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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 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>
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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>
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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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<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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@ -128,7 +128,7 @@
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</div>
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<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>
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</div>
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<div class="section level2">
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@ -137,9 +137,11 @@
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<span> <span class="va">x</span>,</span>
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<span> Becker <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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||||
<span> Lancefield <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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||||
<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>
|
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<span> remove_from_input <span class="op">=</span> <span class="fu">mo_cleaning_regex</span><span class="op">(</span><span class="op">)</span>,</span>
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<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>
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<span> <span class="va">...</span></span>
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@ -147,11 +149,15 @@
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<span></span>
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<span><span class="fu">is.mo</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span>
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||||
<span></span>
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||||
<span><span class="fu">mo_failures</span><span class="op">(</span><span class="op">)</span></span>
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||||
<span></span>
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||||
<span><span class="fu">mo_uncertainties</span><span class="op">(</span><span class="op">)</span></span>
|
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<span></span>
|
||||
<span><span class="fu">mo_renamed</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
|
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<span><span class="fu">mo_renamed</span><span class="op">(</span><span class="op">)</span></span>
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<span></span>
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||||
<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>
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</div>
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<div class="section level2">
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@ -161,17 +167,21 @@
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||||
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||||
|
||||
<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>
|
||||
|
||||
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||||
<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">-></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">-></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">-></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">-></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">-></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">-></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">-></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">#></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">#></span> NULL (=0.2). Try setting this value lower or even to 0.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> "Zthafilokkoockus oureuz".</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> You can retrieve this list with `mo_failures()`.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> ℹ Function `as.mo()` is uncertain about "stau" (assuming Staphylococcus</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> aureus). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> ℹ Function `as.mo()` is uncertain about "STAU" (assuming Staphylococcus</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> aureus). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> ℹ Function `as.mo()` is uncertain about "S. aureus" (assuming</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Staphylococcus aureus). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> ℹ Function `as.mo()` is uncertain about "S aureus" (assuming Staphylococcus</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> aureus). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> ℹ Function `as.mo()` is uncertain about "Staphylococcus aureus (MRSA)"</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (assuming Staphylococcus aureus). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> ℹ Function `as.mo()` is uncertain about "Zthafilokkoockus oureuz" (assuming</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Staphylococcus aureus). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_STPHY_AURS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> [9] UNKNOWN B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> ℹ Function `as.mo()` is uncertain about "Ureaplasma urealyticus" (assuming</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Ureaplasma urealyticum). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> ℹ Function `as.mo()` is uncertain about "Ureaplasmium urealytica" (assuming</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Ureaplasma urealyticum). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> ℹ Function `as.mo()` is uncertain about "Ureaplazma urealitycium" (assuming</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Ureaplasma urealyticum). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_URPLS_URLY</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> Class <mo></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">#></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">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> ℹ Determining intrinsic resistance based on 'EUCAST Expert Rules' and</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3 (2021). This note</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> will be shown once per session.</span>
|
||||
@ -435,7 +381,7 @@ 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