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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="">2.1.1.9077</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9078</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="2.1.1.9077" id="amr-2119077">AMR 2.1.1.9077<a class="anchor" aria-label="anchor" href="#amr-2119077"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9078" id="amr-2119078">AMR 2.1.1.9078<a class="anchor" aria-label="anchor" href="#amr-2119078"></a></h2>
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p>
<div class="section level5">
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9077">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9077"></a></h5>
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9078">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9078"></a></h5>
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
</div>
<div class="section level3">
<h3 id="breaking-2-1-1-9077">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9077"></a></h3>
<h3 id="breaking-2-1-1-9078">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9078"></a></h3>
<ul><li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over a year ago</li>
</ul></div>
<div class="section level3">
<h3 id="new-2-1-1-9077">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9077"></a></h3>
<h3 id="new-2-1-1-9078">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9078"></a></h3>
<ul><li>One Health implementation
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for animal breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
<li>The <code>clinical_breakpoints</code> data set contains all these breakpoints, and can be downloaded on our <a href="https://msberends.github.io/AMR/articles/datasets.html">download page</a>.</li>
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</ul></li>
</ul></div>
<div class="section level3">
<h3 id="changed-2-1-1-9077">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9077"></a></h3>
<h3 id="changed-2-1-1-9078">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9078"></a></h3>
<ul><li>SIR interpretation
<ul><li>It is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
<li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
<li>To get quantitative values, <code><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double()</a></code> on a <code>sir</code> object will return 1 for S, 2 for SDD/I, and 3 for R (NI will become <code>NA</code>). Other functions using <code>sir</code> classes (e.g., <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code>) are updated to reflect the change to contain NI and SDD.</li>
</ul></li>
<li>
<code><a href="../reference/antibiogram.html">antibiogram()</a></code> function
<ul><li>New argument <code>formatting_type</code> to set any of the 12 options for the formatting of all ‘cells’. This defaults to <code>10</code>, changing the output of antibiograms to cells with <code>5% (15/300)</code> instead of the previous standard of just <code>5</code>.</li>
<li>For this reason, <code>add_total_n</code> is now <code>FALSE</code> at default since the denominators are added to the cells</li>
<li>The <code>ab_transform</code> argument now defaults to <code>"name"</code>, displaying antibiotic column names instead of codes</li>
</ul></li>
<li>
<code>antibiotics</code> data set
<ul><li>Added “clindamycin inducible screening” as <code>CLI1</code>. Since clindamycin is a lincosamide, the antibiotic selector <code><a href="../reference/antibiotic_class_selectors.html">lincosamides()</a></code> now contains the argument <code>only_treatable = TRUE</code> (similar to other antibiotic selectors that contain non-treatable drugs)</li>
<li>Added Amorolfine (<code>AMO</code>, D01AE16), which is now also part of the <code><a href="../reference/antibiotic_class_selectors.html">antifungals()</a></code> selector</li>
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<li>Fixed a bug for when <code><a href="../reference/antibiogram.html">antibiogram()</a></code> returns an empty data set</li>
</ul></div>
<div class="section level3">
<h3 id="other-2-1-1-9077">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9077"></a></h3>
<h3 id="other-2-1-1-9078">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9078"></a></h3>
<ul><li>Greatly updated and expanded documentation</li>
<li>Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
</ul></div>