P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 23:21:56 +02:00
Code Releases Activity

Built site for AMR: 2.1.1.9013@f2d245b

Browse Source
This commit is contained in:
github-actions
2024-03-03 22:05:59 +00:00
parent ab367558fe
commit 0b8e89c845
105 changed files with 341 additions and 327 deletions
Download Patch File Download Diff File Expand all files Collapse all files

26
reference/as.mo.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9012</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9013</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">
@ -253,18 +253,18 @@
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<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>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a> B_KLBSL_PNMN Klebsiella pneumoniae</span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a> B_KLBSL_PNMN_RHNS Klebsiella pneumoniae rhinoscleromatis</span>
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a> <span class="sc">|</span> <span class="er">|</span> <span class="er">|</span> <span class="er">|</span></span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a> <span class="er">|</span> <span class="er">|</span> <span class="er">|</span> <span class="er">|</span></span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a> <span class="er">|</span> <span class="er">|</span> <span class="er">|</span> \<span class="sc">--</span><span class="ot">-&gt;</span> subspecies, a <span class="dv">3-5</span> letter acronym</span>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a> <span class="sc">|</span> <span class="er">|</span> \<span class="sc">---</span><span class="ot">-&gt;</span> species, a <span class="dv">3-6</span> letter acronym</span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a> <span class="sc">|</span> \<span class="sc">---</span><span class="ot">-&gt;</span> genus, a <span class="dv">4-8</span> letter acronym</span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a> \<span class="sc">---</span><span class="ot">-&gt;</span> taxonomic kingdom<span class="sc">:</span> <span class="fu">A</span> (Archaea), <span class="fu">AN</span> (Animalia), <span class="fu">B</span> (Bacteria),</span>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">F</span> (Fungi), <span class="fu">PL</span> (Plantae), <span class="fu">P</span> (Protozoa)</span></code></pre><p></p></div>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a> Code Full name</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a> <span class="sc">---------------</span> <span class="sc">--------------------------------------</span></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a> B_KLBSL Klebsiella</span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a> B_KLBSL_PNMN Klebsiella pneumoniae</span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a> B_KLBSL_PNMN_RHNS Klebsiella pneumoniae rhinoscleromatis</span>
<span id="cb1-6"><a href="#cb1-6" 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" 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" tabindex="-1"></a> <span class="er">|</span> <span class="er">|</span> <span class="er">|</span> \<span class="sc">--</span><span class="ot">-&gt;</span> subspecies, a <span class="dv">3-5</span> letter acronym</span>
<span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a> <span class="sc">|</span> <span class="er">|</span> \<span class="sc">---</span><span class="ot">-&gt;</span> species, a <span class="dv">3-6</span> letter acronym</span>
<span id="cb1-10"><a href="#cb1-10" tabindex="-1"></a> <span class="sc">|</span> \<span class="sc">---</span><span class="ot">-&gt;</span> genus, a <span class="dv">4-8</span> letter acronym</span>
<span id="cb1-11"><a href="#cb1-11" tabindex="-1"></a> \<span class="sc">---</span><span class="ot">-&gt;</span> taxonomic kingdom<span class="sc">:</span> <span class="fu">A</span> (Archaea), <span class="fu">AN</span> (Animalia), <span class="fu">B</span> (Bacteria),</span>
<span id="cb1-12"><a href="#cb1-12" 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 <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.</p>