mirror of
https://github.com/msberends/AMR.git
synced 2026-06-24 10:16:23 +02:00
Built site for AMR@3.0.1.9061: 0c1709c
This commit is contained in:
github-actions
@@ -1,5 +1,5 @@
|
||||
<!DOCTYPE html>
|
||||
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><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-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo"><meta name="description" content='Use this function to get a valid microorganism code (mo) based on arbitrary user input. Determination is done using intelligent rules and the complete taxonomic tree of the kingdoms Animalia, Archaea, Bacteria, Chromista, 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:description" content='Use this function to get a valid microorganism code (mo) based on arbitrary user input. Determination is done using intelligent rules and the complete taxonomic tree of the kingdoms Animalia, Archaea, Bacteria, Chromista, 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://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
|
||||
<!-- 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"><title>Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><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-5.3.8/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.8/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo"><meta name="description" content='Use this function to get a valid microorganism code (mo) based on arbitrary user input. Determination is done using intelligent rules and the complete taxonomic tree of the domains Animalia, Archaea, Bacteria, Chromista, Plantae, and Protozoa, and most microbial species from the domain 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:description" content='Use this function to get a valid microorganism code (mo) based on arbitrary user input. Determination is done using intelligent rules and the complete taxonomic tree of the domains Animalia, Archaea, Bacteria, Chromista, Plantae, and Protozoa, and most microbial species from the domain 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://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
|
||||
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
|
||||
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9061</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -50,19 +50,25 @@
|
||||
</div>
|
||||
|
||||
<div class="ref-description section level2">
|
||||
<p>Use this function to get a valid microorganism code (<code>mo</code>) based on arbitrary user input. Determination is done using intelligent rules and the complete taxonomic tree of the kingdoms Animalia, Archaea, Bacteria, Chromista, 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>
|
||||
<p>Use this function to get a valid microorganism code (<code>mo</code>) based on arbitrary user input. Determination is done using intelligent rules and the complete taxonomic tree of the domains Animalia, Archaea, Bacteria, Chromista, Plantae, and Protozoa, and most microbial species from the domain Fungi (see <em>Source</em>). The input can be almost anything: a full name (like <code>"Staphylococcus aureus"</code>), an abbreviated name (such as <code>"S. aureus"</code>), an abbreviation known in the field (such as <code>"MRSA"</code>), or just a genus. See <em>Examples</em>.</p>
|
||||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
<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">as.mo</span><span class="op">(</span><span class="va">x</span>, Becker <span class="op">=</span> <span class="cn">FALSE</span>, Lancefield <span class="op">=</span> <span class="cn">FALSE</span>,</span>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">as.mo</span><span class="op">(</span></span>
|
||||
<span> <span class="va">x</span>,</span>
|
||||
<span> Becker <span class="op">=</span> <span class="cn">FALSE</span>,</span>
|
||||
<span> Lancefield <span class="op">=</span> <span class="cn">FALSE</span>,</span>
|
||||
<span> 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="cn">NULL</span><span class="op">)</span>,</span>
|
||||
<span> cleaning_regex <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_cleaning_regex"</span>, <span class="fu">mo_cleaning_regex</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
|
||||
<span> only_fungi <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_only_fungi"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
|
||||
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, 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 class="va">...</span><span class="op">)</span></span>
|
||||
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
|
||||
<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span>
|
||||
<span> <span class="va">...</span></span>
|
||||
<span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">is.mo</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
@@ -98,7 +104,7 @@
|
||||
|
||||
|
||||
<dt id="arg-minimum-matching-score">minimum_matching_score<a class="anchor" aria-label="anchor" href="#arg-minimum-matching-score"></a></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>
|
||||
<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 domain</a> and <a href="mo_matching_score.html">human pathogenicity</a>.</p></dd>
|
||||
|
||||
|
||||
<dt id="arg-keep-synonyms">keep_synonyms<a class="anchor" aria-label="anchor" href="#arg-keep-synonyms"></a></dt>
|
||||
@@ -119,7 +125,7 @@
|
||||
|
||||
|
||||
<dt id="arg-only-fungi">only_fungi<a class="anchor" aria-label="anchor" href="#arg-only-fungi"></a></dt>
|
||||
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if only fungi must be found, making sure that e.g. misspellings always return records from the kingdom of Fungi. This can be set globally for <a href="mo_property.html">all microorganism functions</a> with the package option <code><a href="AMR-options.html">AMR_only_fungi</a></code>, i.e. <code>options(AMR_only_fungi = TRUE)</code>.</p></dd>
|
||||
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if only fungi must be found, making sure that e.g. misspellings always return records from the domain of Fungi. This can be set globally for <a href="mo_property.html">all microorganism functions</a> with the package option <code><a href="AMR-options.html">AMR_only_fungi</a></code>, i.e. <code>options(AMR_only_fungi = TRUE)</code>.</p></dd>
|
||||
|
||||
|
||||
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
|
||||
@@ -151,7 +157,7 @@
|
||||
<span id="cb1-8"><a href="#cb1-8" 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" 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" 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" tabindex="-1"></a> \<span class="sc">---</span><span class="ot">-></span> 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="cb1-11"><a href="#cb1-11" tabindex="-1"></a> \<span class="sc">---</span><span class="ot">-></span> domain<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" tabindex="-1"></a> <span class="fu">C</span> (Chromista), <span class="fu">F</span> (Fungi), <span class="fu">PL</span> (Plantae),</span>
|
||||
<span id="cb1-13"><a href="#cb1-13" tabindex="-1"></a> <span class="fu">P</span> (Protozoa)</span></code></pre><p></p></div>
|
||||
<p>Values that cannot be coerced will be considered 'unknown' and will return the MO code <code>UNKNOWN</code> with a warning.</p>
|
||||
@@ -161,7 +167,7 @@
|
||||
<h3 id="coping-with-uncertain-results">Coping with Uncertain Results<a class="anchor" aria-label="anchor" href="#coping-with-uncertain-results"></a></h3>
|
||||
|
||||
|
||||
<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, the <a href="microorganisms.html">taxonomic kingdom</a>, and the <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 inspect 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>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, the <a href="microorganisms.html">taxonomic domain</a>, and the <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 inspect 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>cleaning_regex</code> argument is used to clean the input. 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>cleaning_regex</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>
|
||||
@@ -181,8 +187,8 @@
|
||||
<h3 id="coagulase-negative-and-coagulase-positive-staphylococci">Coagulase-negative and Coagulase-positive Staphylococci<a class="anchor" aria-label="anchor" href="#coagulase-negative-and-coagulase-positive-staphylococci"></a></h3>
|
||||
|
||||
|
||||
<p>With <code>Becker = TRUE</code>, the following staphylococci will be converted to their corresponding coagulase group:</p><ul><li><p>Coagulase-negative: <em>S. americanisciuri</em>, <em>S. argensis</em>, <em>S. arlettae</em>, <em>S. auricularis</em>, <em>S. borealis</em>, <em>S. brunensis</em>, <em>S. caeli</em>, <em>S. caledonicus</em>, <em>S. canis</em>, <em>S. capitis</em>, <em>S. capitis capitis</em>, <em>S. capitis urealyticus</em>, <em>S. capitis ureolyticus</em>, <em>S. caprae</em>, <em>S. carnosus</em>, <em>S. carnosus carnosus</em>, <em>S. carnosus utilis</em>, <em>S. casei</em>, <em>S. caseolyticus</em>, <em>S. chromogenes</em>, <em>S. cohnii</em>, <em>S. cohnii cohnii</em>, <em>S. cohnii urealyticum</em>, <em>S. cohnii urealyticus</em>, <em>S. condimenti</em>, <em>S. croceilyticus</em>, <em>S. debuckii</em>, <em>S. devriesei</em>, <em>S. durrellii</em>, <em>S. edaphicus</em>, <em>S. epidermidis</em>, <em>S. equorum</em>, <em>S. equorum equorum</em>, <em>S. equorum linens</em>, <em>S. felis</em>, <em>S. fleurettii</em>, <em>S. gallinarum</em>, <em>S. haemolyticus</em>, <em>S. hominis</em>, <em>S. hominis hominis</em>, <em>S. hominis novobiosepticus</em>, <em>S. jettensis</em>, <em>S. kloosii</em>, <em>S. lentus</em>, <em>S. lloydii</em>, <em>S. lugdunensis</em>, <em>S. marylandisciuri</em>, <em>S. massiliensis</em>, <em>S. microti</em>, <em>S. muscae</em>, <em>S. nepalensis</em>, <em>S. pasteuri</em>, <em>S. petrasii</em>, <em>S. petrasii croceilyticus</em>, <em>S. petrasii jettensis</em>, <em>S. petrasii petrasii</em>, <em>S. petrasii pragensis</em>, <em>S. pettenkoferi</em>, <em>S. piscifermentans</em>, <em>S. pragensis</em>, <em>S. pseudoxylosus</em>, <em>S. pulvereri</em>, <em>S. ratti</em>, <em>S. rostri</em>, <em>S. saccharolyticus</em>, <em>S. saprophyticus</em>, <em>S. saprophyticus bovis</em>, <em>S. saprophyticus saprophyticus</em>, <em>S. schleiferi</em>, <em>S. schleiferi schleiferi</em>, <em>S. sciuri</em>, <em>S. sciuri carnaticus</em>, <em>S. sciuri lentus</em>, <em>S. sciuri rodentium</em>, <em>S. sciuri sciuri</em>, <em>S. shinii</em>, <em>S. simulans</em>, <em>S. stepanovicii</em>, <em>S. succinus</em>, <em>S. succinus casei</em>, <em>S. succinus succinus</em>, <em>S. taiwanensis</em>, <em>S. urealyticus</em>, <em>S. ureilyticus</em>, <em>S. veratri</em>, <em>S. vitulinus</em>, <em>S. vitulus</em>, <em>S. warneri</em>, and <em>S. xylosus</em></p></li>
|
||||
<li><p>Coagulase-positive: <em>S. agnetis</em>, <em>S. argenteus</em>, <em>S. coagulans</em>, <em>S. cornubiensis</em>, <em>S. delphini</em>, <em>S. hyicus</em>, <em>S. hyicus chromogenes</em>, <em>S. hyicus hyicus</em>, <em>S. intermedius</em>, <em>S. lutrae</em>, <em>S. pseudintermedius</em>, <em>S. roterodami</em>, <em>S. schleiferi coagulans</em>, <em>S. schweitzeri</em>, <em>S. simiae</em>, and <em>S. singaporensis</em></p></li>
|
||||
<p>With <code>Becker = TRUE</code>, the following staphylococci will be converted to their corresponding coagulase group:</p><ul><li><p>Coagulase-negative: <em>S. americanisciuri</em>, <em>S. argensis</em>, <em>S. arlettae</em>, <em>S. auricularis</em>, <em>S. borealis</em>, <em>S. brunensis</em>, <em>S. caeli</em>, <em>S. caledonicus</em>, <em>S. canis</em>, <em>S. capitis</em>, <em>S. capitis capitis</em>, <em>S. capitis urealyticus</em>, <em>S. capitis ureolyticus</em>, <em>S. caprae</em>, <em>S. carnosus</em>, <em>S. carnosus carnosus</em>, <em>S. carnosus utilis</em>, <em>S. casei</em>, <em>S. caseolyticus</em>, <em>S. caseorum</em>, <em>S. chromogenes</em>, <em>S. cohnii</em>, <em>S. cohnii cohnii</em>, <em>S. cohnii urealyticum</em>, <em>S. cohnii urealyticus</em>, <em>S. cohnii ureilyticus</em>, <em>S. condimenti</em>, <em>S. croceilyticus</em>, <em>S. debuckii</em>, <em>S. devriesei</em>, <em>S. durrellii</em>, <em>S. edaphicus</em>, <em>S. epidermidis</em>, <em>S. equorum</em>, <em>S. equorum equorum</em>, <em>S. equorum linens</em>, <em>S. felis</em>, <em>S. fleurettii</em>, <em>S. gallinarum</em>, <em>S. haemolyticus</em>, <em>S. halotolerans</em>, <em>S. hominis</em>, <em>S. hominis hominis</em>, <em>S. hominis novobiosepticus</em>, <em>S. hsinchuensis</em>, <em>S. jettensis</em>, <em>S. kloosii</em>, <em>S. lentus</em>, <em>S. lloydii</em>, <em>S. lugdunensis</em>, <em>S. marylandisciuri</em>, <em>S. massiliensis</em>, <em>S. microti</em>, <em>S. muscae</em>, <em>S. nepalensis</em>, <em>S. pasteuri</em>, <em>S. petrasii</em>, <em>S. petrasii croceilyticus</em>, <em>S. petrasii jettensis</em>, <em>S. petrasii petrasii</em>, <em>S. petrasii pragensis</em>, <em>S. pettenkoferi</em>, <em>S. piscifermentans</em>, <em>S. pragensis</em>, <em>S. pseudoxylosus</em>, <em>S. pulvereri</em>, <em>S. ratti</em>, <em>S. rostri</em>, <em>S. saccharolyticus</em>, <em>S. saprophyticus</em>, <em>S. saprophyticus bovis</em>, <em>S. saprophyticus saprophyticus</em>, <em>S. schleiferi</em>, <em>S. schleiferi schleiferi</em>, <em>S. sciuri</em>, <em>S. sciuri carnaticus</em>, <em>S. sciuri lentus</em>, <em>S. sciuri rodentium</em>, <em>S. sciuri sciuri</em>, <em>S. shinii</em>, <em>S. simulans</em>, <em>S. stepanovicii</em>, <em>S. succinus</em>, <em>S. succinus casei</em>, <em>S. succinus succinus</em>, <em>S. taiwanensis</em>, <em>S. urealyticus</em>, <em>S. ureilyticus</em>, <em>S. veratri</em>, <em>S. vitulinus</em>, <em>S. vitulus</em>, <em>S. warneri</em>, and <em>S. xylosus</em></p></li>
|
||||
<li><p>Coagulase-positive: <em>S. agnetis</em>, <em>S. argenteus</em>, <em>S. coagulans</em>, <em>S. cornubiensis</em>, <em>S. delphini</em>, <em>S. hyicus</em>, <em>S. hyicus chromogenes</em>, <em>S. hyicus hyicus</em>, <em>S. intermedius</em>, <em>S. lutrae</em>, <em>S. pseudintermedius</em>, <em>S. roterodami</em>, <em>S. schleiferi coagulans</em>, <em>S. schweitzeri</em>, <em>S. simiae</em>, <em>S. singaporensis</em>, and <em>S. ursi</em></p></li>
|
||||
</ul><p>This is based on:</p><ul><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>
|
||||
@@ -211,14 +217,14 @@
|
||||
|
||||
|
||||
<ul><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>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 June 24th, 2024.</p></li>
|
||||
<li><p>Freese, HM <em>et al.</em> (2026). <strong>TYGS and LPSN in 2025: a Global Core Biodata Resource for genome-based classification and nomenclature of prokaryotes within DSMZ Digital Diversity.</strong> Nucleic Acids Research, 54, D884–D891; <a href="https://doi.org/10.1093/nar/gkaf1110" class="external-link">doi:10.1093/nar/gkaf1110</a>
|
||||
. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on 7th of May, 2026.</p></li>
|
||||
<li><p>Vincent, R <em>et al</em> (2013). <strong>MycoBank gearing up for new horizons.</strong> IMA Fungus, 4(2), 371-9; <a href="https://doi.org/10.5598/imafungus.2013.04.02.16" class="external-link">doi:10.5598/imafungus.2013.04.02.16</a>
|
||||
. Accessed from <a href="https://www.mycobank.org" class="external-link">https://www.mycobank.org</a> on June 24th, 2024.</p></li>
|
||||
<li><p>GBIF Secretariat (2023). 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 June 24th, 2024.</p></li>
|
||||
. Accessed from <a href="https://www.mycobank.org" class="external-link">https://www.mycobank.org</a> on 7th of May, 2026.</p></li>
|
||||
<li><p>Banki, O. <em>et al.</em> (2026). Catalogue of Life (2026-04-18 XR). Catalogue of Life Foundation, Amsterdam, Netherlands. <a href="https://doi.org/10.48580/dgxjw" class="external-link">doi:10.48580/dgxjw</a>
|
||||
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on 7th of May, 2026.</p></li>
|
||||
<li><p>Reimer, LC <em>et al.</em> (2022). <strong><em>BacDive</em> in 2022: the knowledge base for standardized bacterial and archaeal data.</strong> Nucleic Acids Res., 50(D1):D741-D74; <a href="https://doi.org/10.1093/nar/gkab961" class="external-link">doi:10.1093/nar/gkab961</a>
|
||||
. Accessed from <a href="https://bacdive.dsmz.de" class="external-link">https://bacdive.dsmz.de</a> on July 16th, 2024.</p></li>
|
||||
. Accessed from <a href="https://bacdive.dsmz.de" class="external-link">https://bacdive.dsmz.de</a> on 7th of May, 2026.</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 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://www.cdc.gov/phin/php/phinvads/" class="external-link">https://www.cdc.gov/phin/php/phinvads/</a></p></li>
|
||||
<li><p>Bartlett A <em>et al.</em> (2022). <strong>A comprehensive list of bacterial pathogens infecting humans</strong> <em>Microbiology</em> 168:001269; <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a></p></li>
|
||||
</ul></div>
|
||||
@@ -233,7 +239,7 @@
|
||||
<li><p>\(l_n\) is the length of \(n\);</p></li>
|
||||
<li><p>\(lev\) 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 \(x\) into \(n\);</p></li>
|
||||
<li><p>\(p_n\) is the human pathogenic prevalence group of \(n\), as described below;</p></li>
|
||||
<li><p>\(k_n\) is the taxonomic kingdom of \(n\), set as Bacteria = 1, Fungi = 1.25, Protozoa = 1.5, Chromista = 1.75, Archaea = 2, others = 3.</p></li>
|
||||
<li><p>\(k_n\) is the taxonomic domain ('kingdom' until taxonomic reclassification of 2024) of \(n\), set as Bacteria = 1, Fungi = 1.25, Protozoa = 1.5, Chromista = 1.75, Archaea = 2, others = 3.</p></li>
|
||||
</ul><p>The grouping into human pathogenic prevalence \(p\) is based on recent work from Bartlett <em>et al.</em> (2022, <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a>
|
||||
) who extensively studied medical-scientific literature to categorise all bacterial species into these groups:</p><ul><li><p><strong>Established</strong>, if a taxonomic species has infected at least three persons in three or more references. These records have <code>prevalence = 1.15</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
|
||||
<li><p><strong>Putative</strong>, if a taxonomic species has fewer than three known cases. These records have <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
|
||||
@@ -241,7 +247,7 @@
|
||||
<li><p>Any genus present in the <strong>established</strong> list also has <code>prevalence = 1.15</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
|
||||
<li><p>Any other genus present in the <strong>putative</strong> list has <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
|
||||
<li><p>Any other species or subspecies of which the genus is present in the two aforementioned groups, has <code>prevalence = 1.5</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
|
||||
<li><p>Any <em>non-bacterial</em> genus, species or subspecies of which the genus is present in the following list, has <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set: <em>Absidia</em>, <em>Acanthamoeba</em>, <em>Acremonium</em>, <em>Actinomucor</em>, <em>Aedes</em>, <em>Alternaria</em>, <em>Amoeba</em>, <em>Ancylostoma</em>, <em>Angiostrongylus</em>, <em>Anisakis</em>, <em>Anopheles</em>, <em>Apophysomyces</em>, <em>Arthroderma</em>, <em>Aspergillus</em>, <em>Aureobasidium</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Bipolaris</em>, <em>Blastobotrys</em>, <em>Blastocystis</em>, <em>Blastomyces</em>, <em>Candida</em>, <em>Capillaria</em>, <em>Chaetomium</em>, <em>Chilomastix</em>, <em>Chrysonilia</em>, <em>Chrysosporium</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Clavispora</em>, <em>Coccidioides</em>, <em>Cokeromyces</em>, <em>Conidiobolus</em>, <em>Coniochaeta</em>, <em>Contracaecum</em>, <em>Cordylobia</em>, <em>Cryptococcus</em>, <em>Cryptosporidium</em>, <em>Cunninghamella</em>, <em>Curvularia</em>, <em>Cyberlindnera</em>, <em>Debaryozyma</em>, <em>Demodex</em>, <em>Dermatobia</em>, <em>Dientamoeba</em>, <em>Diphyllobothrium</em>, <em>Dirofilaria</em>, <em>Echinostoma</em>, <em>Entamoeba</em>, <em>Enterobius</em>, <em>Epidermophyton</em>, <em>Exidia</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Fasciola</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Geotrichum</em>, <em>Giardia</em>, <em>Graphium</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Hansenula</em>, <em>Hendersonula</em>, <em>Heterophyes</em>, <em>Histomonas</em>, <em>Histoplasma</em>, <em>Hortaea</em>, <em>Hymenolepis</em>, <em>Hypomyces</em>, <em>Hysterothylacium</em>, <em>Kloeckera</em>, <em>Kluyveromyces</em>, <em>Kodamaea</em>, <em>Lacazia</em>, <em>Leishmania</em>, <em>Lichtheimia</em>, <em>Lodderomyces</em>, <em>Lomentospora</em>, <em>Madurella</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Metagonimus</em>, <em>Meyerozyma</em>, <em>Microsporidium</em>, <em>Microsporum</em>, <em>Millerozyma</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Nannizzia</em>, <em>Necator</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oesophagostomum</em>, <em>Oidiodendron</em>, <em>Opisthorchis</em>, <em>Paecilomyces</em>, <em>Paracoccidioides</em>, <em>Pediculus</em>, <em>Penicillium</em>, <em>Phaeoacremonium</em>, <em>Phaeomoniella</em>, <em>Phialophora</em>, <em>Phlebotomus</em>, <em>Phoma</em>, <em>Pichia</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Pneumocystis</em>, <em>Pseudallescheria</em>, <em>Pseudoscopulariopsis</em>, <em>Pseudoterranova</em>, <em>Pulex</em>, <em>Purpureocillium</em>, <em>Quambalaria</em>, <em>Rhinocladiella</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Saccharomyces</em>, <em>Saksenaea</em>, <em>Saprochaete</em>, <em>Sarcoptes</em>, <em>Scedosporium</em>, <em>Schistosoma</em>, <em>Schizosaccharomyces</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Spirometra</em>, <em>Sporobolomyces</em>, <em>Sporopachydermia</em>, <em>Sporothrix</em>, <em>Sporotrichum</em>, <em>Stachybotrys</em>, <em>Strongyloides</em>, <em>Syncephalastrum</em>, <em>Syngamus</em>, <em>Taenia</em>, <em>Talaromyces</em>, <em>Teleomorph</em>, <em>Toxocara</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>Ulocladium</em>, <em>Ustilago</em>, <em>Verticillium</em>, <em>Wallemia</em>, <em>Wangiella</em>, <em>Wickerhamomyces</em>, <em>Wuchereria</em>, <em>Yarrowia</em>, or <em>Zygosaccharomyces</em>;</p></li>
|
||||
<li><p>Any <em>non-bacterial</em> genus, species or subspecies of which the genus is present in the following list, has <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set: <em>Absidia</em>, <em>Acanthamoeba</em>, <em>Acremonium</em>, <em>Actinomucor</em>, <em>Aedes</em>, <em>Alternaria</em>, <em>Amoeba</em>, <em>Ancylostoma</em>, <em>Angiostrongylus</em>, <em>Anisakis</em>, <em>Anopheles</em>, <em>Apophysomyces</em>, <em>Arthroderma</em>, <em>Aspergillus</em>, <em>Aureobasidium</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Bipolaris</em>, <em>Blastobotrys</em>, <em>Blastocystis</em>, <em>Blastomyces</em>, <em>Candida</em>, <em>Capillaria</em>, <em>Chaetomium</em>, <em>Chilomastix</em>, <em>Chrysonilia</em>, <em>Chrysosporium</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Clavispora</em>, <em>Coccidioides</em>, <em>Cokeromyces</em>, <em>Conidiobolus</em>, <em>Coniochaeta</em>, <em>Contracaecum</em>, <em>Cordylobia</em>, <em>Cryptococcus</em>, <em>Cryptosporidium</em>, <em>Cunninghamella</em>, <em>Curvularia</em>, <em>Cyberlindnera</em>, <em>Debaryozyma</em>, <em>Demodex</em>, <em>Dermatobia</em>, <em>Dientamoeba</em>, <em>Diphyllobothrium</em>, <em>Dirofilaria</em>, <em>Echinostoma</em>, <em>Entamoeba</em>, <em>Enterobius</em>, <em>Epidermophyton</em>, <em>Exidia</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Fasciola</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Geotrichum</em>, <em>Giardia</em>, <em>Graphium</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Hansenula</em>, <em>Hendersonula</em>, <em>Heterophyes</em>, <em>Histomonas</em>, <em>Histoplasma</em>, <em>Hortaea</em>, <em>Hymenolepis</em>, <em>Hypomyces</em>, <em>Hysterothylacium</em>, <em>Kloeckera</em>, <em>Kluyveromyces</em>, <em>Kodamaea</em>, <em>Lacazia</em>, <em>Leishmania</em>, <em>Lichtheimia</em>, <em>Lodderomyces</em>, <em>Lomentospora</em>, <em>Madurella</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Metagonimus</em>, <em>Meyerozyma</em>, <em>Microascus</em>, <em>Microsporidium</em>, <em>Microsporum</em>, <em>Millerozyma</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Nannizzia</em>, <em>Necator</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oesophagostomum</em>, <em>Oidiodendron</em>, <em>Opisthorchis</em>, <em>Paecilomyces</em>, <em>Paracoccidioides</em>, <em>Pediculus</em>, <em>Penicillium</em>, <em>Phaeoacremonium</em>, <em>Phaeomoniella</em>, <em>Phialophora</em>, <em>Phlebotomus</em>, <em>Phoma</em>, <em>Pichia</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Plasmodium</em>, <em>Pneumocystis</em>, <em>Pseudallescheria</em>, <em>Pseudoscopulariopsis</em>, <em>Pseudoterranova</em>, <em>Pulex</em>, <em>Purpureocillium</em>, <em>Quambalaria</em>, <em>Rhinocladiella</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Saccharomyces</em>, <em>Saksenaea</em>, <em>Saprochaete</em>, <em>Sarcoptes</em>, <em>Scedosporium</em>, <em>Schistosoma</em>, <em>Schizophyllum</em>, <em>Schizosaccharomyces</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Spirometra</em>, <em>Sporobolomyces</em>, <em>Sporopachydermia</em>, <em>Sporothrix</em>, <em>Sporotrichum</em>, <em>Stachybotrys</em>, <em>Strongyloides</em>, <em>Syncephalastrum</em>, <em>Syngamus</em>, <em>Taenia</em>, <em>Talaromyces</em>, <em>Teleomorph</em>, <em>Toxocara</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>Ulocladium</em>, <em>Ustilago</em>, <em>Verticillium</em>, <em>Wallemia</em>, <em>Wangiella</em>, <em>Wickerhamomyces</em>, <em>Wuchereria</em>, <em>Yarrowia</em>, or <em>Zygosaccharomyces</em>;</p></li>
|
||||
<li><p>All other records have <code>prevalence = 2.0</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
|
||||
</ul><p>When calculating the matching score, 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> (\(m = 0.381\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
|
||||
|
||||
Reference in New Issue
Block a user