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(v0.9.0.9020) as.mo() improvement

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dr. M.S. (Matthijs) Berends
2020-02-09 22:04:29 +01:00
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docs/reference/as.mo.html
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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">0.9.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9020</span>
</span>
</div>
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</pre>
<p>Values that cannot be coered will be considered 'unknown' and will get the MO code <code>UNKNOWN</code>.</p>
<p>Use the <code><a href='mo_property.html'>mo_property_*</a></code> functions to get properties based on the returned code, see Examples.</p>
<p>Use the <code><a href='mo_property.html'>mo_*</a></code> functions to get properties based on the returned code, see Examples.</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>
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<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 highly prevalent microorganism found in humans) will return the microbial ID of <em>Escherichia coli</em> and not <em>Entamoeba coli</em> (a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
<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>
<h3>Coping with uncertain results</h3>