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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="">2.1.1.9092</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9093</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="2.1.1.9092" id="amr-2119092">AMR 2.1.1.9092<a class="anchor" aria-label="anchor" href="#amr-2119092"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9093" id="amr-2119093">AMR 2.1.1.9093<a class="anchor" aria-label="anchor" href="#amr-2119093"></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-2-1-1-9092">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-2-1-1-9092"></a></h5>
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9093">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-2-1-1-9093"></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-2-1-1-9092">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9092"></a></h3>
<h3 id="breaking-2-1-1-9093">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9093"></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-2-1-1-9092">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9092"></a></h3>
<h3 id="new-2-1-1-9093">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9093"></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>
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</ul></li>
</ul></div>
<div class="section level3">
<h3 id="changed-2-1-1-9092">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9092"></a></h3>
<h3 id="changed-2-1-1-9093">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9093"></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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<code><a href="../reference/custom_eucast_rules.html">custom_eucast_rules()</a></code> now supports multiple antibiotics and antibiotic groups to be affected by a single rule</li>
<li>
<code><a href="../reference/mo_property.html">mo_info()</a></code> now contains an extra element <code>rank</code> and <code>group_members</code> (with the contents of the new <code><a href="../reference/mo_property.html">mo_group_members()</a></code> function)</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>
<li>Updated all ATC codes from WHOCC</li>
<li>Updated all antibiotic DDDs from WHOCC</li>
<li>Added over 1,500 trade names for antibiotics</li>
<li>Fix for using a manual value for <code>mo_transform</code> in <code><a href="../reference/antibiogram.html">antibiogram()</a></code>
</li>
<li>Fix for mapping ‘high level’ antibiotics in <code><a href="../reference/as.ab.html">as.ab()</a></code> (amphotericin B-high, gentamicin-high, kanamycin-high, streptomycin-high, tobramycin-high)</li>
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<li>Genera from the World Health Organization’s (WHO) Priority Pathogen List now have the highest prevalence</li>
</ul></li>
<li>Fixed a bug for when <code><a href="../reference/antibiogram.html">antibiogram()</a></code> returns an empty data set</li>
<li>Fixed a bug for <code><a href="../reference/proportion.html">sir_confidence_interval()</a></code> when there are no isolates available</li>
<li>Updated the prevalence calculation to include genera from the World Health Organization’s (WHO) Priority Pathogen List</li>
<li>Improved algorithm of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> when using the phenotype-based method, to prioritise records with the highest availability of SIR values</li>
</ul></div>
<div class="section level3">
<h3 id="other-2-1-1-9092">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9092"></a></h3>
<ul><li>Greatly updated and expanded documentation</li>
<h3 id="other-2-1-1-9093">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9093"></a></h3>
<ul><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>
<li>Greatly updated and expanded documentation</li>
<li>Added Larisse Bolton, Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
<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-2-1-1-9092">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9092"></a></h3>
<h3 id="older-versions-2-1-1-9093">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9093"></a></h3>
<p>This changelog only contains changes from AMR v3.0 (October 2024) 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>