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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="">2.1.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9033</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="2.1.1.9032" id="amr-2119032">AMR 2.1.1.9032<a class="anchor" aria-label="anchor" href="#amr-2119032"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9033" id="amr-2119033">AMR 2.1.1.9033<a class="anchor" aria-label="anchor" href="#amr-2119033"></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!)</em></p>
<div class="section level5">
<h5 id="a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9032">A New Milestone: One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9032"></a></h5>
<h5 id="a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9033">A New Milestone: One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9033"></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</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-2-1-1-9032">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9032"></a></h3>
<h3 id="breaking-2-1-1-9033">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9033"></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-2-1-1-9032">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9032"></a></h3>
<h3 id="new-2-1-1-9033">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9033"></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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<li>
<code><a href="../reference/as.sir.html">as.sir()</a></code> now returns additional factor levels “N” for non-interpretable and “SDD” for susceptible dose-dependent. Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and N.</li>
<li>The function group <code>scale_*_mic()</code>, namely: <code><a href="../reference/plot.html">scale_x_mic()</a></code>, <code><a href="../reference/plot.html">scale_y_mic()</a></code>, <code><a href="../reference/plot.html">scale_colour_mic()</a></code> and <code><a href="../reference/plot.html">scale_fill_mic()</a></code>. They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.</li>
<li>Function <code><a href="../reference/as.mic.html">limit_mic_range()</a></code>, which allows to limit MIC values to a manually set range. This is the powerhouse behind the <code>scale_*_mic()</code> functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.</li>
<li>Function <code><a href="../reference/mo_property.html">mo_group_members()</a></code> to retrieve the member microorganisms. For example, <code>mo_group_members("Strep group C")</code> returns a vector of all microorganisms that are in that group.</li>
<li>Function <code><a href="../reference/as.mic.html">rescale_mic()</a></code>, which allows to rescale MIC values to a manually set range. This is the powerhouse behind the <code>scale_*_mic()</code> functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.</li>
<li>Function <code><a href="../reference/mo_property.html">mo_group_members()</a></code> to retrieve the member microorganisms of a microorganism group. For example, <code>mo_group_members("Strep group C")</code> returns a vector of all microorganisms that are in that group.</li>
</ul></div>
<div class="section level3">
<h3 id="changed-2-1-1-9032">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9032"></a></h3>
<h3 id="changed-2-1-1-9033">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9033"></a></h3>
<ul><li>For SIR interpretation, it is now possible to use column names for argument <code>ab</code> and <code>mo</code>: <code>as.sir(..., ab = "column1", mo = "column2")</code>. This greatly improves the flexibility for users.</li>
<li>For MICs:
<ul><li>Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960)</li>
<li>Added new argument <code>keep_operators</code> to <code><a href="../reference/as.mic.html">as.mic()</a></code>. This can be <code>"all"</code> (default), <code>"none"</code>, or <code>"edges"</code>. This argument is also available in the new <code><a href="../reference/as.mic.html">limit_mic_range()</a></code> and <code>scale_*_mic()</code> functions.</li>
<li>Added new argument <code>keep_operators</code> to <code><a href="../reference/as.mic.html">as.mic()</a></code>. This can be <code>"all"</code> (default), <code>"none"</code>, or <code>"edges"</code>. This argument is also available in the new <code><a href="../reference/as.mic.html">rescale_mic()</a></code> and <code>scale_*_mic()</code> functions.</li>
<li>Comparisons of MIC values are now more strict. For example, <code>&gt;32</code> is higher than (and never equal to) <code>32</code>. Thus, <code>as.mic("&gt;32") == as.mic(32)</code> now returns <code>FALSE</code>, and <code>as.mic("&gt;32") &gt; as.mic(32)</code> now returns <code>TRUE</code>.</li>
</ul></li>
<li>Updated <code><a href="../reference/italicise_taxonomy.html">italicise_taxonomy()</a></code> to support HTML output</li>
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<li>Improved overall algorithm of <code><a href="../reference/as.ab.html">as.ab()</a></code> for better performance and accuracy</li>
</ul></div>
<div class="section level3">
<h3 id="other-2-1-1-9032">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9032"></a></h3>
<h3 id="other-2-1-1-9033">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9033"></a></h3>
<ul><li>Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
</ul></div>
</div>