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(v1.5.0.9008) Internal data sets to pkg, speed for auto col determination

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dr. M.S. (Matthijs) Berends
2021-01-22 10:20:41 +01:00
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commit 1ba44776a1
87 changed files with 408 additions and 292 deletions
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docs/news/index.html
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@ -81,7 +81,7 @@
</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">1.5.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
</span>
</div>
@ -236,13 +236,13 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1509007" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0.9007">
<a href="#amr-1509007" class="anchor"></a>AMR 1.5.0.9007<small> Unreleased </small>
<div id="amr-1509008" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0.9008">
<a href="#amr-1509008" class="anchor"></a>AMR 1.5.0.9008<small> Unreleased </small>
</h1>
<div id="last-updated-18-january-2021" class="section level2">
<div id="last-updated-22-january-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-18-january-2021" class="anchor"></a><small>Last updated: 18 January 2021</small>
<a href="#last-updated-22-january-2021" class="anchor"></a><small>Last updated: 22 January 2021</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
@ -285,7 +285,9 @@
</li>
<li>Added Pretomanid (PMD, J04AK08) to the <code>antibiotics</code> data set</li>
<li>WHONET code <code>"PNV"</code> will now correctly be interpreted as <code>PHN</code>, the antibiotic code for phenoxymethylpenicillin (‘peni V’)</li>
<li>Fix for verbose output of <code><a href="../reference/mdro.html">mdro(..., verbose = TRUE)</a></code> for German guideline (3MGRN and 4MGRN) and <em>P. aeruginosa</em> in Dutch guideline (BRMO)</li>
<li>Fix for verbose output of <code><a href="../reference/mdro.html">mdro(..., verbose = TRUE)</a></code> for German guideline (3MGRN and 4MGRN) and Dutch guideline (BRMO, only <em>P. aeruginosa</em>)</li>
<li>
<code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> now returns <code>FALSE</code> immediately if the input does not contain any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.</li>
</ul>
</div>
<div id="other" class="section level3">
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<a href="#other" class="anchor"></a>Other</h3>
<ul>
<li>Big documentation updates</li>
<li>Loading the package (i.e., <code><a href="https://msberends.github.io/AMR/">library(AMR)</a></code>) now is ~50 times faster than before</li>
</ul>
</div>
</div>