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mirror of https://github.com/msberends/AMR.git synced 2025-07-09 03:22:00 +02:00

eucast rules fix, 1st isolate fix, website update

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2018-12-31 01:48:53 +01:00
parent 469b145d8c
commit 2e4d703338
51 changed files with 1473 additions and 1760 deletions

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<div class="ref-description">
<p>A data set containing the complete microbial taxonomy of the kingdoms Bacteria, Fungi and Protozoa. MO codes can be looked up using <code>as.mo</code>.</p>
<p>A data set containing the complete microbial taxonomy of the kingdoms Bacteria, Fungi and Protozoa. MO codes can be looked up using <code><a href='as.mo.html'>as.mo</a></code>.</p>
</div>
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<dt><code>subkingdom</code></dt><dd><p>Taxonomic subkingdom of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>kingdom</code></dt><dd><p>Taxonomic kingdom of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>gramstain</code></dt><dd><p>Gram of microorganism, like <code>"Gram negative"</code></p></dd>
<dt><code>prevalence</code></dt><dd><p>An integer based on estimated prevalence of the microorganism in humans. Used internally by <code>as.mo</code>, otherwise quite meaningless. It has a value of 25 for manually added items and a value of 1000 for all unprevalent microorganisms whose genus was somewhere in the top 250 (with another species).</p></dd>
<dt><code>prevalence</code></dt><dd><p>An integer based on estimated prevalence of the microorganism in humans. Used internally by <code><a href='as.mo.html'>as.mo</a></code>, otherwise quite meaningless. It has a value of 25 for manually added items and a value of 1000 for all unprevalent microorganisms whose genus was somewhere in the top 250 (with another species).</p></dd>
<dt><code>ref</code></dt><dd><p>Author(s) and year of concerning publication as found in ITIS, see Source</p></dd>
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<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code>as.mo</code> <code>mo_property</code> <code>microorganisms.umcg</code></p></div>
<div class='dont-index'><p><code><a href='as.mo.html'>as.mo</a></code> <code><a href='mo_property.html'>mo_property</a></code> <code><a href='microorganisms.umcg.html'>microorganisms.umcg</a></code></p></div>
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