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Built site for AMR: 1.8.2.9037@3d9faf8

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2022-10-29 17:07:26 +00:00
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9035</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="1.8.2.9035" id="amr-1829035">AMR 1.8.2.9035<a class="anchor" aria-label="anchor" href="#amr-1829035"></a></h2>
<h2 class="pkg-version" data-toc-text="1.8.2.9037" id="amr-1829037">AMR 1.8.2.9037<a class="anchor" aria-label="anchor" href="#amr-1829037"></a></h2>
<p>This version will eventually become v2.0! We’re happy to reach a new major milestone soon!</p>
<div class="section level4">
<h4 id="breaking-1-8-2-9035">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9035"></a></h4>
<h4 id="breaking-1-8-2-9037">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9037"></a></h4>
<ul><li>Removed all species of the taxonomic kingdom Chromista from the package. This was done for multiple reasons:
<ul><li>CRAN allows packages to be around 5 MB maximum, some packages are exempted but this package is not one of them</li>
<li>Chromista are not relevant when it comes to antimicrobial resistance, thus lacking the primary scope of this package</li>
@ -143,7 +143,7 @@
<li>Removal of interpretation guidelines older than 10 years, the oldest now included guidelines of EUCAST and CLSI are from 2013</li>
</ul></div>
<div class="section level4">
<h4 id="new-1-8-2-9035">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9035"></a></h4>
<h4 id="new-1-8-2-9037">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9037"></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>
<li>All new algorithm for <code><a href="../reference/as.mo.html">as.mo()</a></code> (and thus all <code>mo_*()</code> functions) while still following our original set-up as described in our paper (DOI 10.18637/jss.v104.i03).
<ul><li>A new argument <code>keep_synonyms</code> allows to <em>not</em> correct for updated taxonomy, in favour of the now deleted argument <code>allow_uncertain</code>
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<li>Support for antimicrobial interpretation of anaerobic bacteria, by adding a ‘placeholder’ code <code>B_ANAER</code> to the <code>microorganisms</code> data set and add the breakpoints of anaerobics to the <code>rsi_interpretation</code> data set, which is used by <code><a href="../reference/as.rsi.html">as.rsi()</a></code> when interpreting MIC and disk diffusion values</li>
</ul></div>
<div class="section level4">
<h4 id="changed-1-8-2-9035">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9035"></a></h4>
<h4 id="changed-1-8-2-9037">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9037"></a></h4>
<ul><li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</li>
<li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on <code>NA</code> values (e.g. <code>as.rsi(as.disk(NA), ...)</code>)</li>
<li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on drug-drug combinations with multiple breakpoints for different body sites</li>
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<li>Antimicrobial interpretation ‘SDD’ (susceptible dose-dependent, coined by CLSI) will be interpreted as ‘I’ to comply with EUCAST’s ‘I’ in <code><a href="../reference/as.rsi.html">as.rsi()</a></code>
</li>
<li>Fix for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> in case of higher taxonomic ranks (order, class, phylum)</li>
<li>Updated DDDs and ATCs for the <code>antibiotics</code> data set - ATC codes J04AB06 (enviomycin) and D06AX14 (ozenoxacin) were added</li>
</ul></div>
<div class="section level4">
<h4 id="other-1-8-2-9035">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9035"></a></h4>
<h4 id="other-1-8-2-9037">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9037"></a></h4>
<ul><li>New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions</li>
<li>Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, and Jonas Salm as contributors, to thank them for their valuable input</li>
<li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>