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(v0.9.0.9014) Machine reading guidelines

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dr. M.S. (Matthijs) Berends
2020-01-27 11:05:39 +01:00
parent 423d1d3c41
commit 9a3891efe4
21 changed files with 14042 additions and 36 deletions
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docs/news/index.html
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@ -84,7 +84,7 @@
</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">0.9.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9014</span>
</span>
</div>
@ -231,31 +231,36 @@
</div>
<div id="amr-0-9-0-9013" class="section level1">
<div id="amr-0-9-0-9014" class="section level1">
<h1 class="page-header">
<a href="#amr-0-9-0-9013" class="anchor"></a>AMR 0.9.0.9013<small> Unreleased </small>
<a href="#amr-0-9-0-9014" class="anchor"></a>AMR 0.9.0.9014<small> Unreleased </small>
</h1>
<div id="last-updated-26-jan-2020" class="section level2">
<div id="last-updated-27-jan-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-26-jan-2020" class="anchor"></a><small>Last updated: 26-Jan-2020</small>
<a href="#last-updated-27-jan-2020" class="anchor"></a><small>Last updated: 27-Jan-2020</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h3>
<ul>
<li>
<p>Support for LOINC codes in the <code>antibiotics</code> data set. Use <code><a href="../reference/ab_property.html">ab_loinc()</a></code> to retrieve LOINC codes, or use LOINC code for input in any <code>ab_*</code> function:</p>
<p>Support for LOINC codes in the <code>antibiotics</code> data set. Use <code><a href="../reference/ab_property.html">ab_loinc()</a></code> to retrieve LOINC codes, or use a LOINC code for input in any <code>ab_*</code> function:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="../reference/ab_property.html">ab_loinc</a></span>(<span class="st">"ampicillin"</span>)</a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="co">#&gt; [1] "21066-6" "3355-5" "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"</span></a>
<a class="sourceLine" id="cb1-3" data-line-number="3"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="st">"21066-6"</span>)</a>
<a class="sourceLine" id="cb1-4" data-line-number="4"><span class="co">#&gt; [1] "Ampicillin"</span></a></code></pre></div>
<a class="sourceLine" id="cb1-4" data-line-number="4"><span class="co">#&gt; [1] "Ampicillin"</span></a>
<a class="sourceLine" id="cb1-5" data-line-number="5"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="st">"21066-6"</span>)</a>
<a class="sourceLine" id="cb1-6" data-line-number="6"><span class="co">#&gt; [1] "J01CA01"</span></a></code></pre></div>
</li>
<li><p>The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2019 to translate MIC and disk diffusion values to R/SI: <a href="https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt" class="uri">https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This <strong>allows machine reading these guidelines</strong>, which is currently almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.</p></li>
</ul>
</div>
<div id="changes" class="section level3">
<h3 class="hasAnchor">
<a href="#changes" class="anchor"></a>Changes</h3>
<ul>
<li>Bugfix for some WHONET microorganism codes that were not interpreted correctly when using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>
</li>
<li>Speed improvement for <code><a href="../reference/as.mo.html">as.mo()</a></code> (and consequently all <code>mo_*</code> functions that use <code><a href="../reference/as.mo.html">as.mo()</a></code> internally), especially for the <em>G. species</em> format (G for genus), like <em>E. coli</em> and <em>K penumoniae</em>
</li>
<li>Better support for determination of <em>Salmonella</em> biovars</li>
@ -1441,7 +1446,7 @@ 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-0-9-0-9013">0.9.0.9013</a></li>
<li><a href="#amr-0-9-0-9014">0.9.0.9014</a></li>
<li><a href="#amr-0-9-0">0.9.0</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>