor" aria-label="anchor" href="#microbial-prevalence-of-pathogens-in-humans"></a></h3>
<p>The intelligent rules consider the prevalence of microorganisms in humans grouped into three groups, which is available as the <code>prevalence</code> columns in the <a href="microorganisms.html">microorganisms</a> and <a href="microorganisms.old.html">microorganisms.old</a> data sets. The grouping into human pathogenic prevalence is explained in the section <em>Matching Score for Microorganisms</em> below.</p>
<p>The coercion rules consider the prevalence of microorganisms in humans grouped into three groups, which is available as the <code>prevalence</code> columns in the <a href="microorganisms.html">microorganisms</a> data set. The grouping into human pathogenic prevalence is explained in the section <em>Matching Score for Microorganisms</em> below.</p>
</div>
</div>
@@ -262,13 +258,17 @@
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
<ol><li><p>Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870-926; <a href="https://doi.org/10.1128/CMR.00109-13" class="external-link">doi:10.1128/CMR.00109-13</a></p></li>
<li><p>Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect; <a href="https://doi.org/10.1016/j.cmi.2019.02.028" class="external-link">doi:10.1016/j.cmi.2019.02.028</a></p></li>
<li><p>Becker K <em>et al.</em> <strong>Emergence of coagulase-negative staphylococci</strong> 2020. Expert Rev Anti Infect Ther. 18(4):349-366; <a href="https://doi.org/10.1080/14787210.2020.1730813" class="external-link">doi:10.1080/14787210.2020.1730813</a></p></li>
<li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571-95; <a href="https://doi.org/10.1084/jem.57.4.571" class="external-link">doi:10.1084/jem.57.4.571</a></p></li>
<li><p>Catalogue of Life: 2019 Annual Checklist, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a></p></li>
<li><p>List of Prokaryotic names with Standing in Nomenclature (5 October 2021), <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a></p></li>
<li><p>US Edition of SNOMED CT from 1 September 2020, retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009</a></p></li>
<ol><li><p>Berends MS <em>et al.</em> (2022). <strong>AMR: An R Package for Working with Antimicrobial Resistance Data</strong>. <em>Journal of Statistical Software</em>, 104(3), 1-31; <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">doi:10.18637/jss.v104.i03</a></p></li>
<li><p>Becker K <em>et al.</em> (2014). <strong>Coagulase-Negative Staphylococci.</strong> <em>Clin Microbiol Rev.</em> 27(4): 870-926; <a href="https://doi.org/10.1128/CMR.00109-13" class="external-link">doi:10.1128/CMR.00109-13</a></p></li>
<li><p>Becker K <em>et al.</em> (2019). <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> <em>Clin Microbiol Infect</em>; <a href="https://doi.org/10.1016/j.cmi.2019.02.028" class="external-link">doi:10.1016/j.cmi.2019.02.028</a></p></li>
<li><p>Becker K <em>et al.</em> (2020). <strong>Emergence of coagulase-negative staphylococci</strong> <em>Expert Rev Anti Infect Ther.</em> 18(4):349-366; <a href="https://doi.org/10.1080/14787210.2020.1730813" class="external-link">doi:10.1080/14787210.2020.1730813</a></p></li>
<li><p>Lancefield RC (1933). <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. <em>J Exp Med.</em> 57(4): 571-95; <a href="https://doi.org/10.1084/jem.57.4.571" class="external-link">doi:10.1084/jem.57.4.571</a></p></li>
<li><p>Berends MS <em>et al.</em> (2022). <strong>Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019</strong> <em>Microorganisms</em> 10(9), 1801; <a href="https://doi.org/10.3390/microorganisms10091801" class="external-link">doi:10.3390/microorganisms10091801</a></p></li>
<li><p>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong> International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a>
. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on 12 September, 2022.</p></li>
<li><p>GBIF Secretariat (November 26, 2021). GBIF Backbone Taxonomy. Checklist dataset <a href="https://doi.org/10.15468/39omei" class="external-link">doi:10.15468/39omei</a>
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on 12 September, 2022.</p></li>
<li><p>Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link">https://phinvads.cdc.gov</a></p></li>
</ol></div>
<div class="section level2">
<h2 id="matching-score-for-microorganisms">Matching Score for Microorganisms<a class="anchor" aria-label="anchor" href="#matching-score-for-microorganisms"></a></h2>
@@ -279,21 +279,15 @@
<p>where:</p><ul><li><p><i>x</i> is the user input;</p></li>
<li><p><i>n</i> is a taxonomic name (genus, species, and subspecies);</p></li>
<li><p><i>l<sub>n</sub></i> is the length of <i>n</i>;</p></li>
<li><p><i>lev</i> is the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance" class="external-link">Levenshtein distance function</a>, which counts any insertion, deletion and substitution as 1 that is needed to change <i>x</i> into <i>n</i>;</p></li>
<li><p><i>lev</i> is the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance" class="external-link">Levenshtein distance function</a> (counting any insertion as 1, and any deletion or substitution as 2) that is needed to change <i>x</i> into <i>n</i>;</p></li>
<li><p><i>p<sub>n</sub></i> is the human pathogenic prevalence group of <i>n</i>, as described below;</p></li>
<li><p><i>k<sub>n</sub></i> is the taxonomic kingdom of <i>n</i>, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.</p></li>
</ul><p>The grouping into human pathogenic prevalence (\(p\)) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. <strong>Group 1</strong> (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is <em>Enterococcus</em>, <em>Staphylococcus</em> or <em>Streptococcus</em>. This group consequently contains all common Gram-negative bacteria, such as <em>Pseudomonas</em> and <em>Legionella</em> and all species within the order Enterobacterales. <strong>Group 2</strong> consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is <em>Absidia</em>, <em>Acremonium</em>, <em>Actinotignum</em>, <em>Alternaria</em>, <em>Anaerosalibacter</em>, <em>Apophysomyces</em>, <em>Arachnia</em>, <em>Aspergillus</em>, <em>Aureobacterium</em>, <em>Aureobasidium</em>, <em>Bacteroides</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Branhamella</em>, <em>Calymmatobacterium</em>, <em>Candida</em>, <em>Capnocytophaga</em>, <em>Catabacter</em>, <em>Chaetomium</em>, <em>Chryseobacterium</em>, <em>Chryseomonas</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Flavobacterium</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Fusobacterium</em>, <em>Hendersonula</em>, <em>Hypomyces</em>, <em>Koserella</em>, <em>Lelliottia</em>, <em>Leptosphaeria</em>, <em>Leptotrichia</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Mycoplasma</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oidiodendron</em>, <em>Phoma</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Prevotella</em>, <em>Pseudallescheria</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Stomatococcus</em>, <em>Treponema</em>, <em>Trichoderma</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Tritirachium</em> or <em>Ureaplasma</em>. <strong>Group 3</strong> consists of all other microorganisms.</p>
</ul><p>The grouping into human pathogenic prevalence (\(p\)) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence:</p>
<p><strong>Group 1</strong> (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is <em>Enterococcus</em>, <em>Staphylococcus</em> or <em>Streptococcus</em>. This group consequently contains all common Gram-negative bacteria, such as <em>Pseudomonas</em> and <em>Legionella</em> and all species within the order Enterobacterales.</p>
<p><strong>Group 2</strong> consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is <em>Absidia</em>, <em>Acanthamoeba</em>, <em>Acholeplasma</em>, <em>Acremonium</em>, <em>Actinotignum</em>, <em>Aedes</em>, <em>Alistipes</em>, <em>Alloprevotella</em>, <em>Alternaria</em>, <em>Amoeba</em>, <em>Anaerosalibacter</em>, <em>Ancylostoma</em>, <em>Angiostrongylus</em>, <em>Anisakis</em>, <em>Anopheles</em>, <em>Apophysomyces</em>, <em>Arachnia</em>, <em>Aspergillus</em>, <em>Aureobasidium</em>, <em>Bacteroides</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Bergeyella</em>, <em>Blastocystis</em>, <em>Blastomyces</em>, <em>Borrelia</em>, <em>Brachyspira</em>, <em>Branhamella</em>, <em>Butyricimonas</em>, <em>Candida</em>, <em>Capillaria</em>, <em>Capnocytophaga</em>, <em>Catabacter</em>, <em>Cetobacterium</em>, <em>Chaetomium</em>, <em>Chlamydia</em>, <em>Chlamydophila</em>, <em>Chryseobacterium</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Contracaecum</em>, <em>Cordylobia</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Deinococcus</em>, <em>Demodex</em>, <em>Dermatobia</em>, <em>Dientamoeba</em>, <em>Diphyllobothrium</em>, <em>Dirofilaria</em>, <em>Dysgonomonas</em>, <em>Echinostoma</em>, <em>Elizabethkingia</em>, <em>Empedobacter</em>, <em>Entamoeba</em>, <em>Enterobius</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Fasciola</em>, <em>Flavobacterium</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Fusobacterium</em>, <em>Giardia</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Hendersonula</em>, <em>Heterophyes</em>, <em>Histomonas</em>, <em>Histoplasma</em>, <em>Hymenolepis</em>, <em>Hypomyces</em>, <em>Hysterothylacium</em>, <em>Leishmania</em>, <em>Lelliottia</em>, <em>Leptosphaeria</em>, <em>Leptotrichia</em>, <em>Lucilia</em>, <em>Lumbricus</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Metagonimus</em>, <em>Meyerozyma</em>, <em>Microsporidium</em>, <em>Microsporum</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Mycoplasma</em>, <em>Myroides</em>, <em>Necator</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Odoribacter</em>, <em>Oesophagostomum</em>, <em>Oidiodendron</em>, <em>Opisthorchis</em>, <em>Ornithobacterium</em>, <em>Parabacteroides</em>, <em>Pediculus</em>, <em>Pedobacter</em>, <em>Phlebotomus</em>, <em>Phocaeicola</em>, <em>Phocanema</em>, <em>Phoma</em>, <em>Pichia</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Pneumocystis</em>, <em>Porphyromonas</em>, <em>Prevotella</em>, <em>Pseudallescheria</em>, <em>Pseudoterranova</em>, <em>Pulex</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Riemerella</em>, <em>Saccharomyces</em>, <em>Sarcoptes</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Sphingobacterium</em>, <em>Spirometra</em>, <em>Spiroplasma</em>, <em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Streptobacillus</em>, <em>Strongyloides</em>, <em>Syngamus</em>, <em>Taenia</em>, <em>Tannerella</em>, <em>Tenacibaculum</em>, <em>Terrimonas</em>, <em>Toxocara</em>, <em>Treponema</em>, <em>Trichinella</em>, <em>Trichobilharzia</em>, <em>Trichoderma</em>, <em>Trichomonas</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Trichostrongylus</em>, <em>Trichuris</em>, <em>Tritirachium</em>, <em>Trombicula</em>, <em>Trypanosoma</em>, <em>Tunga</em>, <em>Ureaplasma</em>, <em>Victivallis</em>, <em>Wautersiella</em>, <em>Weeksella</em> or <em>Wuchereria</em>.</p>
<p><strong>Group 3</strong> consists of all other microorganisms.</p>
<p>All characters in \(x\) and \(n\) are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.</p>
<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.079\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
<p>Since <code>AMR</code> version 1.8.1, common microorganism abbreviations are ignored in determining the matching score. These abbreviations are currently: AIEC, ATEC, BORSA, CRSM, DAEC, EAEC, EHEC, EIEC, EPEC, ETEC, GISA, MRPA, MRSA, MRSE, MSSA, MSSE, NMEC, PISP, PRSP, STEC, UPEC, VISA, VISP, VRE, VRSA and VRSP.</p>
</div>
<div class="section level2">
<h2 id="catalogue-of-life">Catalogue of Life<a class="anchor" aria-label="anchor" href="#catalogue-of-life"></a></h2>
<p><img src="figures/logo_col.png" height="40" style='margin-bottom:"5"'><br>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/CatalogueOfLife/general" class="external-link">CoL+ project</a> is finished, which we await.</p>
<p><a href="catalogue_of_life.html">Click here</a> for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</p>
<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.119\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
</div>
<div class="section level2">
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
@@ -311,87 +305,45 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># These examples all return "B_STPHY_AURS", the ID of S. aureus:</span></span></span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"sau"</span><span class="op">)</span> <span class="co"># WHONET code</span></span></span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> <span class="st">"sau"</span>, <span class="co"># WHONET code</span></span></span>
<span class="r-in"><span> <span class="st">"stau"</span>,</span></span>
<span class="r-in"><span> <span class="st">"STAU"</span>,</span></span>
<span class="r-in"><span> <span class="st">"staaur"</span>,</span></span>
<span class="r-in"><span> <span class="st">"S. aureus"</span>,</span></span>
<span class="r-in"><span> <span class="st">"S aureus"</span>,</span></span>
<span class="r-in"><span> <span class="st">"Staphylococcus aureus"</span>,</span></span>
<span class="r-in"><span> <span class="st">"Staphylococcus aureus (MRSA,"</span>,</span></span>
<span class="r-in"><span> <span class="st">"Zthafilokkoockus oureuz"</span>, <span class="co"># handles incorrect spelling</span></span></span>
<span class="r-in"><span> <span class="st">"MRSA"</span>, <span class="co"># Methicillin Resistant S. aureus</span></span></span>
<span class="r-in"><span> <span class="st">"VISA"</span>, <span class="co"># Vancomycin Intermediate S. aureus</span></span></span>
<span class="r-in"><span> <span class="st">"VRSA"</span>, <span class="co"># Vancomycin Resistant S. aureus</span></span></span>
<span class="r-in"><span> <span class="fl">115329001</span> <span class="co"># SNOMED CT code</span></span></span>
<span class="r-in"><span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>No hits found for "Zthafilokkoockus oureuz" with minimum_matching_score =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> NULL (=0.2). Try setting this value lower or even to 0.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>The following input could not be coerced and was returned as "UNKNOWN":</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Zthafilokkoockus oureuz".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> You can retrieve this list with `mo_failures()`.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mo&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STPHY_AURS</span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"stau"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "stau" (assuming Staphylococcus</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> aureus). Run `mo_uncertainties()` to review this.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mo&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STPHY_AURS</span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"STAU"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "STAU" (assuming Staphylococcus</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> aureus). Run `mo_uncertainties()` to review this.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mo&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STPHY_AURS</span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"staaur"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mo&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STPHY_AURS</span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "S. aureus" (assuming</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Staphylococcus aureus). Run `mo_uncertainties()` to review this.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mo&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STPHY_AURS</span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S aureus"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "S aureus" (assuming Staphylococcus</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> aureus). Run `mo_uncertainties()` to review this.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mo&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STPHY_AURS</span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mo&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STPHY_AURS</span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Staphylococcus aureus (MRSA)"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "Staphylococcus aureus (MRSA)"</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (assuming Staphylococcus aureus). Run `mo_uncertainties()` to review this.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mo&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STPHY_AURS</span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Zthafilokkoockus oureuz"</span><span class="op">)</span> <span class="co"># handles incorrect spelling</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "Zthafilokkoockus oureuz" (assuming</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Staphylococcus aureus). Run `mo_uncertainties()` to review this.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mo&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STPHY_AURS</span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span> <span class="co"># Methicillin Resistant S. aureus</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mo&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STPHY_AURS</span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span> <span class="co"># Vancomycin Intermediate S. aureus</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mo&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STPHY_AURS</span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"VRSA"</span><span class="op">)</span> <span class="co"># Vancomycin Resistant S. aureus</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mo&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STPHY_AURS</span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="fl">115329001</span><span class="op">)</span> <span class="co"># SNOMED CT code</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mo&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STPHY_AURS</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [5] B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS_AURS</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] UNKNOWN B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] B_STPHY_AURS </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Dyslexia is no problem - these all work:</span></span></span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplasma urealyticum"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> <span class="st">"Ureaplasma urealyticum"</span>,</span></span>
<span class="r-in"><span> <span class="st">"Ureaplasma urealyticus"</span>,</span></span>
<span class="r-in"><span> <span class="st">"Ureaplasmium urealytica"</span>,</span></span>
<span class="r-in"><span> <span class="st">"Ureaplazma urealitycium"</span></span></span>
<span class="r-in"><span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mo&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_URPLS_URLY</span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplasma urealyticus"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "Ureaplasma urealyticus" (assuming</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Ureaplasma urealyticum). Run `mo_uncertainties()` to review this.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mo&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_URPLS_URLY</span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplasmium urealytica"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "Ureaplasmium urealytica" (assuming</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Ureaplasma urealyticum). Run `mo_uncertainties()` to review this.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mo&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_URPLS_URLY</span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplazma urealitycium"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "Ureaplazma urealitycium" (assuming</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Ureaplasma urealyticum). Run `mo_uncertainties()` to review this.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mo&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_URPLS_URLY</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_URPLS_URLY B_URPLS_URLY B_URPLS_URLY B_URPLS_URLY</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Streptococcus group A"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mo&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STRPT_GRPA</span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"GAS"</span><span class="op">)</span> <span class="co"># Group A Streptococci</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mo&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STRPT_GRPA</span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"GBS"</span><span class="op">)</span> <span class="co"># Group B Streptococci</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mo&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STRPT_GRPB</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span><span class="op">)</span> <span class="co"># will remain species: B_STPHY_EPDR</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mo&gt;</span>
@@ -408,17 +360,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STRPT_GRPA</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># All mo_* functions use as.mo() internally too (see ?mo_property):</span></span></span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># returns "Escherichia"</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> coli). Run `mo_uncertainties()` to review this.</span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Escherichia"</span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># returns "Gram negative"</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> coli). Run `mo_uncertainties()` to review this.</span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"ESCO"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gram-negative"</span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"E. coli"</span>, <span class="st">"vanco"</span><span class="op">)</span> <span class="co"># returns TRUE</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> coli). Run `mo_uncertainties()` to review this.</span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"ESCCOL"</span>, ab <span class="op">=</span> <span class="st">"vanco"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Determining intrinsic resistance based on 'EUCAST Expert Rules' and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3 (2021). This note</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> will be shown once per session.</span>
@@ -435,7 +381,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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@@ -1,5 +1,5 @@
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</small>
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@@ -484,16 +484,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 13</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_consid…¹ mo_in…² mo_conside…³ guide…⁴</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-09-01 <span style="color: #949494;">13:35:41</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-09-01 <span style="color: #949494;">13:35:41</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-09-01 <span style="color: #949494;">13:35:41</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-09-01 <span style="color: #949494;">13:35:41</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-09-01 <span style="color: #949494;">13:35:41</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-09-01 <span style="color: #949494;">13:35:42</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-09-01 <span style="color: #949494;">13:35:42</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-09-01 <span style="color: #949494;">13:35:42</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-09-01 <span style="color: #949494;">13:35:42</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-09-01 <span style="color: #949494;">13:35:42</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-10-05 <span style="color: #949494;">10:29:43</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-10-05 <span style="color: #949494;">10:29:43</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-10-05 <span style="color: #949494;">10:29:43</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-10-05 <span style="color: #949494;">10:29:43</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-10-05 <span style="color: #949494;">10:29:43</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-10-05 <span style="color: #949494;">10:29:44</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-10-05 <span style="color: #949494;">10:29:44</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-10-05 <span style="color: #949494;">10:29:44</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-10-05 <span style="color: #949494;">10:29:44</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-10-05 <span style="color: #949494;">10:29:44</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 6 more variables: ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S &lt;dbl&gt;, breakpoint_R &lt;dbl&gt;, input &lt;dbl&gt;, interpretation &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># and abbreviated variable names ¹​ab_considered, ²​mo_input, ³​mo_considered,</span></span>
@@ -506,8 +506,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"AMP"</span>,</span></span>
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "S. pneumoniae" (assuming</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Streptococcus pneumoniae). Run `mo_uncertainties()` to review this.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
@@ -554,7 +552,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-in"><span> <span class="fu">as.rsi</span><span class="op">(</span><span class="op">)</span> <span class="co"># automatically determines urine isolates</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">NIT</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, uti <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, uti <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2022...</span>
@@ -617,8 +615,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for `col_mo`.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> coli). Run `mo_uncertainties()` to review this.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of column 'NIT' (nitrofurantoin) according to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
@@ -626,19 +622,29 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-msg co"><span class="r-pr">#&gt;</span> infection.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Use `as.rsi(uti = FALSE)` to prevent this.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for `col_mo`.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> coli). Run `mo_uncertainties()` to review this.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of column 'NIT' (nitrofurantoin) according to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in mutate_at(., vars(AMP:NIT), as.rsi, mo = "E. coli", uti = TRUE):</span> Can't subset columns that don't exist.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">✖</span> Column `NIT` doesn't exist.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'CIP' (ciprofloxacin) according to EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'GEN' (gentamicin) according to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'TOB' (tobramycin) according to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> microorganism AMP CIP GEN TOB ERY</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli S I S S R</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># For CLEANING existing R/SI values ------------------------------------</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">as.rsi</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `as.rsi()`: 3 results truncated (50%) that were invalid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> interpretations: "A", "B" and "C"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `as.rsi()`: 3 results in column '24' truncated (50%) that were invalid</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial interpretations: "A", "B" and "C"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;rsi&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S I R &lt;NA&gt; &lt;NA&gt; &lt;NA&gt;</span>
<span class="r-in"><span><span class="fu">as.rsi</span><span class="op">(</span><span class="st">"&lt;= 0.002; S"</span><span class="op">)</span> <span class="co"># will return "S"</span></span></span>
@@ -700,7 +706,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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reference/atc_online.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
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@@ -231,7 +231,7 @@
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6
reference/availability.html
View File

@@ -1,5 +1,5 @@
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reference/bug_drug_combinations.html
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@@ -266,16 +266,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 80 × 6</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab S I R total</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Gram-negative PEN 8 0 717 725</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Gram-negative OXA 6 0 0 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Gram-negative FLC 6 0 0 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Gram-negative AMX 226 0 405 631</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Gram-negative AMC 463 89 174 726</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Gram-negative AMP 226 0 405 631</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Gram-negative TZP 554 11 76 641</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Gram-negative PEN 17 1 726 744</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Gram-negative OXA 9 0 1 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Gram-negative FLC 11 0 1 12</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Gram-negative AMX 231 1 407 639</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Gram-negative AMC 473 89 175 737</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Gram-negative AMP 231 1 407 639</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Gram-negative TZP 556 11 76 643</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Gram-negative CZO 94 2 110 206</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Gram-negative FEP 470 1 14 485</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Gram-negative CXM 539 22 142 703</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Gram-negative CXM 546 22 144 712</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 70 more rows</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Use 'format()' on this result to get a publishable/printable format.</span>
<span class="r-in"><span></span></span>
@@ -315,7 +315,7 @@
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<img src="../logo.svg" class="logo" alt=""><h1>The Catalogue of Life</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/catalogue_of_life.R" class="external-link"><code>R/catalogue_of_life.R</code></a></small>
<div class="d-none name"><code>catalogue_of_life.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>This package contains the complete taxonomic tree (last updated: 5 October 2021) of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (CoL), supplemented with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN).</p>
</div>
<div class="section level2">
<h2 id="catalogue-of-life">Catalogue of Life<a class="anchor" aria-label="anchor" href="#catalogue-of-life"></a></h2>
<p><img src="figures/logo_col.png" height="40" style='margin-bottom:"5"'><br>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/CatalogueOfLife/general" class="external-link">CoL+ project</a> is finished, which we await.</p>
<p>Click here for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</p>
</div>
<div class="section level2">
<h2 id="included-taxa">Included Taxa<a class="anchor" aria-label="anchor" href="#included-taxa"></a></h2>
<p>Included are:</p><ul><li><p>All ~58,000 (sub)species from the kingdoms of Archaea, Bacteria, Chromista and Protozoa</p></li>
<li><p>All ~5,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Microascales, Mucorales, Onygenales, Pneumocystales, Saccharomycetales, Schizosaccharomycetales and Tremellales, as well as ~4,600 other fungal (sub)species. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant fungi are covered (such as all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Cryptococcus</em>, <em>Histplasma</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~2,200 (sub)species from ~50 other relevant genera from the kingdom of Animalia (such as <em>Strongyloides</em> and <em>Taenia</em>)</p></li>
<li><p>All ~14,000 previously accepted names of all included (sub)species (these were taxonomically renamed)</p></li>
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
<li><p>The responsible author(s) and year of scientific publication</p></li>
</ul><p>The Catalogue of Life (<a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.9 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.</p>
<p>The syntax used to transform the original data to a cleansed <span style="R">R</span> format, can be found here: <a href="https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R</a>.</p>
</div>
<div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
<div class="dont-index"><p>Data set <a href="microorganisms.html">microorganisms</a> for the actual data. <br>
Function <code><a href="as.mo.html">as.mo()</a></code> to use the data for intelligent determination of microorganisms.</p></div>
</div>
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Get version info of included data set</span></span></span>
<span class="r-in"><span><span class="fu"><a href="catalogue_of_life_version.html">catalogue_of_life_version</a></span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Included in this AMR package (v1.8.1.9049) are:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Catalogue of Life: 2019 Annual Checklist</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Available at: http://www.catalogueoflife.org</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Number of included microbial species: 49,029</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> List of Prokaryotic names with Standing in Nomenclature (5 October 2021)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Available at: https://lpsn.dsmz.de</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Number of included bacterial species: 21,701</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> =&gt; Total number of species included: 70,764</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> =&gt; Total number of synonyms included: 14,338</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> See for more info `?microorganisms` and `?catalogue_of_life`.</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Get a note when a species was renamed</span></span></span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_shortname</a></span><span class="op">(</span><span class="st">"Chlamydophila psittaci"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Chlamydophila psittaci (Everett et al. , 1999) was renamed back to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Chlamydia psittaci (Page, 1968) [B_CHLMY_PSTT]</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "C. psittaci"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Get any property from the entire taxonomic tree for all included species</span></span></span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_class</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gammaproteobacteria"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_family</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Enterobacteriaceae"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span><span class="op">)</span> <span class="co"># based on kingdom and phylum, see ?mo_gramstain</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gram-negative"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_ref</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Castellani et al., 1919"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Do not get mistaken - this package is about microorganisms</span></span></span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_kingdom</a></span><span class="op">(</span><span class="st">"C. elegans"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "C. elegans" (assuming Cladosporium</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> elegans). Run `mo_uncertainties()` to review this.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Fungi"</span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"C. elegans"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "C. elegans" (assuming Cladosporium</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> elegans). Run `mo_uncertainties()` to review this.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Cladosporium elegans"</span>
</code></pre></div>
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<img src="../logo.svg" class="logo" alt=""><h1>Version info of included Catalogue of Life</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/catalogue_of_life.R" class="external-link"><code>R/catalogue_of_life.R</code></a></small>
<div class="d-none name"><code>catalogue_of_life_version.Rd</code></div>
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<div class="ref-description section level2">
<p>This function returns information about the included data from the Catalogue of Life.</p>
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<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">catalogue_of_life_version</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
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<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a>, which prints in pretty format</p>
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<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>For LPSN, see <a href="microorganisms.html">microorganisms</a>.</p>
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<div class="section level2">
<h2 id="catalogue-of-life">Catalogue of Life<a class="anchor" aria-label="anchor" href="#catalogue-of-life"></a></h2>
<p><img src="figures/logo_col.png" height="40" style='margin-bottom:"5"'><br>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/CatalogueOfLife/general" class="external-link">CoL+ project</a> is finished, which we await.</p>
<p><a href="catalogue_of_life.html">Click here</a> for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code>catalogue_of_life_version()</code>.</p>
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<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
<div class="dont-index"><p><a href="microorganisms.html">microorganisms</a></p></div>
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<p></p><p><code>AMR</code> (for R). Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><a target="_blank" href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
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count_resistant() should be used to count resistant isolates, count_susceptible() should be used to count susceptible isolates."><title>Count Available Isolates — count • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.2/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Count Available Isolates — count"><meta property="og:description" content="These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in summarise() from the dplyr package and also support grouped variables, see Examples.
count_resistant() should be used to count resistant isolates, count_susceptible() should be used to count susceptible isolates."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@univgroningen"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -372,7 +372,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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@@ -161,28 +161,80 @@
<p>If you are familiar with the <code><a href="https://dplyr.tidyverse.org/reference/case_when.html" class="external-link">case_when()</a></code> function of the <code>dplyr</code> package, you will recognise the input method to set your own rules. Rules must be set using what <span style="R">R</span> considers to be the 'formula notation'. The rule itself is written <em>before</em> the tilde (<code>~</code>) and the consequence of the rule is written <em>after</em> the tilde:</p>
<p></p><div class="sourceCode {r}"><pre><code></code></pre><p></p></div>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_eucast_rules.html">custom_eucast_rules</a></span><span class="op">(</span><span class="va">TZP</span> <span class="op">==</span> <span class="st">"S"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"S"</span>,</span>
<span> <span class="va">TZP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></span></code></pre><p></p></div>
<p>These are two custom EUCAST rules: if TZP (piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must be made "R". These rules can also be printed to the console, so it is immediately clear how they work:</p>
<p></p><div class="sourceCode {r}"><pre><code></code></pre><p></p></div>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">x</span></span>
<span><span class="co">#&gt; A set of custom EUCAST rules:</span></span>
<span><span class="co">#&gt;</span></span>
<span><span class="co">#&gt; 1. If TZP is "S" then set to S :</span></span>
<span><span class="co">#&gt; amoxicillin (AMX), ampicillin (AMP)</span></span>
<span><span class="co">#&gt;</span></span>
<span><span class="co">#&gt; 2. If TZP is "R" then set to R :</span></span>
<span><span class="co">#&gt; amoxicillin (AMX), ampicillin (AMP)</span></span></code></pre><p></p></div>
<p>The rules (the part <em>before</em> the tilde, in above example <code>TZP == "S"</code> and <code>TZP == "R"</code>) must be evaluable in your data set: it should be able to run as a filter in your data set without errors. This means for the above example that the column <code>TZP</code> must exist. We will create a sample data set and test the rules set:</p>
<p></p><div class="sourceCode {r}"><pre><code></code></pre><p></p></div>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span>,</span>
<span> TZP <span class="op">=</span> <span class="fu"><a href="../reference/as.rsi.html">as.rsi</a></span><span class="op">(</span><span class="st">"R"</span><span class="op">)</span>,</span>
<span> ampi <span class="op">=</span> <span class="fu"><a href="../reference/as.rsi.html">as.rsi</a></span><span class="op">(</span><span class="st">"S"</span><span class="op">)</span>,</span>
<span> cipro <span class="op">=</span> <span class="fu"><a href="../reference/as.rsi.html">as.rsi</a></span><span class="op">(</span><span class="st">"S"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="va">df</span></span>
<span><span class="co">#&gt; mo TZP ampi cipro</span></span>
<span><span class="co">#&gt; 1 Escherichia coli R S S</span></span>
<span><span class="co">#&gt; 2 Klebsiella pneumoniae R S S</span></span>
<span></span>
<span><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">df</span>, rules <span class="op">=</span> <span class="st">"custom"</span>, custom_rules <span class="op">=</span> <span class="va">x</span>, info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
<span><span class="co">#&gt; mo TZP ampi cipro</span></span>
<span><span class="co">#&gt; 1 Escherichia coli R R S</span></span>
<span><span class="co">#&gt; 2 Klebsiella pneumoniae R R S</span></span></code></pre><p></p></div>
</div>
<div class="section">
<h3 id="using-taxonomic-properties-in-rules">Using taxonomic properties in rules<a class="anchor" aria-label="anchor" href="#using-taxonomic-properties-in-rules"></a></h3>
<p>There is one exception in variables used for the rules: all column names of the <a href="microorganisms.html">microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: <code>r vector_and(colnames(microorganisms), sort = FALSE)</code>. Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p>
<p></p><div class="sourceCode {r}"><pre><code></code></pre><p></p></div>
<p>There is one exception in variables used for the rules: all column names of the <a href="microorganisms.html">microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence" and "snomed". Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_eucast_rules.html">custom_eucast_rules</a></span><span class="op">(</span><span class="va">TZP</span> <span class="op">==</span> <span class="st">"S"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"S"</span>,</span>
<span> <span class="va">TZP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">df</span>, rules <span class="op">=</span> <span class="st">"custom"</span>, custom_rules <span class="op">=</span> <span class="va">y</span>, info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
<span><span class="co">#&gt; mo TZP ampi cipro</span></span>
<span><span class="co">#&gt; 1 Escherichia coli R S S</span></span>
<span><span class="co">#&gt; 2 Klebsiella pneumoniae R R S</span></span></code></pre><p></p></div>
</div>
<div class="section">
<h3 id="usage-of-antibiotic-group-names">Usage of antibiotic group names<a class="anchor" aria-label="anchor" href="#usage-of-antibiotic-group-names"></a></h3>
<p>It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part <em>after</em> the tilde. In above examples, the antibiotic group <code>aminopenicillins</code> is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the agents that will be matched when running the rule.</p>
<p><code>r paste0(" * ", sapply(DEFINED_AB_GROUPS, function(x) paste0("\"", tolower(gsub("^AB_", "", x)), "\"\\cr(", vector_and(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), quotes = FALSE), ")"), USE.NAMES = FALSE), "\n", collapse = "")</code></p>
</div>
<p>It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part <em>after</em> the tilde. In above examples, the antibiotic group <code>aminopenicillins</code> is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the agents that will be matched when running the rule.</p><ul><li><p>"aminoglycosides"<br>(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin and tobramycin-high)</p></li>
<li><p>"aminopenicillins"<br>(amoxicillin and ampicillin)</p></li>
<li><p>"antifungals"<br>(5-fluorocytosine, amphotericin B, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole and voriconazole)</p></li>
<li><p>"antimycobacterials"<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, morinamide, p-aminosalicylic acid, pretomanid, prothionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone/isoniazid, tiocarlide and viomycin)</p></li>
<li><p>"betalactams"<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin and ticarcillin/clavulanic acid)</p></li>
<li><p>"carbapenems"<br>(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil and tebipenem)</p></li>
<li><p>"cephalosporins"<br>(cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef and loracarbef)</p></li>
<li><p>"cephalosporins_1st"<br>(cefacetrile, cefadroxil, cefaloridine, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, cephalexin, cephalothin, cephapirin and cephradine)</p></li>
<li><p>"cephalosporins_2nd"<br>(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil and loracarbef)</p></li>
<li><p>"cephalosporins_3rd"<br>(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone and latamoxef)</p></li>
<li><p>"cephalosporins_4th"<br>(cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol, cefoselis, cefozopran, cefpirome and cefquinome)</p></li>
<li><p>"cephalosporins_5th"<br>(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor and ceftolozane/tazobactam)</p></li>
<li><p>"cephalosporins_except_caz"<br>(cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef and loracarbef)</p></li>
<li><p>"fluoroquinolones"<br>(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)</p></li>
<li><p>"glycopeptides"<br>(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin and vancomycin-macromethod)</p></li>
<li><p>"glycopeptides_except_lipo"<br>(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin and vancomycin-macromethod)</p></li>
<li><p>"lincosamides"<br>(acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin, lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin and tylvalosin)</p></li>
<li><p>"lipoglycopeptides"<br>(dalbavancin, oritavancin and telavancin)</p></li>
<li><p>"macrolides"<br>(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin and tylvalosin)</p></li>
<li><p>"oxazolidinones"<br>(cadazolid, cycloserine, linezolid, tedizolid and thiacetazone)</p></li>
<li><p>"penicillins"<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, cefepime/nacubactam, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin and ticarcillin/clavulanic acid)</p></li>
<li><p>"polymyxins"<br>(colistin, polymyxin B and polymyxin B/polysorbate 80)</p></li>
<li><p>"quinolones"<br>(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)</p></li>
<li><p>"streptogramins"<br>(pristinamycin and quinupristin/dalfopristin)</p></li>
<li><p>"tetracyclines"<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline and tigecycline)</p></li>
<li><p>"tetracyclines_except_tgc"<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline and tetracycline)</p></li>
<li><p>"trimethoprims"<br>(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim and trimethoprim/sulfamethoxazole)</p></li>
<li><p>"ureidopenicillins"<br>(azlocillin, mezlocillin, piperacillin and piperacillin/tazobactam)</p></li>
</ul></div>
</div>
@@ -251,7 +303,7 @@
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6
reference/dosage.html
View File

@@ -1,5 +1,5 @@
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@@ -10,7 +10,7 @@
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reference/eucast_rules.html
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To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see Details."><title>Apply EUCAST Rules — eucast_rules • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.2/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Apply EUCAST Rules — eucast_rules"><meta property="og:description" content="Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, https://eucast.org), see Source. Use eucast_dosage() to get a data.frame with advised dosages of a certain bug-drug combination, which is based on the dosage data set.
To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see Details."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@univgroningen"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see Details."><title>Apply EUCAST Rules — eucast_rules • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.2/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Apply EUCAST Rules — eucast_rules"><meta property="og:description" content="Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, https://www.eucast.org), see Source. Use eucast_dosage() to get a data.frame with advised dosages of a certain bug-drug combination, which is based on the dosage data set.
To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see Details."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@@ -130,7 +130,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</div>
<div class="ref-description section level2">
<p>Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <a href="https://eucast.org" class="external-link">https://eucast.org</a>), see <em>Source</em>. Use <code>eucast_dosage()</code> to get a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with advised dosages of a certain bug-drug combination, which is based on the <a href="dosage.html">dosage</a> data set.</p>
<p>Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <a href="https://www.eucast.org" class="external-link">https://www.eucast.org</a>), see <em>Source</em>. Use <code>eucast_dosage()</code> to get a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with advised dosages of a certain bug-drug combination, which is based on the <a href="dosage.html">dosage</a> data set.</p>
<p>To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see <em>Details</em>.</p>
</div>
@@ -229,12 +229,15 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p><strong>Note:</strong> This function does not translate MIC values to RSI values. Use <code><a href="as.rsi.html">as.rsi()</a></code> for that. <br><strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. <br></p>
<p>The file containing all EUCAST rules is located here: <a href="https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv</a>. <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The file used as input for this <code>AMR</code> package contains the taxonomy updated until <code><a href="catalogue_of_life.html">r CATALOGUE_OF_LIFE$yearmonth_LPSN</a></code>.</p><div class="section">
<p>The file containing all EUCAST rules is located here: <a href="https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv</a>. <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The <code>AMR</code> package contains the full microbial taxonomy updated until 12 September, 2022, see <a href="microorganisms.html">microorganisms</a>.</p><div class="section">
<h3 id="custom-rules">Custom Rules<a class="anchor" aria-label="anchor" href="#custom-rules"></a></h3>
<p>Custom rules can be created using <code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code>, e.g.:</p>
<p></p><div class="sourceCode {r}"><pre><code></code></pre><p></p></div>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_eucast_rules.html">custom_eucast_rules</a></span><span class="op">(</span><span class="va">AMC</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"R"</span>,</span>
<span> <span class="va">AMC</span> <span class="op">==</span> <span class="st">"I"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"I"</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">example_isolates</span>, rules <span class="op">=</span> <span class="st">"custom"</span>, custom_rules <span class="op">=</span> <span class="va">x</span><span class="op">)</span></span></code></pre><p></p></div>
</div>
<div class="section">
@@ -374,7 +377,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
</div>
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reference/example_isolates.html
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@@ -1,5 +1,5 @@
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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler et al. in 2007 (doi:10.1086/511864
). To determine patient episodes not necessarily based on microorganisms, use is_new_episode() that also supports grouping with the dplyr package."><title>Determine First Isolates — first_isolate • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.2/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Determine First Isolates — first_isolate"><meta property="og:description" content="Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler et al. in 2007 (doi:10.1086/511864
). To determine patient episodes not necessarily based on microorganisms, use is_new_episode() that also supports grouping with the dplyr package."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@univgroningen"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
). To determine patient episodes not necessarily based on microorganisms, use is_new_episode() that also supports grouping with the dplyr package."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -12,7 +12,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</small>
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@@ -350,7 +350,7 @@
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu"><a href="mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Including isolates from ICU.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for `mo_is_gram_negative()`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 437 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 460 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
@@ -363,7 +363,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-03-16 4FC193 69 M Clinical B_PSDMN_AERG R NA NA R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-04-01 496896 46 F ICU B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-04-23 EE2510 69 F ICU B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 427 more rows, and 36 more variables: AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 450 more rows, and 36 more variables: AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CZO &lt;rsi&gt;, FEP &lt;rsi&gt;, CXM &lt;rsi&gt;, FOX &lt;rsi&gt;, CTX &lt;rsi&gt;, CAZ &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CRO &lt;rsi&gt;, GEN &lt;rsi&gt;, TOB &lt;rsi&gt;, AMK &lt;rsi&gt;, KAN &lt;rsi&gt;, TMP &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># SXT &lt;rsi&gt;, NIT &lt;rsi&gt;, FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;,</span></span>
@@ -462,7 +462,7 @@
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reference/g.test.html
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@@ -10,7 +10,7 @@
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140
reference/get_episode.html
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@@ -1,5 +1,5 @@
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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument episode_days. This can be used to determine clinical episodes for any epidemiological analysis. The get_episode() function returns the index number of the episode per group, while the is_new_episode() function returns values TRUE/FALSE to indicate whether an item in a vector is the start of a new episode."><title>Determine (New) Episodes for Patients — get_episode • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.2/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Determine (New) Episodes for Patients — get_episode"><meta property="og:description" content="These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument episode_days. This can be used to determine clinical episodes for any epidemiological analysis. The get_episode() function returns the index number of the episode per group, while the is_new_episode() function returns values TRUE/FALSE to indicate whether an item in a vector is the start of a new episode."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@univgroningen"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument episode_days. This can be used to determine clinical episodes for any epidemiological analysis. The get_episode() function returns the index number of the episode per group, while the is_new_episode() function returns values TRUE/FALSE to indicate whether an item in a vector is the start of a new episode."><title>Determine (New) Episodes for Patients — get_episode • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.2/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Determine (New) Episodes for Patients — get_episode"><meta property="og:description" content="These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument episode_days. This can be used to determine clinical episodes for any epidemiological analysis. The get_episode() function returns the index number of the episode per group, while the is_new_episode() function returns values TRUE/FALSE to indicate whether an item in a vector is the start of a new episode."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
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@@ -177,41 +177,43 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">200</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 47 61 41 30 22 55 11 62 22 52 58 11 11 17 15 28 11 13 37 59 31 18 8 48 41</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 45 3 64 1 53 8 64 55 62 41 23 58 64 51 18 16 8 64 40 47 50 20 9 15 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 24 58 8 37 7 21 67 30 17 14 1 43 41 9 17 45 44 13 21 31 29 39 2 66 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 12 61 52 30 67 58 65 63 30 56 26 60 66 40 60 43 51 35 65 64 7 64 25 54 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 19 9 7 9 63 52 41 67 5 33 21 20 42 4 17 35 66 19 34 37 18 23 33 8 7</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 51 41 60 38 2 67 58 10 42 38 1 29 49 10 22 46 67 1 3 39 61 27 32 5 63</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 12 16 3 53 7 49 31 23 11 22 29 37 30 45 32 35 45 1 56 46 23 18 49 64 30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 27 8 1 6 32 9 10 18 12 20 37 46 49 9 24 10 67 57 8 55 48 62 65 31 61</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 32 7 22 29 55 15 62 34 39 13 4 28 30 43 26 34 55 46 3 16 62 49 38 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 13 1 39 52 20 48 55 10 43 60 31 14 9 29 32 8 18 52 57 48 54 62 43 49 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 13 57 21 43 61 52 17 4 56 10 31 18 59 3 41 20 37 6 32 5 48 43 49 12 58</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 63 63 49 38 44 35 10 60 9 55 63 48 58 11 43 7 61 45 32 60 62 2 58 53 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 40 35 16 29 29 46 13 25 25 15 45 58 30 59 44 64 57 45 14 34 3 18 4 28 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 2 29 61 27 46 23 40 50 61 60 41 15 3 45 44 18 55 60 37 37 28 15 47 42 41</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 8 27 26 15 7 50 33 2 63 64 23 12 41 62 8 16 62 49 9 12 22 32 10 9 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 51 30 36 11 57 19 37 9 34 7 2 27 17 54 19 55 35 6 53 28 17 56 4 32 45</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE FALSE TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] TRUE TRUE TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE TRUE TRUE FALSE FALSE TRUE TRUE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE TRUE FALSE TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] TRUE FALSE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE FALSE TRUE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-06-23 798871 82 M Clinical B_ENTRC_FCLS NA NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-06-06 24D393 20 F Clinical B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-06-19 402950 53 F Clinical B_STPHY_HMNS R NA S NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 5 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-06-07 710157 76 M Outpatie… B_STPHY_CONS S NA S NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-06-22 FD8039 75 F ICU B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-07-15 C42193 84 M ICU B_STPHY_HMNS R NA R R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2002-07-15 426426 67 F ICU B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> 2002-06-04 082413 78 M ICU B_STRPT_PNMN S NA NA S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 36 more variables: AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;, CZO &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FEP &lt;rsi&gt;, CXM &lt;rsi&gt;, FOX &lt;rsi&gt;, CTX &lt;rsi&gt;, CAZ &lt;rsi&gt;, CRO &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># GEN &lt;rsi&gt;, TOB &lt;rsi&gt;, AMK &lt;rsi&gt;, KAN &lt;rsi&gt;, TMP &lt;rsi&gt;, SXT &lt;rsi&gt;,</span></span>
@@ -247,16 +249,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: condition [3]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 023456 2012-11-24 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> A79917 2016-05-21 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 257844 2011-05-22 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> F50462 2008-05-11 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 3CF3C4 2006-06-26 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> E29972 2014-11-22 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 406502 2004-02-29 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> D10538 2016-08-13 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 336698 2006-07-02 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> DF7736 2014-02-19 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 614772 2002-02-27 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 650870 2009-11-12 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 82C90B 2003-09-19 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> B52127 2007-06-03 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> B13757 2009-02-12 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 097186 2015-10-28 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> C82046 2005-08-08 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> D80438 2017-07-03 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 09B453 2010-03-21 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 5B78D5 2011-09-19 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -268,19 +270,19 @@
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [178]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [188]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2012-11-24 023456 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2016-05-21 A79917 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2011-05-22 257844 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU 2008-05-11 F50462 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2006-06-26 3CF3C4 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Outpatient 2014-11-22 E29972 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2004-02-29 406502 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ICU 2016-08-13 D10538 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2006-07-02 336698 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> ICU 2014-02-19 DF7736 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2002-02-27 614772 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Outpatient 2009-11-12 650870 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2003-09-19 82C90B 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU 2007-06-03 B52127 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Outpatient 2009-02-12 B13757 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2015-10-28 097186 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2005-08-08 C82046 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2017-07-03 D80438 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2010-03-21 09B453 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2011-09-19 5B78D5 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -295,9 +297,9 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 119 14 54 79</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 48 12 32 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 11 6 9 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 122 15 53 75</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 49 12 33 39</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 17 8 13 15</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
@@ -327,19 +329,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [185]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [193]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 023456 B_PROTS_MRBL Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> A79917 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 257844 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> F50462 B_STPHY_CONS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 3CF3C4 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> E29972 B_STPHY_HMNS Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 406502 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> D10538 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 336698 B_NESSR_SICC Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> DF7736 B_STRPT_PYGN ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 614772 B_STPHY_HMNS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 650870 B_ESCHR_COLI Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 82C90B B_STPHY_EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> B52127 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> B13757 B_STPHY_EPDR Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 097186 B_STPHY_CPTS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> C82046 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> D80438 B_CRYNB_STRT Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 09B453 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 5B78D5 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
@@ -353,7 +355,7 @@
</div>
<div class="pkgdown-footer-right">
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 200px;"></a></p>
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a></p>
</div>
</footer></div>

6
reference/ggplot_pca.html
View File

@@ -1,5 +1,5 @@
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@@ -10,7 +10,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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reference/index.html
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<!DOCTYPE html>
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -138,12 +138,12 @@
<dl><dt>
<code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code>
<code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_reset_session()</a></code> <code><a href="as.mo.html">mo_cleaning_regex()</a></code>
</dt>
<dd>Transform Input to a Microorganism Code</dd>
</dl><dl><dt>
<code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_domain()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_is_gram_negative()</a></code> <code><a href="mo_property.html">mo_is_gram_positive()</a></code> <code><a href="mo_property.html">mo_is_yeast()</a></code> <code><a href="mo_property.html">mo_is_intrinsic_resistant()</a></code> <code><a href="mo_property.html">mo_snomed()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_lpsn()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_synonyms()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code>
<code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_domain()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_status()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_is_gram_negative()</a></code> <code><a href="mo_property.html">mo_is_gram_positive()</a></code> <code><a href="mo_property.html">mo_is_yeast()</a></code> <code><a href="mo_property.html">mo_is_intrinsic_resistant()</a></code> <code><a href="mo_property.html">mo_snomed()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_lpsn()</a></code> <code><a href="mo_property.html">mo_gbif()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_synonyms()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code>
</dt>
<dd>Get Properties of a Microorganism</dd>
</dl><dl><dt>
@@ -307,7 +307,7 @@
<dl><dt>
<code><a href="AMR.html">AMR</a></code>
<code><a href="AMR.html">AMR</a></code> <code><a href="AMR.html">AMR-package</a></code>
</dt>
<dd>The <code>AMR</code> Package</dd>
</dl><dl><dt>
@@ -319,17 +319,12 @@
<code><a href="microorganisms.html">microorganisms</a></code>
</dt>
<dd>Data Set with 70,764 Microorganisms</dd>
<dd>Data Set with 48,787 Microorganisms</dd>
</dl><dl><dt>
<code><a href="microorganisms.codes.html">microorganisms.codes</a></code>
</dt>
<dd>Data Set with 5,604 Common Microorganism Codes</dd>
</dl><dl><dt>
<code><a href="microorganisms.old.html">microorganisms.old</a></code>
</dt>
<dd>Data Set with Previously Accepted Taxonomic Names</dd>
<dd>Data Set with 5,411 Common Microorganism Codes</dd>
</dl><dl><dt>
<code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code>
@@ -347,16 +342,6 @@
<dd>Data Set with Treatment Dosages as Defined by EUCAST</dd>
</dl><dl><dt>
<code><a href="catalogue_of_life.html">catalogue_of_life</a></code>
</dt>
<dd>The Catalogue of Life</dd>
</dl><dl><dt>
<code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>
</dt>
<dd>Version info of included Catalogue of Life</dd>
</dl><dl><dt>
<code><a href="WHOCC.html">WHOCC</a></code>
</dt>
<dd>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</dd>
@@ -493,7 +478,7 @@
</div>
<div class="pkgdown-footer-right">
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 200px;"></a></p>
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a></p>
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12
reference/intrinsic_resistant.html
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@@ -1,5 +1,5 @@
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<![endif]--></head><body>
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -138,7 +138,7 @@
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 134,956 observations and 2 variables:</p><ul><li><p><code>mo</code><br> Microorganism ID</p></li>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 134,659 observations and 2 variables:</p><ul><li><p><code>mo</code><br> Microorganism ID</p></li>
<li><p><code>ab</code><br> Antibiotic ID</p></li>
</ul></div>
<div class="section level2">
@@ -156,7 +156,7 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">intrinsic_resistant</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 134,956 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 134,659 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> B_GRAMP ATM </span>
@@ -169,7 +169,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B_ABTRP NAL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B_ABTRP PLB </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B_ABTRP TEM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 134,946 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 134,649 more rows</span></span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
@@ -181,7 +181,7 @@
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6
reference/italicise_taxonomy.html
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "K. pneumoniae" (assuming</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Klebsiella pneumoniae). Run `mo_uncertainties()` to review this.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 16</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo fullname kingdom phylum class order family genus species subsp…¹</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> B_KLBSL_PNMN Klebsiel… Bacter… Prote… Gamm… Ente… Enter… Kleb… pneumo… <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 6 more variables: rank &lt;chr&gt;, ref &lt;chr&gt;, species_id &lt;dbl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># source &lt;chr&gt;, prevalence &lt;dbl&gt;, snomed &lt;list&gt;, and abbreviated variable</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># name ¹​subspecies</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 22</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo fullname status kingdom phylum class order family genus species</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> B_KLBSL_PNMN Klebsiell… accep… Bacter… Pseud… Gamm… Ente… Enter… Kleb… pneumo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 12 more variables: subspecies &lt;chr&gt;, rank &lt;chr&gt;, ref &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># source &lt;chr&gt;, lpsn &lt;chr&gt;, lpsn_parent &lt;chr&gt;, lpsn_renamed_to &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># gbif &lt;chr&gt;, gbif_parent &lt;chr&gt;, gbif_renamed_to &lt;chr&gt;, prevalence &lt;dbl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># snomed &lt;list&gt;</span></span>
<span class="r-in"><span><span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="st">"B_KLBSL_PNMN"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 16</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo fullname kingdom phylum class order family genus species subsp…¹</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> B_KLBSL_PNMN Klebsiel… Bacter… Prote… Gamm… Ente… Enter… Kleb… pneumo… <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 6 more variables: rank &lt;chr&gt;, ref &lt;chr&gt;, species_id &lt;dbl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># source &lt;chr&gt;, prevalence &lt;dbl&gt;, snomed &lt;list&gt;, and abbreviated variable</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># name ¹​subspecies</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 22</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo fullname status kingdom phylum class order family genus species</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> B_KLBSL_PNMN Klebsiell… accep… Bacter… Pseud… Gamm… Ente… Enter… Kleb… pneumo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 12 more variables: subspecies &lt;chr&gt;, rank &lt;chr&gt;, ref &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># source &lt;chr&gt;, lpsn &lt;chr&gt;, lpsn_parent &lt;chr&gt;, lpsn_renamed_to &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># gbif &lt;chr&gt;, gbif_parent &lt;chr&gt;, gbif_renamed_to &lt;chr&gt;, prevalence &lt;dbl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># snomed &lt;list&gt;</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> date <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span></span></span>
@@ -211,18 +211,17 @@
<span class="r-in"><span> <span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> coli) and "S. aureus" (assuming Staphylococcus aureus). Run</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> `mo_uncertainties()` to review these uncertainties.</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">df</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "date" "bacteria"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df_joined</span> <span class="op">&lt;-</span> <span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="va">df</span>, <span class="st">"bacteria"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">df_joined</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "date" "bacteria" "fullname" "kingdom" "phylum" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [6] "class" "order" "family" "genus" "species" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] "subspecies" "rank" "ref" "species_id" "source" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "prevalence" "snomed" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "date" "bacteria" "fullname" "status" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [5] "kingdom" "phylum" "class" "order" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] "family" "genus" "species" "subspecies" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "rank" "ref" "source" "lpsn" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [17] "lpsn_parent" "lpsn_renamed_to" "gbif" "gbif_parent" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] "gbif_renamed_to" "prevalence" "snomed" </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@@ -231,19 +230,23 @@
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Joining, by = "mo"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "date" "patient" "age" "gender" "ward" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [6] "mo" "PEN" "OXA" "FLC" "AMX" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] "AMC" "AMP" "TZP" "CZO" "FEP" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "CXM" "FOX" "CTX" "CAZ" "CRO" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] "GEN" "TOB" "AMK" "KAN" "TMP" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] "SXT" "NIT" "FOS" "LNZ" "CIP" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [31] "MFX" "VAN" "TEC" "TCY" "TGC" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [36] "DOX" "ERY" "CLI" "AZM" "IPM" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [41] "MEM" "MTR" "CHL" "COL" "MUP" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [46] "RIF" "fullname" "kingdom" "phylum" "class" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] "order" "family" "genus" "species" "subspecies"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [56] "rank" "ref" "species_id" "source" "prevalence"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] "snomed" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "date" "patient" "age" "gender" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [5] "ward" "mo" "PEN" "OXA" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] "FLC" "AMX" "AMC" "AMP" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "TZP" "CZO" "FEP" "CXM" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [17] "FOX" "CTX" "CAZ" "CRO" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] "GEN" "TOB" "AMK" "KAN" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "TMP" "SXT" "NIT" "FOS" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [29] "LNZ" "CIP" "MFX" "VAN" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [33] "TEC" "TCY" "TGC" "DOX" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] "ERY" "CLI" "AZM" "IPM" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [41] "MEM" "MTR" "CHL" "COL" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [45] "MUP" "RIF" "fullname" "status" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] "kingdom" "phylum" "class" "order" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [53] "family" "genus" "species" "subspecies" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [57] "rank" "ref" "source" "lpsn" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] "lpsn_parent" "lpsn_renamed_to" "gbif" "gbif_parent" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [65] "gbif_renamed_to" "prevalence" "snomed" </span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>
@@ -256,7 +259,7 @@
</div>
<div class="pkgdown-footer-right">
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 200px;"></a></p>
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a></p>
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6
reference/key_antimicrobials.html
View File

@@ -1,5 +1,5 @@
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@@ -167,9 +167,9 @@
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.888967</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.044605</span>
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.05684207</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.01569241</span>
</code></pre></div>
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reference/mdro.html
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@@ -1,5 +1,5 @@
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -195,10 +195,10 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.0625 0.001 0.25 &gt;=128 0.025 1 0.5 0.005 1 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.25 256 16 0.001 8 8 0.002 8 0.0625 16 </span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.41123292 -1.57568929 -0.02085462 1.73584774 -0.66925895 0.36952368</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.17433453 -1.12247412 0.36952368 1.15028028</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.3351460 1.3348700 0.6668636 -1.6654448 0.4998620 0.4998620</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.4984432 0.4998620 -0.6691492 0.6668636</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@@ -208,38 +208,38 @@
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 2 2 &lt;=0.25 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 4 2 2 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &gt;=16 2 &lt;=0.25 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D &lt;=1 0.25 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E &gt;=16 &lt;=0.125 &lt;=0.25 0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F &gt;=16 &lt;=0.125 4 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &lt;=1 2 &lt;=0.25 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 0.25 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &lt;=1 1 0.5 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 8 2 0.5 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 4 2 1 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 8 2 1 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 4 0.25 &gt;=4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D &lt;=1 0.125 0.5 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E &lt;=1 0.5 2 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F &lt;=1 0.25 &gt;=4 &lt;=0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 4 &gt;=4 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 0.25 &gt;=4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 8 1 2 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 4 0.5 2 4</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "id" and "tobr"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.15641280 0.42857996 0.14992674 -0.42197963 -0.81679006 0.57661476</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.30349990 0.01816313 -0.02817569 0.55357349</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.40198724 0.61497293 0.04169761 -1.42617241 -0.07813388 -0.65411731</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.53631944 0.17661937 0.17391127 0.21291573</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E &gt;=16 &lt;=0.125 &lt;=0.25 0.25 -0.81679006</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D &lt;=1 0.25 2 2 -0.42197963</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &lt;=1 2 &lt;=0.25 4 -0.30349990</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 2 2 &lt;=0.25 4 -0.15641280</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &lt;=1 1 0.5 &gt;=16 -0.02817569</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 0.25 4 2 0.01816313</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &gt;=16 2 &lt;=0.25 2 0.14992674</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 4 2 2 4 0.42857996</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 8 2 0.5 &gt;=16 0.55357349</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F &gt;=16 &lt;=0.125 4 &gt;=16 0.57661476</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D &lt;=1 0.125 0.5 0.5 -1.42617241</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F &lt;=1 0.25 &gt;=4 &lt;=0.25 -0.65411731</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E &lt;=1 0.5 2 8 -0.07813388</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 4 0.25 &gt;=4 1 0.04169761</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 8 1 2 0.5 0.17391127</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 0.25 &gt;=4 2 0.17661937</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 4 0.5 2 4 0.21291573</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 4 2 1 8 0.40198724</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 4 &gt;=4 2 2 0.53631944</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 8 2 1 8 0.61497293</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -251,17 +251,17 @@
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C &gt;=16 2 &lt;=0.25 2 0.14992674 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 H 4 0.25 4 2 0.01816313 0.1317636</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 I &lt;=1 1 0.5 &gt;=16 -0.02817569 0.1781024</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 B 4 2 2 4 0.42857996 0.2786532</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 A 2 2 &lt;=0.25 4 -0.15641280 0.3063395</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 J 8 2 0.5 &gt;=16 0.55357349 0.4036468</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 F &gt;=16 &lt;=0.125 4 &gt;=16 0.57661476 0.4266880</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 G &lt;=1 2 &lt;=0.25 4 -0.30349990 0.4534266</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 D &lt;=1 0.25 2 2 -0.42197963 0.5719064</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 E &gt;=16 &lt;=0.125 &lt;=0.25 0.25 -0.81679006 0.9667168</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C 4 0.25 &gt;=4 1 0.04169761 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 E &lt;=1 0.5 2 8 -0.07813388 0.1198315</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 I 8 1 2 0.5 0.17391127 0.1322137</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 H 4 0.25 &gt;=4 2 0.17661937 0.1349218</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 J 4 0.5 2 4 0.21291573 0.1712181</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 A 4 2 1 8 0.40198724 0.3602896</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 4 &gt;=4 2 2 0.53631944 0.4946218</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 B 8 2 1 8 0.61497293 0.5732753</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 F &lt;=1 0.25 &gt;=4 &lt;=0.25 -0.65411731 0.6958149</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 D &lt;=1 0.125 0.5 0.5 -1.42617241 1.4678700</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -301,7 +301,7 @@
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -122,7 +122,7 @@
</nav><div class="container template-reference-topic">
<div class="row">
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 5,604 Common Microorganism Codes</h1>
<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 5,411 Common Microorganism Codes</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
<div class="d-none name"><code>microorganisms.codes.Rd</code></div>
</div>
@@ -138,20 +138,12 @@
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 5,604 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism</p></li>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 5,411 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism</p></li>
<li><p><code>mo</code><br> ID of the microorganism in the <a href="microorganisms.html">microorganisms</a> data set</p></li>
</ul></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
</div>
<div class="section level2">
<h2 id="catalogue-of-life">Catalogue of Life<a class="anchor" aria-label="anchor" href="#catalogue-of-life"></a></h2>
<p><img src="figures/logo_col.png" height="40" style='margin-bottom:"5"'><br>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/CatalogueOfLife/general" class="external-link">CoL+ project</a> is finished, which we await.</p>
<p><a href="catalogue_of_life.html">Click here</a> for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</p>
</div>
<div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
@@ -161,7 +153,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">microorganisms.codes</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 5,604 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 5,411 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> code mo </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> _FAM_A- B_GRAMN </span>
@@ -174,7 +166,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> _FAM_AS F_FUNGUS </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> _FAM_AT UNKNOWN</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> _FAM_AV UNKNOWN</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 5,594 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 5,401 more rows</span></span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
@@ -186,7 +178,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 70,764 Microorganisms</h1>
<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 48,787 Microorganisms</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
<div class="d-none name"><code>microorganisms.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>A data set containing the full microbial taxonomy (<strong>last updated: 5 October 2021</strong>) of six kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using <code><a href="as.mo.html">as.mo()</a></code>.</p>
<p>A data set containing the full microbial taxonomy (<strong>last updated: 12 September, 2022</strong>) of five kingdoms from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF). This data set is the backbone of this <code>AMR</code> package. MO codes can be looked up using <code><a href="as.mo.html">as.mo()</a></code>.</p>
</div>
<div class="section level2">
@@ -138,44 +138,61 @@
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 70,764 observations and 16 variables:</p><ul><li><p><code>mo</code><br> ID of microorganism as used by this package</p></li>
<li><p><code>fullname</code><br> Full name, like <code>"Escherichia coli"</code></p></li>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 48,787 observations and 22 variables:</p><ul><li><p><code>mo</code><br> ID of microorganism as used by this package</p></li>
<li><p><code>fullname</code><br> Full name, like <code>"Escherichia coli"</code>. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon.</p></li>
<li><p><code>status</code> <br> Status of the taxon, either "accepted" or "synonym"</p></li>
<li><p><code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br> Taxonomic rank of the microorganism</p></li>
<li><p><code>rank</code><br> Text of the taxonomic rank of the microorganism, like <code>"species"</code> or <code>"genus"</code></p></li>
<li><p><code>ref</code><br> Author(s) and year of concerning scientific publication</p></li>
<li><p><code>species_id</code><br> ID of the species as used by the Catalogue of Life</p></li>
<li><p><code>source</code><br> Either "CoL", "LPSN" or "manually added" (see <em>Source</em>)</p></li>
<li><p><code>rank</code><br> Text of the taxonomic rank of the microorganism, such as <code>"species"</code> or <code>"genus"</code></p></li>
<li><p><code>ref</code><br> Author(s) and year of related scientific publication. This contains only the <em>first surname</em> and year of the <em>latest</em> authors, e.g. "Wallis <em>et al.</em> 2006 <em>emend.</em> Smith and Jones 2018" becomes "Smith <em>et al.</em>, 2018". This field is directly retrieved from the source specified in the column <code>source</code>. Moreover, accents were removed to comply with CRAN that only allows ASCII characters, e.g. "Váňová" becomes "Vanova".</p></li>
<li><p><code>lpsn</code><br> Identifier ('Record number') of the List of Prokaryotic names with Standing in Nomenclature (LPSN). This will be the first/highest LPSN identifier to keep one identifier per row. For example, <em>Acetobacter ascendens</em> has LPSN Record number 7864 and 11011. Only the first is available in the <code>microorganisms</code> data set.</p></li>
<li><p><code>lpsn_parent</code><br> LPSN identifier of the parent taxon</p></li>
<li><p><code>lpsn_renamed_to</code><br> LPSN identifier of the currently valid taxon</p></li>
<li><p><code>gbif</code><br> Identifier ('taxonID') of the Global Biodiversity Information Facility (GBIF)</p></li>
<li><p><code>gbif_parent</code><br> GBIF identifier of the parent taxon</p></li>
<li><p><code>gbif_renamed_to</code><br> GBIF identifier of the currently valid taxon</p></li>
<li><p><code>source</code><br> Either "GBIF", "LPSN" or "manually added" (see <em>Source</em>)</p></li>
<li><p><code>prevalence</code><br> Prevalence of the microorganism, see <code><a href="as.mo.html">as.mo()</a></code></p></li>
<li><p><code>snomed</code><br> Systematized Nomenclature of Medicine (SNOMED) code of the microorganism, according to the US Edition of SNOMED CT from 1 September 2020 (see <em>Source</em>). Use <code><a href="mo_property.html">mo_snomed()</a></code> to retrieve it quickly, see <code><a href="mo_property.html">mo_property()</a></code>.</p></li>
<li><p><code>snomed</code><br> Systematized Nomenclature of Medicine (SNOMED) code of the microorganism, version of 1 July, 2021 (see <em>Source</em>). Use <code><a href="mo_property.html">mo_snomed()</a></code> to retrieve it quickly, see <code><a href="mo_property.html">mo_property()</a></code>.</p></li>
</ul></div>
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
<p>Catalogue of Life: 2019 Annual Checklist as currently implemented in this <code>AMR</code> package:</p><ul><li><p>Annual Checklist (public online taxonomic database), <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a></p></li>
</ul><p>List of Prokaryotic names with Standing in Nomenclature (5 October 2021) as currently implemented in this <code>AMR</code> package:</p><ul><li><p>Parte, A.C., Sarda Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Goker, M. (2020). List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a></p></li>
<li><p>Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; <a href="https://doi.org/10.1099/ijsem.0.002786" class="external-link">doi:10.1099/ijsem.0.002786</a></p></li>
<li><p>Parte, A.C. (2014). LPSN - List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613-D616; <a href="https://doi.org/10.1093/nar/gkt1111" class="external-link">doi:10.1093/nar/gkt1111</a></p></li>
<li><p>Euzeby, J.P. (1997). List of Bacterial Names with Standing in Nomenclature: a Folder Available on the Internet. International Journal of Systematic Bacteriology, 47, 590-592; <a href="https://doi.org/10.1099/00207713-47-2-590" class="external-link">doi:10.1099/00207713-47-2-590</a></p></li>
</ul><p>US Edition of SNOMED CT from 1 September 2020 as currently implemented in this <code>AMR</code> package:</p><ul><li><p>Retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009</a></p></li>
<ul><li><p>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong> International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a>
. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on 12 September, 2022.</p></li>
<li><p>GBIF Secretariat (November 26, 2021). GBIF Backbone Taxonomy. Checklist dataset <a href="https://doi.org/10.15468/39omei" class="external-link">doi:10.15468/39omei</a>
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on 12 September, 2022.</p></li>
<li><p>Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link">https://phinvads.cdc.gov</a></p></li>
</ul></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>Please note that entries are only based on the Catalogue of Life and the LPSN (see below). Since these sources incorporate entries based on (recent) publications in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), it can happen that the year of publication is sometimes later than one might expect.</p>
<p>Please note that entries are only based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF) (see below). Since these sources incorporate entries based on (recent) publications in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), it can happen that the year of publication is sometimes later than one might expect.</p>
<p>For example, <em>Staphylococcus pettenkoferi</em> was described for the first time in Diagnostic Microbiology and Infectious Disease in 2002 (<a href="https://doi.org/10.1016/s0732-8893%2802%2900399-1" class="external-link">doi:10.1016/s0732-8893(02)00399-1</a>
), but it was not before 2007 that a publication in IJSEM followed (<a href="https://doi.org/10.1099/ijs.0.64381-0" class="external-link">doi:10.1099/ijs.0.64381-0</a>
). Consequently, the <code>AMR</code> package returns 2007 for <code>mo_year("S. pettenkoferi")</code>.</p><div class="section">
). Consequently, the <code>AMR</code> package returns 2007 for <code>mo_year("S. pettenkoferi")</code>.</p>
</div>
<div class="section level2">
<h2 id="included-taxa">Included Taxa<a class="anchor" aria-label="anchor" href="#included-taxa"></a></h2>
<p>Included taxonomic data are:</p><ul><li><p>All ~34,000 (sub)species from the kingdoms of Archaea and Bacteria</p></li>
<li><p>~7,400 (sub)species from the kingdom of Fungi. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package. Only relevant fungi are covered (such as all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Cryptococcus</em>, <em>Histoplasma</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>~4,900 (sub)species from the kingdom of Protozoa</p></li>
<li><p>~1,500 (sub)species from ~50 other relevant genera from the kingdom of Animalia (such as <em>Strongyloides</em> and <em>Taenia</em>)</p></li>
<li><p>All ~9,400 previously accepted names of all included (sub)species (these were taxonomically renamed)</p></li>
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
<li><p>The identifier of the parent taxons</p></li>
<li><p>The year and first author of the related scientific publication</p></li>
</ul><div class="section">
<h3 id="manual-additions">Manual additions<a class="anchor" aria-label="anchor" href="#manual-additions"></a></h3>
<p>For convenience, some entries were added manually:</p><ul><li><p>11 entries of <em>Streptococcus</em> (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)</p></li>
<li><p>2 entries of <em>Staphylococcus</em> (coagulase-negative (CoNS) and coagulase-positive (CoPS))</p></li>
<li><p>3 entries of <em>Trichomonas</em> (<em>T. vaginalis</em>, and its family and genus)</p></li>
<li><p>4 entries of <em>Toxoplasma</em> (<em>T. gondii</em>, and its order, family and genus)</p></li>
<li><p>1 entry of <em>Candida</em> (<em>C. krusei</em>), that is not (yet) in the Catalogue of Life</p></li>
<li><p>1 entry of <em>Blastocystis</em> (<em>B. hominis</em>), although it officially does not exist (Noel <em>et al.</em> 2005, PMID 15634993)</p></li>
<li><p>1 entry of <em>Moraxella</em> (<em>M. catarrhalis</em>), which was formally named <em>Branhamella catarrhalis</em> (Catlin, 1970) though this change was never accepted within the field of clinical microbiology</p></li>
<li><p>5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)</p></li>
<li><p>6 families under the Enterobacterales order, according to Adeolu <em>et al.</em> (2016, PMID 27620848), that are not (yet) in the Catalogue of Life</p></li>
</ul></div>
</ul><p>The syntax used to transform the original data to a cleansed <span style="R">R</span> format, can be found here: <a href="https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R</a>.</p>
</div>
<div class="section">
<h3 id="direct-download">Direct download<a class="anchor" aria-label="anchor" href="#direct-download"></a></h3>
@@ -189,16 +206,8 @@
<h2 id="about-the-records-from-lpsn-see-source-">About the Records from LPSN (see <em>Source</em>)<a class="anchor" aria-label="anchor" href="#about-the-records-from-lpsn-see-source-"></a></h2>
<p>LPSN is the main source for bacteriological taxonomy of this <code>AMR</code> package.</p>
<p>The List of Prokaryotic names with Standing in Nomenclature (LPSN) provides comprehensive information on the nomenclature of prokaryotes. LPSN is a free to use service founded by Jean P. Euzeby in 1997 and later on maintained by Aidan C. Parte.</p>
<p>As of February 2020, the regularly augmented LPSN database at DSMZ is the basis of the new LPSN service. The new database was implemented for the Type-Strain Genome Server and augmented in 2018 to store all kinds of nomenclatural information. Data from the previous version of LPSN and from the Prokaryotic Nomenclature Up-to-date (PNU) service were imported into the new system. PNU had been established in 1993 as a service of the Leibniz Institute DSMZ, and was curated by Norbert Weiss, Manfred Kracht and Dorothea Gleim.</p>
</div>
<div class="section level2">
<h2 id="catalogue-of-life">Catalogue of Life<a class="anchor" aria-label="anchor" href="#catalogue-of-life"></a></h2>
<p><img src="figures/logo_col.png" height="40" style='margin-bottom:"5"'><br>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/CatalogueOfLife/general" class="external-link">CoL+ project</a> is finished, which we await.</p>
<p><a href="catalogue_of_life.html">Click here</a> for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</p>
</div>
<div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
@@ -208,21 +217,23 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">microorganisms</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 70,764 × 16</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo fullname kingdom phylum class order family genus species</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> F_FUNGUS (unknown fu… Fungi (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> B_GRAMN (unknown Gr… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B_GRAMP (unknown Gr… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> UNKNOWN (unknown na… (unkno… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> F_YEAST (unknown ye… Fungi (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B_[FAM]_ABDTBCTR Abditibacte… Bacter… Abdit… Abdi… Abdi… <span style="color: #949494;">"</span>Abdi… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B_[ORD]_ABDTBCTR Abditibacte… Bacter… Abdit… Abdi… Abdi… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B_ABDTB Abditibacte… Bacter… Abdit… Abdi… Abdi… <span style="color: #949494;">"</span>Abdi… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B_ABDTB_UTST Abditibacte… Bacter… Abdit… Abdi… Abdi… <span style="color: #949494;">"</span>Abdi… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">"</span>utste…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> C_ABDTD Abditodentr… Chromi… Foram… Glob… Rota… <span style="color: #949494;">"</span>Boli… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 70,754 more rows, and 7 more variables: subspecies &lt;chr&gt;, rank &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ref &lt;chr&gt;, species_id &lt;dbl&gt;, source &lt;chr&gt;, prevalence &lt;dbl&gt;, snomed &lt;list&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 48,787 × 22</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo fullname status kingdom phylum class order family genus</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> F_FUNGUS (unknown fun… accep… Fungi (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> B_GRAMN (unknown Gra… accep… Bacter… (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B_GRAMP (unknown Gra… accep… Bacter… (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> UNKNOWN (unknown nam… accep… (unkno… (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> F_YEAST (unknown yea… accep… Fungi (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B_[CLS]_ABDTBCTR Abditibacter… accep… Bacter… Armat… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B_[FAM]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">"</span>Abdi… <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B_[ORD]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B_[CLS]_ADTBCTRA Abditibacter… accep… Bacter… Abdit… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B_[PHL]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 48,777 more rows, and 13 more variables: species &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># subspecies &lt;chr&gt;, rank &lt;chr&gt;, ref &lt;chr&gt;, source &lt;chr&gt;, lpsn &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># lpsn_parent &lt;chr&gt;, lpsn_renamed_to &lt;chr&gt;, gbif &lt;chr&gt;, gbif_parent &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># gbif_renamed_to &lt;chr&gt;, prevalence &lt;dbl&gt;, snomed &lt;list&gt;</span></span>
</code></pre></div>
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@@ -234,7 +245,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with Previously Accepted Taxonomic Names</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
<div class="d-none name"><code>microorganisms.old.Rd</code></div>
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<div class="ref-description section level2">
<p>A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by <code><a href="as.mo.html">as.mo()</a></code>.</p>
</div>
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">microorganisms.old</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 14,338 observations and 4 variables:</p><ul><li><p><code>fullname</code><br> Old full taxonomic name of the microorganism</p></li>
<li><p><code>fullname_new</code><br> New full taxonomic name of the microorganism</p></li>
<li><p><code>ref</code><br> Author(s) and year of concerning scientific publication</p></li>
<li><p><code>prevalence</code><br> Prevalence of the microorganism, see <code><a href="as.mo.html">as.mo()</a></code></p></li>
</ul></div>
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
<p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a> (check included annual version with <code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>).</p>
<p>Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; <a href="https://doi.org/10.1099/ijsem.0.002786" class="external-link">doi:10.1099/ijsem.0.002786</a></p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
</div>
<div class="section level2">
<h2 id="catalogue-of-life">Catalogue of Life<a class="anchor" aria-label="anchor" href="#catalogue-of-life"></a></h2>
<p><img src="figures/logo_col.png" height="40" style='margin-bottom:"5"'><br>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/CatalogueOfLife/general" class="external-link">CoL+ project</a> is finished, which we await.</p>
<p><a href="catalogue_of_life.html">Click here</a> for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</p>
</div>
<div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
<div class="dont-index"><p><code><a href="as.mo.html">as.mo()</a></code> <code><a href="mo_property.html">mo_property()</a></code> <a href="microorganisms.html">microorganisms</a></p></div>
</div>
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">microorganisms.old</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 14,338 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> fullname fullname_new ref preva…¹</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Abaphospora petrucciana Nectria petrucciana Kirschst, 19… 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Abathostoma stercoris Echinocyclidium stercoris Berger in Co… 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Abbottina tannerbankensis Nonion tannerbankensis McCulloch, 1… 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Abditodentrix rhomboidalis Tortoplectella rhomboidalis Millett, 1899 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Abiotrophia adiacens Granulicatella adiacens Kawamura et … 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Abiotrophia balaenopterae Granulicatella balaenopterae Lawson et al… 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Abiotrophia elegans Granulicatella elegans Roggenkamp e… 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Absidia blakesleeana Lichtheimia blakesleeana Lendn, 1924 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Absidia butleri Gongronella butleri Lendn, 1926 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Absidia corymbifera Lichtheimia corymbifera Sacc et al.,… 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 14,328 more rows, and abbreviated variable name ¹​prevalence</span></span>
</code></pre></div>
</div>
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<p></p><p><code>AMR</code> (for R). Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><a target="_blank" href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -146,6 +146,11 @@
<dd><p>A full taxonomic name, that exists in <code><a href="microorganisms.html">microorganisms$fullname</a></code></p></dd>
</dl></div>
<div class="section level2">
<h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
<p>This algorithm was described in: Berends MS <em>et al.</em> (2022). <strong>AMR: An R Package for Working with Antimicrobial Resistance Data</strong>. <em>Journal of Statistical Software</em>, 104(3), 1-31; <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">doi:10.18637/jss.v104.i03</a>
.</p>
</div>
<div class="section level2">
<h2 id="matching-score-for-microorganisms">Matching Score for Microorganisms<a class="anchor" aria-label="anchor" href="#matching-score-for-microorganisms"></a></h2>
@@ -155,13 +160,15 @@
<p>where:</p><ul><li><p><i>x</i> is the user input;</p></li>
<li><p><i>n</i> is a taxonomic name (genus, species, and subspecies);</p></li>
<li><p><i>l<sub>n</sub></i> is the length of <i>n</i>;</p></li>
<li><p><i>lev</i> is the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance" class="external-link">Levenshtein distance function</a>, which counts any insertion, deletion and substitution as 1 that is needed to change <i>x</i> into <i>n</i>;</p></li>
<li><p><i>lev</i> is the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance" class="external-link">Levenshtein distance function</a> (counting any insertion as 1, and any deletion or substitution as 2) that is needed to change <i>x</i> into <i>n</i>;</p></li>
<li><p><i>p<sub>n</sub></i> is the human pathogenic prevalence group of <i>n</i>, as described below;</p></li>
<li><p><i>k<sub>n</sub></i> is the taxonomic kingdom of <i>n</i>, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.</p></li>
</ul><p>The grouping into human pathogenic prevalence (\(p\)) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. <strong>Group 1</strong> (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is <em>Enterococcus</em>, <em>Staphylococcus</em> or <em>Streptococcus</em>. This group consequently contains all common Gram-negative bacteria, such as <em>Pseudomonas</em> and <em>Legionella</em> and all species within the order Enterobacterales. <strong>Group 2</strong> consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is <em>Absidia</em>, <em>Acremonium</em>, <em>Actinotignum</em>, <em>Alternaria</em>, <em>Anaerosalibacter</em>, <em>Apophysomyces</em>, <em>Arachnia</em>, <em>Aspergillus</em>, <em>Aureobacterium</em>, <em>Aureobasidium</em>, <em>Bacteroides</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Branhamella</em>, <em>Calymmatobacterium</em>, <em>Candida</em>, <em>Capnocytophaga</em>, <em>Catabacter</em>, <em>Chaetomium</em>, <em>Chryseobacterium</em>, <em>Chryseomonas</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Flavobacterium</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Fusobacterium</em>, <em>Hendersonula</em>, <em>Hypomyces</em>, <em>Koserella</em>, <em>Lelliottia</em>, <em>Leptosphaeria</em>, <em>Leptotrichia</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Mycoplasma</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oidiodendron</em>, <em>Phoma</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Prevotella</em>, <em>Pseudallescheria</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Stomatococcus</em>, <em>Treponema</em>, <em>Trichoderma</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Tritirachium</em> or <em>Ureaplasma</em>. <strong>Group 3</strong> consists of all other microorganisms.</p>
</ul><p>The grouping into human pathogenic prevalence (\(p\)) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence:</p>
<p><strong>Group 1</strong> (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is <em>Enterococcus</em>, <em>Staphylococcus</em> or <em>Streptococcus</em>. This group consequently contains all common Gram-negative bacteria, such as <em>Pseudomonas</em> and <em>Legionella</em> and all species within the order Enterobacterales.</p>
<p><strong>Group 2</strong> consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is <em>Absidia</em>, <em>Acanthamoeba</em>, <em>Acholeplasma</em>, <em>Acremonium</em>, <em>Actinotignum</em>, <em>Aedes</em>, <em>Alistipes</em>, <em>Alloprevotella</em>, <em>Alternaria</em>, <em>Amoeba</em>, <em>Anaerosalibacter</em>, <em>Ancylostoma</em>, <em>Angiostrongylus</em>, <em>Anisakis</em>, <em>Anopheles</em>, <em>Apophysomyces</em>, <em>Arachnia</em>, <em>Aspergillus</em>, <em>Aureobasidium</em>, <em>Bacteroides</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Bergeyella</em>, <em>Blastocystis</em>, <em>Blastomyces</em>, <em>Borrelia</em>, <em>Brachyspira</em>, <em>Branhamella</em>, <em>Butyricimonas</em>, <em>Candida</em>, <em>Capillaria</em>, <em>Capnocytophaga</em>, <em>Catabacter</em>, <em>Cetobacterium</em>, <em>Chaetomium</em>, <em>Chlamydia</em>, <em>Chlamydophila</em>, <em>Chryseobacterium</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Contracaecum</em>, <em>Cordylobia</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Deinococcus</em>, <em>Demodex</em>, <em>Dermatobia</em>, <em>Dientamoeba</em>, <em>Diphyllobothrium</em>, <em>Dirofilaria</em>, <em>Dysgonomonas</em>, <em>Echinostoma</em>, <em>Elizabethkingia</em>, <em>Empedobacter</em>, <em>Entamoeba</em>, <em>Enterobius</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Fasciola</em>, <em>Flavobacterium</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Fusobacterium</em>, <em>Giardia</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Hendersonula</em>, <em>Heterophyes</em>, <em>Histomonas</em>, <em>Histoplasma</em>, <em>Hymenolepis</em>, <em>Hypomyces</em>, <em>Hysterothylacium</em>, <em>Leishmania</em>, <em>Lelliottia</em>, <em>Leptosphaeria</em>, <em>Leptotrichia</em>, <em>Lucilia</em>, <em>Lumbricus</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Metagonimus</em>, <em>Meyerozyma</em>, <em>Microsporidium</em>, <em>Microsporum</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Mycoplasma</em>, <em>Myroides</em>, <em>Necator</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Odoribacter</em>, <em>Oesophagostomum</em>, <em>Oidiodendron</em>, <em>Opisthorchis</em>, <em>Ornithobacterium</em>, <em>Parabacteroides</em>, <em>Pediculus</em>, <em>Pedobacter</em>, <em>Phlebotomus</em>, <em>Phocaeicola</em>, <em>Phocanema</em>, <em>Phoma</em>, <em>Pichia</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Pneumocystis</em>, <em>Porphyromonas</em>, <em>Prevotella</em>, <em>Pseudallescheria</em>, <em>Pseudoterranova</em>, <em>Pulex</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Riemerella</em>, <em>Saccharomyces</em>, <em>Sarcoptes</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Sphingobacterium</em>, <em>Spirometra</em>, <em>Spiroplasma</em>, <em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Streptobacillus</em>, <em>Strongyloides</em>, <em>Syngamus</em>, <em>Taenia</em>, <em>Tannerella</em>, <em>Tenacibaculum</em>, <em>Terrimonas</em>, <em>Toxocara</em>, <em>Treponema</em>, <em>Trichinella</em>, <em>Trichobilharzia</em>, <em>Trichoderma</em>, <em>Trichomonas</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Trichostrongylus</em>, <em>Trichuris</em>, <em>Tritirachium</em>, <em>Trombicula</em>, <em>Trypanosoma</em>, <em>Tunga</em>, <em>Ureaplasma</em>, <em>Victivallis</em>, <em>Wautersiella</em>, <em>Weeksella</em> or <em>Wuchereria</em>.</p>
<p><strong>Group 3</strong> consists of all other microorganisms.</p>
<p>All characters in \(x\) and \(n\) are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.</p>
<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.079\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
<p>Since <code>AMR</code> version 1.8.1, common microorganism abbreviations are ignored in determining the matching score. These abbreviations are currently: AIEC, ATEC, BORSA, CRSM, DAEC, EAEC, EHEC, EIEC, EPEC, ETEC, GISA, MRPA, MRSA, MRSE, MSSA, MSSE, NMEC, PISP, PRSP, STEC, UPEC, VISA, VISP, VRE, VRSA and VRSP.</p>
<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.119\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
</div>
<div class="section level2">
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
@@ -177,23 +184,24 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> coli). Run `mo_uncertainties()` to review this.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mo&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_ESCHR_COLI</span>
<span class="r-in"><span><span class="fu"><a href="as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Matching scores are based on pathogenicity in humans and the resemblance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> between the input and the full taxonomic name. See `?mo_matching_score`.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Matching scores are based on the resemblance between the input and the full</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> taxonomic name, and the pathogenicity in humans. See `?mo_matching_score`.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> "E. coli" -&gt; Escherichia coli (B_ESCHR_COLI, 0.688)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Also matched: Entamoeba coli (0.079)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> "K. pneumoniae" -&gt; Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Based on input "K pneumoniae"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Also matched: Klebsiella pneumoniae ozaenae (0.707), Klebsiella pneumoniae</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> pneumoniae (0.688), Klebsiella pneumoniae rhinoscleromatis (0.658) and</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Kroppenstedtia pulmonis (0.304)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">mo_matching_score</span><span class="op">(</span></span></span>
<span class="r-in"><span> x <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
<span class="r-in"><span> n <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span>, <span class="st">"Entamoeba coli"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.68750000 0.07936508</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.6875000 0.1190476</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
@@ -205,7 +213,7 @@
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<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a></p>
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@@ -1,5 +1,5 @@
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<![endif]--></head><body>
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -133,63 +133,225 @@
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mo_name</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mo_name</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_fullname</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_fullname</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_shortname</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_shortname</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_subspecies</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_subspecies</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_species</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_species</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_genus</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_genus</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_family</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_family</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_order</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_order</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_class</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_class</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_phylum</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_phylum</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_kingdom</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_kingdom</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_domain</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_domain</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_type</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_type</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_status</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_is_gram_negative</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_gramstain</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_is_gram_positive</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_is_gram_negative</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_is_yeast</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_is_gram_positive</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_is_intrinsic_resistant</span><span class="op">(</span><span class="va">x</span>, <span class="va">ab</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_is_yeast</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_snomed</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_is_intrinsic_resistant</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> <span class="va">ab</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_ref</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_snomed</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_authors</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_ref</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_year</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_authors</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_lpsn</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_year</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_rank</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_lpsn</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_taxonomy</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_gbif</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_synonyms</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_rank</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_info</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_taxonomy</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_url</span><span class="op">(</span><span class="va">x</span>, open <span class="op">=</span> <span class="cn">FALSE</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mo_synonyms</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_property</span><span class="op">(</span><span class="va">x</span>, property <span class="op">=</span> <span class="st">"fullname"</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
<span><span class="fu">mo_info</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_url</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> open <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_property</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> property <span class="op">=</span> <span class="st">"fullname"</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
@@ -199,11 +361,15 @@
<dt>language</dt>
<dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can be overwritten by setting the option <code>AMR_locale</code>, e.g. <code>options(AMR_locale = "de")</code>, see <a href="translate.html">translate</a>. Also used to translate text like "no growth". Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dd><p>language to translate text like "no growth", which defaults to the system language (see <code><a href="translate.html">get_AMR_locale()</a></code>)</p></dd>
<dt>keep_synonyms</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is <code>FALSE</code>, which will return a note if old taxonomic names were processed. The default can be set with <code>options(AMR_keep_synonyms = TRUE)</code> or <code>options(AMR_keep_synonyms = FALSE)</code>.</p></dd>
<dt>...</dt>
<dd><p>other arguments passed on to <code><a href="as.mo.html">as.mo()</a></code>, such as 'allow_uncertain' and 'ignore_pattern'</p></dd>
<dd><p>other arguments passed on to <code><a href="as.mo.html">as.mo()</a></code>, such as 'minimum_matching_score', 'ignore_pattern', and 'remove_from_input'</p></dd>
<dt>ab</dt>
@@ -215,7 +381,7 @@
<dt>property</dt>
<dd><p>one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "species_id", "source", "prevalence" or "snomed", or must be <code>"shortname"</code></p></dd>
<dd><p>one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence" or "snomed", or must be <code>"shortname"</code></p></dd>
</dl></div>
<div class="section level2">
@@ -230,9 +396,9 @@
</ul></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for <code>mo_ref()</code>, <code>mo_authors()</code> and <code>mo_year()</code>. Please refer to this example, knowing that <em>Escherichia blattae</em> was renamed to <em>Shimwellia blattae</em> in 2010:</p><ul><li><p><code>mo_name("Escherichia blattae")</code> will return <code>"Shimwellia blattae"</code> (with a message about the renaming)</p></li>
<li><p><code>mo_ref("Escherichia blattae")</code> will return <code>"Burgess et al., 1973"</code> (with a message about the renaming)</p></li>
<li><p><code>mo_ref("Shimwellia blattae")</code> will return <code>"Priest et al., 2010"</code> (without a message)</p></li>
<p>All functions will, at default, keep old taxonomic properties. Please refer to this example, knowing that <em>Escherichia blattae</em> was renamed to <em>Shimwellia blattae</em> in 2010:</p><ul><li><p><code>mo_name("Escherichia blattae")</code> will return <code>"Shimwellia blattae"</code> (with a message about the renaming)</p></li>
<li><p><code>mo_ref("Escherichia blattae", keep_synonyms = TRUE)</code> will return <code>"Burgess et al., 1973"</code> (with a warning about the renaming)</p></li>
<li><p><code>mo_ref("Shimwellia blattae", keep_synonyms = FALSE)</code> will return <code>"Priest et al., 2010"</code> (without a message)</p></li>
</ul><p>The short name - <code>mo_shortname()</code> - almost always returns the first character of the genus and the full species, like <code>"E. coli"</code>. Exceptions are abbreviations of staphylococci (such as <em>"CoNS"</em>, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as <em>"GBS"</em>, Group B Streptococci). Please bear in mind that e.g. <em>E. coli</em> could mean <em>Escherichia coli</em> (kingdom of Bacteria) as well as <em>Entamoeba coli</em> (kingdom of Protozoa). Returning to the full name will be done using <code><a href="as.mo.html">as.mo()</a></code> internally, giving priority to bacteria and human pathogens, i.e. <code>"E. coli"</code> will be considered <em>Escherichia coli</em>. In other words, <code>mo_fullname(mo_shortname("Entamoeba coli"))</code> returns <code>"Escherichia coli"</code>.</p>
<p>Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions <code>mo_kingdom()</code> and <code>mo_domain()</code> return the exact same results.</p>
<p>The Gram stain - <code>mo_gramstain()</code> - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, <a href="https://pubmed.ncbi.nlm.nih.gov/11837318" class="external-link">PMID 11837318</a>), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive, except for members of the class Negativicutes which are Gram-negative. Members of other bacterial phyla are all considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
@@ -240,7 +406,7 @@
<p>Intrinsic resistance - <code>mo_is_intrinsic_resistant()</code> - will be determined based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, which is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes/" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3</a> (2021). The <code>mo_is_intrinsic_resistant()</code> functions can be vectorised over arguments <code>x</code> (input for microorganisms) and over <code>ab</code> (input for antibiotics).</p>
<p>All output <a href="translate.html">will be translated</a> where possible.</p>
<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
<p>SNOMED codes - <code>mo_snomed()</code> - are from the US Edition of SNOMED CT from 1 September 2020. See <em>Source</em> and the <a href="microorganisms.html">microorganisms</a> data set for more info.</p>
<p>SNOMED codes - <code>mo_snomed()</code> - are from the version of 1 July, 2021. See <em>Source</em> and the <a href="microorganisms.html">microorganisms</a> data set for more info.</p>
</div>
<div class="section level2">
<h2 id="matching-score-for-microorganisms">Matching Score for Microorganisms<a class="anchor" aria-label="anchor" href="#matching-score-for-microorganisms"></a></h2>
@@ -251,33 +417,31 @@
<p>where:</p><ul><li><p><i>x</i> is the user input;</p></li>
<li><p><i>n</i> is a taxonomic name (genus, species, and subspecies);</p></li>
<li><p><i>l<sub>n</sub></i> is the length of <i>n</i>;</p></li>
<li><p><i>lev</i> is the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance" class="external-link">Levenshtein distance function</a>, which counts any insertion, deletion and substitution as 1 that is needed to change <i>x</i> into <i>n</i>;</p></li>
<li><p><i>lev</i> is the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance" class="external-link">Levenshtein distance function</a> (counting any insertion as 1, and any deletion or substitution as 2) that is needed to change <i>x</i> into <i>n</i>;</p></li>
<li><p><i>p<sub>n</sub></i> is the human pathogenic prevalence group of <i>n</i>, as described below;</p></li>
<li><p><i>k<sub>n</sub></i> is the taxonomic kingdom of <i>n</i>, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.</p></li>
</ul><p>The grouping into human pathogenic prevalence (\(p\)) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. <strong>Group 1</strong> (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is <em>Enterococcus</em>, <em>Staphylococcus</em> or <em>Streptococcus</em>. This group consequently contains all common Gram-negative bacteria, such as <em>Pseudomonas</em> and <em>Legionella</em> and all species within the order Enterobacterales. <strong>Group 2</strong> consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is <em>Absidia</em>, <em>Acremonium</em>, <em>Actinotignum</em>, <em>Alternaria</em>, <em>Anaerosalibacter</em>, <em>Apophysomyces</em>, <em>Arachnia</em>, <em>Aspergillus</em>, <em>Aureobacterium</em>, <em>Aureobasidium</em>, <em>Bacteroides</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Branhamella</em>, <em>Calymmatobacterium</em>, <em>Candida</em>, <em>Capnocytophaga</em>, <em>Catabacter</em>, <em>Chaetomium</em>, <em>Chryseobacterium</em>, <em>Chryseomonas</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Flavobacterium</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Fusobacterium</em>, <em>Hendersonula</em>, <em>Hypomyces</em>, <em>Koserella</em>, <em>Lelliottia</em>, <em>Leptosphaeria</em>, <em>Leptotrichia</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Mycoplasma</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oidiodendron</em>, <em>Phoma</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Prevotella</em>, <em>Pseudallescheria</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Stomatococcus</em>, <em>Treponema</em>, <em>Trichoderma</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Tritirachium</em> or <em>Ureaplasma</em>. <strong>Group 3</strong> consists of all other microorganisms.</p>
</ul><p>The grouping into human pathogenic prevalence (\(p\)) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence:</p>
<p><strong>Group 1</strong> (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is <em>Enterococcus</em>, <em>Staphylococcus</em> or <em>Streptococcus</em>. This group consequently contains all common Gram-negative bacteria, such as <em>Pseudomonas</em> and <em>Legionella</em> and all species within the order Enterobacterales.</p>
<p><strong>Group 2</strong> consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is <em>Absidia</em>, <em>Acanthamoeba</em>, <em>Acholeplasma</em>, <em>Acremonium</em>, <em>Actinotignum</em>, <em>Aedes</em>, <em>Alistipes</em>, <em>Alloprevotella</em>, <em>Alternaria</em>, <em>Amoeba</em>, <em>Anaerosalibacter</em>, <em>Ancylostoma</em>, <em>Angiostrongylus</em>, <em>Anisakis</em>, <em>Anopheles</em>, <em>Apophysomyces</em>, <em>Arachnia</em>, <em>Aspergillus</em>, <em>Aureobasidium</em>, <em>Bacteroides</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Bergeyella</em>, <em>Blastocystis</em>, <em>Blastomyces</em>, <em>Borrelia</em>, <em>Brachyspira</em>, <em>Branhamella</em>, <em>Butyricimonas</em>, <em>Candida</em>, <em>Capillaria</em>, <em>Capnocytophaga</em>, <em>Catabacter</em>, <em>Cetobacterium</em>, <em>Chaetomium</em>, <em>Chlamydia</em>, <em>Chlamydophila</em>, <em>Chryseobacterium</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Contracaecum</em>, <em>Cordylobia</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Deinococcus</em>, <em>Demodex</em>, <em>Dermatobia</em>, <em>Dientamoeba</em>, <em>Diphyllobothrium</em>, <em>Dirofilaria</em>, <em>Dysgonomonas</em>, <em>Echinostoma</em>, <em>Elizabethkingia</em>, <em>Empedobacter</em>, <em>Entamoeba</em>, <em>Enterobius</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Fasciola</em>, <em>Flavobacterium</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Fusobacterium</em>, <em>Giardia</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Hendersonula</em>, <em>Heterophyes</em>, <em>Histomonas</em>, <em>Histoplasma</em>, <em>Hymenolepis</em>, <em>Hypomyces</em>, <em>Hysterothylacium</em>, <em>Leishmania</em>, <em>Lelliottia</em>, <em>Leptosphaeria</em>, <em>Leptotrichia</em>, <em>Lucilia</em>, <em>Lumbricus</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Metagonimus</em>, <em>Meyerozyma</em>, <em>Microsporidium</em>, <em>Microsporum</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Mycoplasma</em>, <em>Myroides</em>, <em>Necator</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Odoribacter</em>, <em>Oesophagostomum</em>, <em>Oidiodendron</em>, <em>Opisthorchis</em>, <em>Ornithobacterium</em>, <em>Parabacteroides</em>, <em>Pediculus</em>, <em>Pedobacter</em>, <em>Phlebotomus</em>, <em>Phocaeicola</em>, <em>Phocanema</em>, <em>Phoma</em>, <em>Pichia</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Pneumocystis</em>, <em>Porphyromonas</em>, <em>Prevotella</em>, <em>Pseudallescheria</em>, <em>Pseudoterranova</em>, <em>Pulex</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Riemerella</em>, <em>Saccharomyces</em>, <em>Sarcoptes</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Sphingobacterium</em>, <em>Spirometra</em>, <em>Spiroplasma</em>, <em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Streptobacillus</em>, <em>Strongyloides</em>, <em>Syngamus</em>, <em>Taenia</em>, <em>Tannerella</em>, <em>Tenacibaculum</em>, <em>Terrimonas</em>, <em>Toxocara</em>, <em>Treponema</em>, <em>Trichinella</em>, <em>Trichobilharzia</em>, <em>Trichoderma</em>, <em>Trichomonas</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Trichostrongylus</em>, <em>Trichuris</em>, <em>Tritirachium</em>, <em>Trombicula</em>, <em>Trypanosoma</em>, <em>Tunga</em>, <em>Ureaplasma</em>, <em>Victivallis</em>, <em>Wautersiella</em>, <em>Weeksella</em> or <em>Wuchereria</em>.</p>
<p><strong>Group 3</strong> consists of all other microorganisms.</p>
<p>All characters in \(x\) and \(n\) are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.</p>
<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.079\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
<p>Since <code>AMR</code> version 1.8.1, common microorganism abbreviations are ignored in determining the matching score. These abbreviations are currently: AIEC, ATEC, BORSA, CRSM, DAEC, EAEC, EHEC, EIEC, EPEC, ETEC, GISA, MRPA, MRSA, MRSE, MSSA, MSSE, NMEC, PISP, PRSP, STEC, UPEC, VISA, VISP, VRE, VRSA and VRSP.</p>
</div>
<div class="section level2">
<h2 id="catalogue-of-life">Catalogue of Life<a class="anchor" aria-label="anchor" href="#catalogue-of-life"></a></h2>
<p><img src="figures/logo_col.png" height="40" style='margin-bottom:"5"'><br>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/CatalogueOfLife/general" class="external-link">CoL+ project</a> is finished, which we await.</p>
<p><a href="catalogue_of_life.html">Click here</a> for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</p>
<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.119\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
</div>
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
<ol><li><p>Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870-926; <a href="https://doi.org/10.1128/CMR.00109-13" class="external-link">doi:10.1128/CMR.00109-13</a></p></li>
<li><p>Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect; <a href="https://doi.org/10.1016/j.cmi.2019.02.028" class="external-link">doi:10.1016/j.cmi.2019.02.028</a></p></li>
<li><p>Becker K <em>et al.</em> <strong>Emergence of coagulase-negative staphylococci</strong> 2020. Expert Rev Anti Infect Ther. 18(4):349-366; <a href="https://doi.org/10.1080/14787210.2020.1730813" class="external-link">doi:10.1080/14787210.2020.1730813</a></p></li>
<li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571-95; <a href="https://doi.org/10.1084/jem.57.4.571" class="external-link">doi:10.1084/jem.57.4.571</a></p></li>
<li><p>Catalogue of Life: 2019 Annual Checklist, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a></p></li>
<li><p>List of Prokaryotic names with Standing in Nomenclature (5 October 2021), <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a></p></li>
<li><p>US Edition of SNOMED CT from 1 September 2020, retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009</a></p></li>
<ol><li><p>Berends MS <em>et al.</em> (2022). <strong>AMR: An R Package for Working with Antimicrobial Resistance Data</strong>. <em>Journal of Statistical Software</em>, 104(3), 1-31; <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">doi:10.18637/jss.v104.i03</a></p></li>
<li><p>Becker K <em>et al.</em> (2014). <strong>Coagulase-Negative Staphylococci.</strong> <em>Clin Microbiol Rev.</em> 27(4): 870-926; <a href="https://doi.org/10.1128/CMR.00109-13" class="external-link">doi:10.1128/CMR.00109-13</a></p></li>
<li><p>Becker K <em>et al.</em> (2019). <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> <em>Clin Microbiol Infect</em>; <a href="https://doi.org/10.1016/j.cmi.2019.02.028" class="external-link">doi:10.1016/j.cmi.2019.02.028</a></p></li>
<li><p>Becker K <em>et al.</em> (2020). <strong>Emergence of coagulase-negative staphylococci</strong> <em>Expert Rev Anti Infect Ther.</em> 18(4):349-366; <a href="https://doi.org/10.1080/14787210.2020.1730813" class="external-link">doi:10.1080/14787210.2020.1730813</a></p></li>
<li><p>Lancefield RC (1933). <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. <em>J Exp Med.</em> 57(4): 571-95; <a href="https://doi.org/10.1084/jem.57.4.571" class="external-link">doi:10.1084/jem.57.4.571</a></p></li>
<li><p>Berends MS <em>et al.</em> (2022). <strong>Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019</strong> <em>Microorganisms</em> 10(9), 1801; <a href="https://doi.org/10.3390/microorganisms10091801" class="external-link">doi:10.3390/microorganisms10091801</a></p></li>
<li><p>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong> International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a>
. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on 12 September, 2022.</p></li>
<li><p>GBIF Secretariat (November 26, 2021). GBIF Backbone Taxonomy. Checklist dataset <a href="https://doi.org/10.15468/39omei" class="external-link">doi:10.15468/39omei</a>
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on 12 September, 2022.</p></li>
<li><p>Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link">https://phinvads.cdc.gov</a></p></li>
</ol></div>
<div class="section level2">
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
@@ -296,7 +460,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class="r-in"><span><span class="fu">mo_kingdom</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteria"</span>
<span class="r-in"><span><span class="fu">mo_phylum</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Proteobacteria"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Pseudomonadota"</span>
<span class="r-in"><span><span class="fu">mo_class</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gammaproteobacteria"</span>
<span class="r-in"><span><span class="fu">mo_order</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
@@ -322,8 +486,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class="r-in"><span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gram-negative"</span>
<span class="r-in"><span><span class="fu">mo_snomed</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.098101e+15 4.468700e+08 1.098201e+15 4.098010e+08 5.641501e+07</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [6] 7.143150e+08</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "1098101000112102" "1098201000112108" "409801009" "446870005" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [5] "56415008" "713926009" "714315002" </span>
<span class="r-in"><span><span class="fu">mo_type</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteria"</span>
<span class="r-in"><span><span class="fu">mo_rank</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
@@ -342,7 +506,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class="r-in"><span><span class="fu">mo_year</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1887</span>
<span class="r-in"><span><span class="fu">mo_lpsn</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 777151</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "777151"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># abbreviations known in the field -----------------------------------------</span></span></span>
<span class="r-in"><span><span class="fu">mo_genus</span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span></span></span>
@@ -361,11 +525,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># known subspecies ---------------------------------------------------------</span></span></span>
<span class="r-in"><span><span class="fu">mo_name</span><span class="op">(</span><span class="st">"doylei"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Campylobacter jejuni doylei"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Doolittlea endobia"</span>
<span class="r-in"><span><span class="fu">mo_genus</span><span class="op">(</span><span class="st">"doylei"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Campylobacter"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Doolittlea"</span>
<span class="r-in"><span><span class="fu">mo_species</span><span class="op">(</span><span class="st">"doylei"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "jejuni"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "endobia"</span>
<span class="r-in"><span><span class="fu">mo_subspecies</span><span class="op">(</span><span class="st">"doylei"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "doylei"</span>
<span class="r-in"><span></span></span>
@@ -377,21 +541,13 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># Becker classification, see ?as.mo ----------------------------------------</span></span></span>
<span class="r-in"><span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. epi"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "S. epi" (assuming Staphylococcus</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> epidermidis). Run `mo_uncertainties()` to review this.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Staphylococcus epidermidis"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Serratia entomophila"</span>
<span class="r-in"><span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. epi"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "S. epi" (assuming Staphylococcus</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> epidermidis). Run `mo_uncertainties()` to review this.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Coagulase-negative Staphylococcus (CoNS)"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Serratia entomophila"</span>
<span class="r-in"><span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"S. epi"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "S. epi" (assuming Staphylococcus</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> epidermidis). Run `mo_uncertainties()` to review this.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "S. epidermidis"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "S. entomophila"</span>
<span class="r-in"><span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"S. epi"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "S. epi" (assuming Staphylococcus</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> epidermidis). Run `mo_uncertainties()` to review this.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "CoNS"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "S. entomophila"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Lancefield classification, see ?as.mo ------------------------------------</span></span></span>
<span class="r-in"><span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyo"</span><span class="op">)</span></span></span>
@@ -475,7 +631,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteria"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $phylum</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Proteobacteria"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Pseudomonadota"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $class</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gammaproteobacteria"</span>
@@ -503,7 +659,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteria"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $phylum</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Proteobacteria"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Pseudomonadota"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $class</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gammaproteobacteria"</span>
@@ -523,6 +679,9 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class="r-out co"><span class="r-pr">#&gt;</span> $subspecies</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ""</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $status</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "accepted"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $synonyms</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> NULL</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
@@ -536,8 +695,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Trevisan, 1887"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $snomed</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.098101e+15 4.468700e+08 1.098201e+15 4.098010e+08 5.641501e+07</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [6] 7.143150e+08</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "1098101000112102" "1098201000112108" "409801009" "446870005" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [5] "56415008" "713926009" "714315002" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
@@ -551,7 +710,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown-footer-right">
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 200px;"></a></p>
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a></p>
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6
reference/mo_source.html
View File

@@ -1,7 +1,7 @@
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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="These functions can be used to predefine your own reference to be used in as.mo() and consequently all mo_* functions (such as mo_genus() and mo_gramstain()).
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@@ -10,7 +10,7 @@
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@@ -297,8 +297,6 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># when providing the microorganism and antibiotic, colours will show interpretations:</span></span></span>
<span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_mic_values</span>, mo <span class="op">=</span> <span class="st">"S. aureus"</span>, ab <span class="op">=</span> <span class="st">"ampicillin"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "S. aureus" (assuming</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Staphylococcus aureus). Run `mo_uncertainties()` to review this.</span>
<span class="r-plt img"><img src="plot-4.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_disk_values</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="plot-5.png" alt="" width="700" height="433"></span>
@@ -330,7 +328,7 @@
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6
reference/proportion.html
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resistance() should be used to calculate resistance, susceptibility() should be used to calculate susceptibility."><title>Calculate Microbial Resistance — proportion • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.2/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Calculate Microbial Resistance — proportion"><meta property="og:description" content="These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in summarise() from the dplyr package and also support grouped variables, see Examples.
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@@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@@ -393,7 +393,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
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@@ -178,42 +178,42 @@
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 64 16 &gt;=256 64 128 &lt;=0.001 0.5 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 16 2 8 8 2 &gt;=256 32 64 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] &gt;=256 16 0.5 0.0625 64 0.01 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.002 64 128 2 4 0.25 0.5 0.025 &gt;=256 0.002 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.0625 0.025 0.0625 32 4 0.025 0.0625 8 &gt;=256 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.002 0.025 0.001 0.01 0.0625</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 41 20 7 37 10 50 20 23 38 32 44 6 34 26 19 46 43 11 32 50 18 12 32 19 37</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 13 15 24 27 29 12 46 43 15 28 20 31 25 17 13 39 19 35 49 14 40 29 45 28 38</span>
<span class="r-in"><span><span class="fu">random_rsi</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;rsi&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S R R R I S I S I R I I S S R R R I R R R I S R R</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S S S S I I S S R S I I I I I S R S I R I I I S I</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 32 8 0.005 4 8 0.025 &gt;=64 0.5 0.001 0.025 0.001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.125 &gt;=64 0.125 0.002 0.01 16 &gt;=64 8 &gt;=64 0.5 0.125 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4 0.125 64 16 0.01 1 64 64 8 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 1 64 64 1 0.025 0.001 0.025 0.25 1 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.125 &gt;=256 64 0.0625 &gt;=256 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 4 8 4 16 8 16 &lt;=1 4 2 4 4 4 2 8 4 &lt;=1 16 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [20] 2 &lt;=1 &lt;=1 4 16 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &gt;=16 1 0.5 2 2 8 2 2 8 0.5 4 &gt;=16 0.5 2 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] 2 1 2 2 &gt;=16 &gt;=16 4 0.5 2 4 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5 0.125 0.25 0.125 0.125 0.125 4 2 0.0625 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.0625 2 0.5 1 1 2 2 4 1 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 2 2 1 0.25 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.25 1 0.25 16 4 16 8 8 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 1 0.25 2 16 0.5 &lt;=0.125 16 8 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 1 &lt;=0.125 0.25 1 0.5 8 0.25 </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 26 40 17 35 19 24 48 16 44 33 47 16 49 50 37 40 41 22 29 46 47 38 22 49 30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 25 41 23 39 8 23 20 8 41 21 18 47 18 40 23 36 42 23 30 45 23 43 8 39 45</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 13 14 15 14 16 17 16 14 11 16 17 12 14 14 12 11 17 13 12 12 11 14 14 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 15 14 11 16 16 16 14 12 12 17 17 12 13 15 11 13 15 14 17 15 13 16 11 12 11</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 23 23 21 23 20 23 18 20 18 27 25 17 16 26 22 20 17 20 19 23 20 24 24 18 25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 18 23 17 23 22 27 15 21 15 17 25 25 22 25 21 15 18 19 17 18 18 17 19 17 18</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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@@ -226,7 +226,7 @@
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@@ -1,5 +1,5 @@
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</small>
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@@ -349,8 +349,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-in"><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">data</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">data</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> coli). Run `mo_uncertainties()` to review this.</span>
<span class="r-plt img"><img src="resistance_predict-4.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
@@ -364,7 +362,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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6
reference/rsi_translation.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</small>
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@@ -189,7 +189,7 @@
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8
reference/skewness.html
View File

@@ -1,7 +1,7 @@
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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Skewness is a measure of the asymmetry of the probability distribution of a real-valued random variable about its mean.
When negative ('left-skewed'): the left tail is longer; the mass of the distribution is concentrated on the right of a histogram. When positive ('right-skewed'): the right tail is longer; the mass of the distribution is concentrated on the left of a histogram. A normal distribution has a skewness of 0."><title>Skewness of the Sample — skewness • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.2/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Skewness of the Sample — skewness"><meta property="og:description" content="Skewness is a measure of the asymmetry of the probability distribution of a real-valued random variable about its mean.
When negative ('left-skewed'): the left tail is longer; the mass of the distribution is concentrated on the right of a histogram. When positive ('right-skewed'): the right tail is longer; the mass of the distribution is concentrated on the left of a histogram. A normal distribution has a skewness of 0."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@univgroningen"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
When negative ('left-skewed'): the left tail is longer; the mass of the distribution is concentrated on the right of a histogram. When positive ('right-skewed'): the right tail is longer; the mass of the distribution is concentrated on the left of a histogram. A normal distribution has a skewness of 0."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</small>
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@@ -166,7 +166,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.1146407</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.03302321</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
@@ -178,7 +178,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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@@ -1,5 +1,5 @@
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -145,7 +145,7 @@
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>language</dt>
<dd><p>language to choose. Use one of these supported language names or ISO-639-1 codes: "English" ("en"), "Chinese" ("zh"), "Danish" ("da"), "Dutch" ("nl"), "French" ("fr"), "German" ("de"), "Greek" ("el"), "Italian" ("it"), "Japanese" ("ja"), "Polish" ("pl"), "Portuguese" ("pt"), "Russian" ("ru"), "Spanish" ("es"), "Swedish" ("sv"), "Turkish" ("tr"), "Ukrainian" ("uk").</p></dd>
<dd><p>language to choose. Use one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Danish (da), Dutch (nl), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Polish (pl), Portuguese (pt), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) or Ukrainian (uk).</p></dd>
<dt>x</dt>
@@ -154,13 +154,23 @@
</dl></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>The currently 16 supported languages are English, Chinese, Danish, Dutch, French, German, Greek, Italian, Japanese, Polish, Portuguese, Russian, Spanish, Swedish, Turkish and Ukrainian. All these languages have translations available for all antimicrobial agents and colloquial microorganism names.</p>
<p>The currently 16 supported languages are English (en), Chinese (zh), Danish (da), Dutch (nl), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Polish (pl), Portuguese (pt), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) or Ukrainian (uk). All these languages have translations available for all antimicrobial agents and colloquial microorganism names.</p>
<p><strong>To silence language notes when this package loads</strong> on a non-English operating system, you can set the option <code>AMR_locale</code> in your <code>.Rprofile</code> file like this:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="co"># Open .Rprofile file</span></span>
<span><span class="fu">utils</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/utils/file.edit.html" class="external-link">file.edit</a></span><span class="op">(</span><span class="st">"~/.Rprofile"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Add e.g. Italian support to that file using:</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>AMR_locale <span class="op">=</span> <span class="st">"Italian"</span><span class="op">)</span></span>
<span><span class="co"># or using:</span></span>
<span><span class="fu">AMR</span><span class="fu">::</span><span class="fu"><a href="../reference/translate.html">set_AMR_locale</a></span><span class="op">(</span><span class="st">"Italian"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># And save the file!</span></span></code></pre><p></p></div>
<p>Please read about adding or updating a language in <a href="https://github.com/msberends/AMR/wiki/" class="external-link">our Wiki</a>.</p><div class="section">
<h3 id="changing-the-default-language">Changing the Default Language<a class="anchor" aria-label="anchor" href="#changing-the-default-language"></a></h3>
<p>The system language will be used at default (as returned by <code>Sys.getenv("LANG")</code> or, if <code>LANG</code> is not set, <code><a href="https://rdrr.io/r/base/locales.html" class="external-link">Sys.getlocale("LC_COLLATE")</a></code>), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:</p><ol><li><p>Setting the R option <code>AMR_locale</code>, either by using <code>set_AMR_locale()</code> or by running e.g. <code>options(AMR_locale = "de")</code>.</p>
<p>Note that setting an <span style="R">R</span> option only works in the same session. Save the command <code>options(AMR_locale = "(your language)")</code> to your <code>.Rprofile</code> file to apply it for every session.</p></li>
<p>The system language will be used at default (as returned by <code>Sys.getenv("LANG")</code> or, if <code>LANG</code> is not set, <code><a href="https://rdrr.io/r/base/locales.html" class="external-link">Sys.getlocale("LC_COLLATE")</a></code>), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:</p><ol><li><p>Setting the R option <code>AMR_locale</code>, either by using e.g. <code>set_AMR_locale("German")</code> or by running e.g. <code>options(AMR_locale = "German")</code>.</p>
<p>Note that setting an <span style="R">R</span> option only works in the same session. Save the command <code>options(AMR_locale = "(your language)")</code> to your <code>.Rprofile</code> file to apply it for every session. Run <code>utils::file.edit("~/.Rprofile")</code> to edit your <code>.Rprofile</code> file.</p></li>
<li><p>Setting the system variable <code>LANGUAGE</code> or <code>LANG</code>, e.g. by adding <code>LANGUAGE="de_DE.utf8"</code> to your <code>.Renviron</code> file in your home directory.</p></li>
</ol><p>Thus, if the R option <code>AMR_locale</code> is set, the system variables <code>LANGUAGE</code> and <code>LANG</code> will be ignored.</p>
</div>
@@ -172,35 +182,45 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Current settings (based on system language)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"Ciprofloxacin"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Ciprofloxacin"</span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Coagulase-negative Staphylococcus"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Coagulase-negative Staphylococcus (CoNS)"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Coagulase-negative Staphylococcus (CoNS)"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># setting another language</span></span></span>
<span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"Greek"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using the Greek language (Ελληνικά) for the AMR package for this session.</span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"Ciprofloxacin"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Σιπροφλοξασίνη"</span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Coagulase-negative Staphylococcus"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Σταφυλόκοκκος με αρνητική πηκτικότητα (CoNS)"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"Spanish"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using the Spanish language (Español) for the AMR package for this</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> session.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using Spanish (Español) for the AMR package for this session.</span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"Ciprofloxacin"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Ciprofloxacina"</span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Coagulase-negative Staphylococcus"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Coagulase-negative Staphylococcus (CoNS)"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Staphylococcus coagulasa negativo (SCN)"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># setting yet another language</span></span></span>
<span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"Greek"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using Greek (Ελληνικά) for the AMR package for this session.</span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"Ciprofloxacin"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Σιπροφλοξασίνη"</span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Coagulase-negative Staphylococcus (CoNS)"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Σταφυλόκοκκος με αρνητική πηκτικότητα (CoNS)"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># setting yet another language</span></span></span>
<span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"Ukrainian"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using Ukrainian (Українська) for the AMR package for this session.</span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"Ciprofloxacin"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Ципрофлоксацин"</span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Coagulase-negative Staphylococcus (CoNS)"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Коагулазонегативний стафілокок (КНС)"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># set_AMR_locale() understands endonyms, English exonyms, and ISO-639-1:</span></span></span>
<span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"Deutsch"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using the German language (Deutsch) for the AMR package for this session.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using German (Deutsch) for the AMR package for this session.</span>
<span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"German"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using the German language (Deutsch) for the AMR package for this session.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using German (Deutsch) for the AMR package for this session.</span>
<span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"de"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using the German language (Deutsch) for the AMR package for this session.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using German (Deutsch) for the AMR package for this session.</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># reset to system default</span></span></span>
<span class="r-in"><span><span class="fu">reset_AMR_locale</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using the English language (English) for the AMR package for this</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> session.</span>
</code></pre></div>
</div>
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@@ -212,7 +232,7 @@
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