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(v1.3.0.9014) as.mo() speed improvement

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dr. M.S. (Matthijs) Berends
2020-09-03 12:31:48 +02:00
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Transform to microorganism ID — as.mo • AMR (for R)</title>
<title>Transform input to a microorganism ID — as.mo • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Transform to microorganism ID — as.mo" />
<meta property="og:title" content="Transform input to a microorganism ID — as.mo" />
<meta property="og:description" content="Use this function to determine a valid microorganism ID (mo). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like &quot;Staphylococcus aureus&quot;), an abbreviated name (like &quot;S. aureus&quot;), an abbreviation known in the field (like &quot;MRSA&quot;), or just a genus. Please see Examples." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
</span>
</div>
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<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
</a>
</li>
<li>
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<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Transform to microorganism ID</h1>
<h1>Transform input to a microorganism ID</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mo.R'><code>R/mo.R</code></a></small>
<div class="hidden name"><code>as.mo.Rd</code></div>
</div>
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Lancefield = <span class='fl'>FALSE</span>,
allow_uncertain = <span class='fl'>TRUE</span>,
reference_df = <span class='fu'><a href='mo_source.html'>get_mo_source</a></span>(),
ignore_pattern = <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"AMR_ignore_pattern"</span>),
<span class='kw'>...</span>
)
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<th>reference_df</th>
<td><p>a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> to be used for extra reference when translating <code>x</code> to a valid <code>mo</code>. See <code><a href='mo_source.html'>set_mo_source()</a></code> and <code><a href='mo_source.html'>get_mo_source()</a></code> to automate the usage of your own codes (e.g. used in your analysis or organisation).</p></td>
</tr>
<tr>
<th>ignore_pattern</th>
<td><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><a href='https://rdrr.io/r/base/options.html'>options(AMR_ignore_pattern = "(not reported|contaminated flora)")</a></code>.</p></td>
</tr>
<tr>
<th>...</th>
<td><p>other parameters passed on to functions</p></td>
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<h3>General info</h3>
<p>A microorganism ID from this package (class: <code>mo</code>) typically looks like these examples:</p><pre> Code Full name
<p>A microorganism ID from this package (class: <code>mo</code>) is human readable and typically looks like these examples:</p><pre> Code Full name
--------------- --------------------------------------
B_KLBSL Klebsiella
B_KLBSL_PNMN Klebsiella pneumoniae
B_KLBSL_PNMN_RHNS Klebsiella pneumoniae rhinoscleromatis
| | | |
| | | |
| | | ---&gt; subspecies, a 4-5 letter acronym
| | ----&gt; species, a 4-5 letter acronym
| ----&gt; genus, a 5-7 letter acronym
----&gt; taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
| | | \---&gt; subspecies, a 4-5 letter acronym
| | \----&gt; species, a 4-5 letter acronym
| \----&gt; genus, a 5-7 letter acronym
\----&gt; taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
C (Chromista), F (Fungi), P (Protozoa)
</pre>