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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 these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with as.mo(), which makes it possible to use microbial abbreviations, codes and names as input. See Examples."><title>Get Properties of a Microorganism — mo_property • 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="Get Properties of a Microorganism — mo_property"><meta property="og:description" content="Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with as.mo(), which makes it possible to use microbial abbreviations, codes and names as input. 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]>
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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 these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with as.mo(), which makes it possible to use microbial abbreviations, codes and names as input. See Examples."><title>Get Properties of a Microorganism — mo_property • 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="Get Properties of a Microorganism — mo_property"><meta property="og:description" content="Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with as.mo(), which makes it possible to use microbial abbreviations, codes and names as input. 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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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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<![endif]--></head><body>
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@ -10,7 +10,7 @@
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<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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<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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@ -133,63 +133,225 @@
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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">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">#></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">#></span> [1] "Proteobacteria"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></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">#></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">#></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">#></span> [6] 7.143150e+08</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "1098101000112102" "1098201000112108" "409801009" "446870005" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></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">#></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">#></span> [1] 777151</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> [1] "Campylobacter jejuni doylei"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> [1] "Campylobacter"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> [1] "jejuni"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></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">#></span> ℹ Function `as.mo()` is uncertain about "S. epi" (assuming Staphylococcus</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> epidermidis). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Staphylococcus epidermidis"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> ℹ Function `as.mo()` is uncertain about "S. epi" (assuming Staphylococcus</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> epidermidis). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Coagulase-negative Staphylococcus (CoNS)"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> ℹ Function `as.mo()` is uncertain about "S. epi" (assuming Staphylococcus</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> epidermidis). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "S. epidermidis"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> ℹ Function `as.mo()` is uncertain about "S. epi" (assuming Staphylococcus</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> epidermidis). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "CoNS"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> [1] "Bacteria"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $phylum</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Proteobacteria"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Pseudomonadota"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $class</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> [1] "Bacteria"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $phylum</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Proteobacteria"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Pseudomonadota"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $class</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> $subspecies</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] ""</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $status</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "accepted"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $synonyms</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> NULL</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> [1] "Trevisan, 1887"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $snomed</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> [6] 7.143150e+08</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "1098101000112102" "1098201000112108" "409801009" "446870005" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [5] "56415008" "713926009" "714315002" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></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>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
Reference in New Issue
Block a user