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(v0.8.0.9007) Enterobacterales order

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2019-10-30 23:02:50 +01:00
parent 7ff2ad8188
commit 09c4b04cd0
22 changed files with 156 additions and 55 deletions

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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">0.8.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9007</span>
</span>
</div>
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</div>
<div id="amr-0-8-0-9006" class="section level1">
<div id="amr-0-8-0-9007" class="section level1">
<h1 class="page-header">
<a href="#amr-0-8-0-9006" class="anchor"></a>AMR 0.8.0.9006<small> Unreleased </small>
<a href="#amr-0-8-0-9007" class="anchor"></a>AMR 0.8.0.9007<small> Unreleased </small>
</h1>
<p><small>Last updated: 27-Oct-2019</small></p>
<p><small>Last updated: 30-Oct-2019</small></p>
<div id="new" class="section level3">
<h3 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h3>
@ -250,8 +250,7 @@
<ul>
<li>When running <code><a href="../reference/as.rsi.html">as.rsi()</a></code> over a data set, it will now print the guideline that will be used if it is not specified by the user</li>
<li>Fix for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>: <em>Stenotrophomonas maltophilia</em> not interpreted “R” to ceftazidime anymore (following EUCAST v3.1)</li>
<li>Fix in taxonomic info for genera that are in multiple kingdoms, like <em>Proteus</em>
</li>
<li>Adopted Adeolu <em>et al.</em> (2016), <a href="https://www.ncbi.nlm.nih.gov/pubmed/27620848">PMID 27620848</a> for the <code>microorganisms</code> data set, which means that the new order Enterobacterales now consists of a part of the existing family <em>Enterobacteriaceae</em>, but that this family has been split into other families as well (like <em>Morganellaceae</em> and <em>Yersiniaceae</em>). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations with <code><a href="../reference/mdro.html">mdro()</a></code> will now use the Enterobacterales order for all guidelines before 2016.</li>
<li>Fix for interpreting MIC values with <code><a href="../reference/as.rsi.html">as.rsi()</a></code> where the input is <code>NA</code>
</li>
<li>Added “imi” as allowed abbreviation for Imipenem</li>
@ -1321,7 +1320,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-8-0-9006">0.8.0.9006</a></li>
<li><a href="#amr-0-8-0-9007">0.8.0.9007</a></li>
<li><a href="#amr-0-8-0">0.8.0</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li>