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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9263</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
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<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>
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<div class="section level2">
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<h2 class="pkg-version" data-toc-text="2.1.1.9263" id="amr-2119263">AMR 2.1.1.9263<a class="anchor" aria-label="anchor" href="#amr-2119263"></a></h2>
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<h2 class="pkg-version" data-toc-text="2.1.1.9266" id="amr-2119266">AMR 2.1.1.9266<a class="anchor" aria-label="anchor" href="#amr-2119266"></a></h2>
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<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://amr-for-r.org/#get-this-package">the instructions here</a>.)</em></p>
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<div class="section level5">
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<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9263">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-2-1-1-9263"></a></h5>
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<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>
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</div>
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<div class="section level3">
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<h3 id="breaking-2-1-1-9263">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9263"></a></h3>
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<h3 id="tldr-2-1-1-9266">tl;dr<a class="anchor" aria-label="anchor" href="#tldr-2-1-1-9266"></a></h3>
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<ul><li>
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<strong>Scope Expansion</strong>: One Health support (Human + Veterinary + Environmental microbiology).</li>
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<li>
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<strong>Data Updates</strong>:
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<ul><li>
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<code>antibiotics</code> renamed to <code>antimicrobials</code>.</li>
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<li>Veterinary antimicrobials and WHOCC codes added.</li>
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<li>MycoBank fungal taxonomy integrated (+20,000 fungi).</li>
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</ul></li>
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<li>
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<strong>Breakpoints & Interpretations</strong>:
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<ul><li>CLSI/EUCAST 2024-2025 breakpoints added; EUCAST 2025 default.</li>
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<li>
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<code><a href="../reference/as.sir.html">as.sir()</a></code> supports NI/SDD levels; parallel computation enabled.</li>
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<li>Custom S/I/R/SDD/NI definitions allowed.</li>
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<li>Improved handling of capped MICs.</li>
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</ul></li>
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<li>
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<strong>New Tools & Functions</strong>:
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<ul><li>WISCA antibiogram support (<code><a href="../reference/antibiogram.html">antibiogram()</a></code>, <code><a href="../reference/antibiogram.html">wisca()</a></code>).</li>
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<li>New ggplot2 extensions: <code>scale_*_mic()</code>, <code>scale_*_sir()</code>, <code><a href="../reference/as.mic.html">rescale_mic()</a></code>.</li>
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<li>New utility functions: <code><a href="../reference/top_n_microorganisms.html">top_n_microorganisms()</a></code>, <code><a href="../reference/mo_property.html">mo_group_members()</a></code>, <code><a href="../reference/as.mic.html">mic_p50()</a></code>, <code><a href="../reference/as.mic.html">mic_p90()</a></code>.</li>
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</ul></li>
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<li>
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<strong>Predictive Modelling</strong>:
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<ul><li>Full tidymodels compatibility for antimicrobial selectors.</li>
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<li>Deprecated <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code> and <code><a href="../reference/resistance_predict.html">sir_predict()</a></code>.</li>
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</ul></li>
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<li>
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<strong>Python Compatibility</strong>: AMR R package now runs in Python.</li>
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<li>
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<strong>Selector Improvements</strong>:
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<ul><li>Added selectors (<code><a href="../reference/antimicrobial_selectors.html">isoxazolylpenicillins()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">monobactams()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">nitrofurans()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">phenicols()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">rifamycins()</a></code>, and <code><a href="../reference/antimicrobial_selectors.html">sulfonamides()</a></code>)</li>
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<li>Selectors renamed from <code>ab_*</code> to <code>amr_*</code>; old names deprecated.</li>
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</ul></li>
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<li>
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<strong>MIC/Disks Handling</strong>:
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<ul><li>MIC strict comparisons, added levels.</li>
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<li>Disk diffusion range expanded (0–50 mm).</li>
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</ul></li>
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<li>
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<strong>EUCAST Rules and MDROs</strong>:
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<ul><li>EUCAST v12–v15 rules implemented.</li>
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<li>Dutch MDRO 2024 guideline support in <code><a href="../reference/mdro.html">mdro()</a></code>.</li>
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</ul></li>
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<li>
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<strong>Infrastructure</strong>:
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<ul><li>New website: <a href="https://amr-for-r.org" class="uri">https://amr-for-r.org</a>.</li>
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<li>Improved <code>vctrs</code> integration for tidyverse workflows.</li>
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<li>Dropped SAS <code>.xpt</code> file support.</li>
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</ul></li>
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<li>
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<strong>Other Fixes & Enhancements</strong>:
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<ul><li>Faster microorganism identification.</li>
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<li>Improved antimicrobial and MIC handling.</li>
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<li>Extended documentation, additional contributors acknowledged.</li>
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</ul></li>
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</ul></div>
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<div class="section level3">
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<h3 id="full-changelog-2-1-1-9266">Full Changelog<a class="anchor" aria-label="anchor" href="#full-changelog-2-1-1-9266"></a></h3>
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<div class="section level4">
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<h4 id="breaking-2-1-1-9266">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9266"></a></h4>
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<ul><li>Dataset <code>antibiotics</code> has been renamed to <code>antimicrobials</code> as the data set contains more than just antibiotics. Using <code>antibiotics</code> will still work, but now returns a warning.</li>
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<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 two years ago.</li>
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<li>Functions <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code> and <code><a href="../reference/resistance_predict.html">sir_predict()</a></code> is now deprecated and will be removed in a future version. Use the <code>tidymodels</code> framework instead, for which we <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">wrote a basic introduction</a>.</li>
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</ul></div>
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<div class="section level3">
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<h3 id="new-2-1-1-9263">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9263"></a></h3>
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<div class="section level4">
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<h4 id="new-2-1-1-9266">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9266"></a></h4>
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<ul><li>
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<strong>One Health implementation</strong>
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<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary 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>
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<li>New functions <code><a href="../reference/as.mic.html">mic_p50()</a></code> and <code><a href="../reference/as.mic.html">mic_p90()</a></code> to retrieve the 50th and 90th percentile of MIC values.</li>
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</ul></li>
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</ul></div>
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<div class="section level3">
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<h3 id="changed-2-1-1-9263">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9263"></a></h3>
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<div class="section level4">
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<h4 id="changed-2-1-1-9266">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9266"></a></h4>
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<ul><li>SIR interpretation
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<ul><li>Support for parallel computing to greatly improve speed using the <code>parallel</code> package (part of base R). Use <code>as.sir(your_data, parallel = TRUE)</code> to run SIR interpretation using multiple cores.</li>
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<li>It is now possible to use column names for arguments <code>guideline</code>, <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>
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</ul></li>
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<li>Added console colours support of <code>sir</code> class for Positron</li>
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</ul></div>
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<div class="section level3">
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<h3 id="other-2-1-1-9263">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9263"></a></h3>
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<ul><li>New website domain: <a href="https://amr-for-r.org" class="uri">https://amr-for-r.org</a>! The old domain (<a href="http://amr-for-r.org" class="external-link uri">http://amr-for-r.org</a>) will remain to work.</li>
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<div class="section level4">
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<h4 id="other-2-1-1-9266">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9266"></a></h4>
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<ul><li>New website domain: <a href="https://amr-for-r.org" class="uri">https://amr-for-r.org</a>! The old domain (<a href="https://msberends.github.io/AMR/" class="external-link uri">https://msberends.github.io/AMR/</a>) will remain to work.</li>
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<li>Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way</li>
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<li>Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations</li>
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<li>Added Prof. Kathryn Holt, Dr. Jane Hawkey, and Dr. Natacha Couto as contributors for their many suggestions, ideas and bugfixes</li>
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<li>Greatly updated and expanded documentation</li>
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<li>Stopped support for SAS (<code>.xpt</code>) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.</li>
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</ul></div>
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</div>
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<div class="section level3">
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<h3 id="older-versions-2-1-1-9263">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9263"></a></h3>
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<h3 id="older-versions-2-1-1-9266">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9266"></a></h3>
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<p>This changelog only contains changes from AMR v3.0 (March 2025) and later.</p>
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<ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li>
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<li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li>
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