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2022-11-28 18:48:45 +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="">1.8.2.9053</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9054</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="1.8.2.9053" id="amr-1829053">AMR 1.8.2.9053<a class="anchor" aria-label="anchor" href="#amr-1829053"></a></h2>
<h2 class="pkg-version" data-toc-text="1.8.2.9054" id="amr-1829054">AMR 1.8.2.9054<a class="anchor" aria-label="anchor" href="#amr-1829054"></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-1-8-2-9053">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9053"></a></h4>
<h4 id="breaking-1-8-2-9054">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9054"></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>
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<li>Using <code>units</code> in <code>ab_ddd(..., units = "...")</code> had been deprecated and is now not supported anymore. Use <code><a href="../reference/ab_property.html">ab_ddd_units()</a></code> instead.</li>
</ul></div>
<div class="section level4">
<h4 id="new-1-8-2-9053">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9053"></a></h4>
<h4 id="new-1-8-2-9054">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9054"></a></h4>
<ul><li>
<strong>EUCAST 2022 and CLSI 2022 guidelines</strong> have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 (v12.0) is now the new default guideline for all MIC and disks diffusion interpretations, and for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> to apply EUCAST Expert Rules.</li>
<li>Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. We are very grateful for the valuable input by our colleagues from other countries. The <code>AMR</code> package is now available in 16 languages. The automatic language determination will give a note at start-up on systems in supported languages.</li>
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</li>
</ul></div>
<div class="section level4">
<h4 id="changed-1-8-2-9053">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9053"></a></h4>
<h4 id="changed-1-8-2-9054">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9054"></a></h4>
<ul><li>Fixes and changes for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>:
<ul><li>On certain EUCAST breakpoints for MIC values</li>
<li>On <code>NA</code> values (e.g. <code>as.rsi(as.disk(NA), ...)</code>)</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>Cleaning columns with <code><a href="../reference/as.rsi.html">as.rsi()</a></code>, <code><a href="../reference/as.mic.html">as.mic()</a></code>, or <code><a href="../reference/as.disk.html">as.disk()</a></code> will now show the column name in the warning for invalid results</li>
</ul></div>
<div class="section level4">
<h4 id="other-1-8-2-9053">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9053"></a></h4>
<h4 id="other-1-8-2-9054">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9054"></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>