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(v0.7.0.9005) ab algorithm update

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dr. M.S. (Matthijs) Berends
2019-06-11 14:18:25 +02:00
parent f6c47c8c88
commit 8f674e19bb
36 changed files with 274 additions and 248 deletions
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docs/news/index.html
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@ -78,7 +78,7 @@
</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="Latest development version">0.7.0.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9005</span>
</span>
</div>
@ -232,9 +232,9 @@
</div>
<div id="amr-0709004" class="section level1">
<div id="amr-0709005" class="section level1">
<h1 class="page-header">
<a href="#amr-0709004" class="anchor"></a>AMR 0.7.0.9004<small> Unreleased </small>
<a href="#amr-0709005" class="anchor"></a>AMR 0.7.0.9005<small> Unreleased </small>
</h1>
<div id="new" class="section level4">
<h4 class="hasAnchor">
@ -247,6 +247,7 @@
<a class="sourceLine" id="cb1-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"UPEC"</span>)</a>
<a class="sourceLine" id="cb1-4" title="4"><span class="co"># "Escherichia coli"</span></a></code></pre></div>
</li>
<li><p>Function <code><a href="../reference/mo_property.html">mo_info()</a></code> as an analogy to <code><a href="../reference/ab_property.html">ab_info()</a></code>. The <code><a href="../reference/mo_property.html">mo_info()</a></code> prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism</p></li>
</ul>
</div>
<div id="changed" class="section level4">
@ -256,6 +257,7 @@
<li>Fixed bug in translation of microorganism names</li>
<li>Fixed bug in determining taxonomic kingdoms</li>
<li>Algorithm improvements for <code><a href="../reference/as.ab.html">as.ab()</a></code> and <code><a href="../reference/as.mo.html">as.mo()</a></code> to understand even more severely misspelled input</li>
<li>Function <code><a href="../reference/as.ab.html">as.ab()</a></code> now allows spaces for coercing antibiotics names</li>
<li>Added <code>ggplot2</code> methods for automatically determining the scale type of classes <code>mo</code> and <code>ab</code>
</li>
<li>Added names of object in the header in frequency tables, even when using pipes</li>
@ -263,6 +265,9 @@
<li>Fixed a bug where setting an antibiotic would not work for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>
</li>
<li>Fixed a EUCAST rule for Staphylococci, where amikacin resistance would not be inferred from tobramycin</li>
<li>Removed <code>latest_annual_release</code> from the <code><a href="../reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> function</li>
<li>Removed antibiotic code <code>PVM1</code> from the <code>antibiotics</code> data set as this was a duplicate of <code>PME</code>
</li>
</ul>
</div>
<div id="other" class="section level4">
@ -1101,7 +1106,7 @@ 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-0709004">0.7.0.9004</a></li>
<li><a href="#amr-0709005">0.7.0.9005</a></li>
<li><a href="#amr-070">0.7.0</a></li>
<li><a href="#amr-061">0.6.1</a></li>
<li><a href="#amr-060">0.6.0</a></li>