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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="">2.1.1.9196</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9198</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="2.1.1.9196" id="amr-2119196">AMR 2.1.1.9196<a class="anchor" aria-label="anchor" href="#amr-2119196"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9198" id="amr-2119198">AMR 2.1.1.9198<a class="anchor" aria-label="anchor" href="#amr-2119198"></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-2-1-1-9196">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-2-1-1-9196"></a></h5>
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9198">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-2-1-1-9198"></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-2-1-1-9196">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9196"></a></h3>
<h3 id="breaking-2-1-1-9198">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9198"></a></h3>
<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>
<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>
</ul></div>
<div class="section level3">
<h3 id="new-2-1-1-9196">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9196"></a></h3>
<h3 id="new-2-1-1-9198">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9198"></a></h3>
<ul><li>
<strong>One Health implementation</strong>
<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>
<li>The CLSI VET09 guideline has been implemented to address cases where veterinary breakpoints are missing (only applies when <code>guideline</code> is set to CLSI)</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>
<li>The (new) <code>antimicrobials</code> data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well.</li>
<li>
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</ul></li>
</ul></div>
<div class="section level3">
<h3 id="changed-2-1-1-9196">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9196"></a></h3>
<h3 id="changed-2-1-1-9198">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9198"></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>
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</ul></li>
<li>
<code>antimicrobials</code> data set
<ul><li>Added agents used for screening, with an ID all ending with <code>-S</code>: benzylpenicillin screening test (<code>PEN-S</code>), beta-lactamase screening test (<code>BTL-S</code>), clindamycin inducible screening test (<code>CLI-S</code>), nalidixic acid screening test (<code>NAL-S</code>), norfloxacin screening test (<code>NOR-S</code>), oxacillin screening test (<code>OXA-S</code>), pefloxacin screening test (<code>PEF-S</code>), and tetracycline screening test (<code>TCY-S</code>). The ID of cefoxitin screening was renamed from <code>FOX1</code> to <code>FOX-S</code>, while the old code remains to work.</li>
<li>For this reason, the antimicrobial selectors <code><a href="../reference/antimicrobial_selectors.html">lincosamides()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">isoxazolylpenicillins()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">quinolones()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">fluoroquinolones()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">tetracyclines()</a></code> now contain the argument <code>only_treatable = TRUE</code> (similar to other antimicrobial selectors that contain non-treatable drugs)</li>
<ul><li>Added agents used for screening, with an ID all ending with <code>-S</code>: benzylpenicillin screening test (<code>PEN-S</code>), beta-lactamase screening test (<code>BTL-S</code>), cefotaxime screening test (<code>CTX-S</code>), clindamycin inducible screening test (<code>CLI-S</code>), nalidixic acid screening test (<code>NAL-S</code>), norfloxacin screening test (<code>NOR-S</code>), oxacillin screening test (<code>OXA-S</code>), pefloxacin screening test (<code>PEF-S</code>), and tetracycline screening test (<code>TCY-S</code>). The ID of cefoxitin screening was renamed from <code>FOX1</code> to <code>FOX-S</code>, while the old code remains to work.</li>
<li>For this reason, the antimicrobial selectors <code><a href="../reference/antimicrobial_selectors.html">cephalosporins()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">cephalosporins_3rd()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">lincosamides()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">isoxazolylpenicillins()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">quinolones()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">fluoroquinolones()</a></code>, and <code><a href="../reference/antimicrobial_selectors.html">tetracyclines()</a></code> now contain the argument <code>only_treatable = TRUE</code> (similar to other antimicrobial 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/antimicrobial_selectors.html">antifungals()</a></code> selector</li>
<li>Added efflux (<code>EFF</code>), to allow mapping to AMRFinderPlus</li>
<li>Added tigemonam (<code>TNM</code>), a monobactam</li>
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<li>Intermediate log2 levels used for MIC plotting are now more common values instead of following a strict dilution range</li>
</ul></li>
<li>
<code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> now has an argument <code>overwrite</code> (default: <code>TRUE</code>) to indicate whether non-<code>NA</code> values should be overwritten</li>
<code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> now has an argument <code>overwrite</code> (default: <code>FALSE</code>) to indicate whether non-<code>NA</code> values should be overwritten</li>
<li>Disks of 0 to 5 mm are now allowed, the newly allowed range for disk diffusion (<code><a href="../reference/as.disk.html">as.disk()</a></code>) is now between 0 and 50 mm</li>
<li>Updated <code><a href="../reference/italicise_taxonomy.html">italicise_taxonomy()</a></code> to support HTML output</li>
<li>
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<li>Added console colours support of <code>sir</code> class for Positron</li>
</ul></div>
<div class="section level3">
<h3 id="other-2-1-1-9196">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9196"></a></h3>
<h3 id="other-2-1-1-9198">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9198"></a></h3>
<ul><li>Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way</li>
<li>Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations</li>
<li>Greatly improved <code>vctrs</code> integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that functions such as <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/bind_rows.html" class="external-link">bind_rows()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/rowwise.html" class="external-link">rowwise()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/c_across.html" class="external-link">c_across()</a></code> are now supported for e.g. columns of class <code>mic</code>. Despite this, this <code>AMR</code> package is still zero-dependent on any other package, including <code>dplyr</code> and <code>vctrs</code>.</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>
</ul></div>
<div class="section level3">
<h3 id="older-versions-2-1-1-9196">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9196"></a></h3>
<h3 id="older-versions-2-1-1-9198">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9198"></a></h3>
<p>This changelog only contains changes from AMR v3.0 (March 2025) and later.</p>
<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>
<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>