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(v1.8.1.9011) update prevalence of some genera

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dr. M.S. (Matthijs) Berends
2022-06-03 12:43:25 +02:00
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commit 1b84564d36
35 changed files with 278 additions and 429 deletions
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@ -17,7 +17,7 @@
</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="Released version">1.8.1.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9011</span>
</span>
</div>
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</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="1.8.1.9010" id="amr-1819010">
<code>AMR</code> 1.8.1.9010<a class="anchor" aria-label="anchor" href="#amr-1819010"></a></h2>
<h2 class="page-header" data-toc-text="1.8.1.9011" id="amr-1819011">
<code>AMR</code> 1.8.1.9011<a class="anchor" aria-label="anchor" href="#amr-1819011"></a></h2>
<div class="section level3">
<h3 id="last-updated-may-1-8-1-9010"><small>Last updated: 16 May 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-may-1-8-1-9010"></a></h3>
<h3 id="last-updated-june-1-8-1-9011"><small>Last updated: 3 June 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-june-1-8-1-9011"></a></h3>
<div class="section level4">
<h4 id="new-1-8-1-9010">New<a class="anchor" aria-label="anchor" href="#new-1-8-1-9010"></a></h4>
<h4 id="new-1-8-1-9011">New<a class="anchor" aria-label="anchor" href="#new-1-8-1-9011"></a></h4>
<ul><li>EUCAST 2022 and CLSI 2022 guidelines have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.</li>
</ul></div>
<div class="section level4">
<h4 id="changed-1-8-1-9010">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9010"></a></h4>
<h4 id="changed-1-8-1-9011">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9011"></a></h4>
<ul><li>Fix for <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</li>
<li>Removed <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> for MIC values, since MIC are not integer values and running <code><a href="https://rdrr.io/r/base/table.html" class="external-link">table()</a></code> on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on <code>factor</code>s work)</li>
<li>
@ -176,6 +176,8 @@
<li>Fixes for reading in text files using <code><a href="../reference/mo_source.html">set_mo_source()</a></code>, which now also allows the source file to contain valid taxonomic names instead of only valid microorganism ID of this package</li>
<li>Using any <code>random_*()</code> function (such as <code><a href="../reference/random.html">random_mic()</a></code>) is now possible by directly calling the package without loading it first: <code>AMR::random_mic(10)</code>
</li>
<li>Changed value in column <code>prevalence</code> of the <code>microorganisms</code> data set from 3 to 2 for these genera: <em>Acholeplasma</em>, <em>Alistipes</em>, <em>Alloprevotella</em>, <em>Bergeyella</em>, <em>Borrelia</em>, <em>Brachyspira</em>, <em>Butyricimonas</em>, <em>Cetobacterium</em>, <em>Chlamydia</em>, <em>Chlamydophila</em>, <em>Deinococcus</em>, <em>Dysgonomonas</em>, <em>Elizabethkingia</em>, <em>Empedobacter</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Myroides</em>, <em>Odoribacter</em>, <em>Ornithobacterium</em>, <em>Parabacteroides</em>, <em>Pedobacter</em>, <em>Phocaeicola</em>, <em>Porphyromonas</em>, <em>Riemerella</em>, <em>Sphingobacterium</em>, <em>Streptobacillus</em>, <em>Tenacibaculum</em>, <em>Terrimonas</em>, <em>Victivallis</em>, <em>Wautersiella</em>, <em>Weeksella</em>
</li>
</ul></div>
</div>
</div>