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@ -33,7 +33,7 @@
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -49,11 +49,11 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9276" id="amr-2119276">AMR 2.1.1.9276<a class="anchor" aria-label="anchor" href="#amr-2119276"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9277" id="amr-2119277">AMR 2.1.1.9277<a class="anchor" aria-label="anchor" href="#amr-2119277"></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://amr-for-r.org/#get-this-package">the instructions here</a>.)</em></p>
<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 class="section level3">
<h3 id="tldr-2-1-1-9276">tl;dr<a class="anchor" aria-label="anchor" href="#tldr-2-1-1-9276"></a></h3>
<h3 id="tldr-2-1-1-9277">tl;dr<a class="anchor" aria-label="anchor" href="#tldr-2-1-1-9277"></a></h3>
<ul><li>Scope Expansion: One Health support (Human + Veterinary + Environmental microbiology).</li>
<li>Data Updates:
<ul><li>
@ -103,15 +103,15 @@
</ul></li>
</ul></div>
<div class="section level3">
<h3 id="full-changelog-2-1-1-9276">Full Changelog<a class="anchor" aria-label="anchor" href="#full-changelog-2-1-1-9276"></a></h3>
<h3 id="full-changelog-2-1-1-9277">Full Changelog<a class="anchor" aria-label="anchor" href="#full-changelog-2-1-1-9277"></a></h3>
<div class="section level4">
<h4 id="breaking-2-1-1-9276">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9276"></a></h4>
<h4 id="breaking-2-1-1-9277">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9277"></a></h4>
<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>
<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> are 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>
</ul></div>
<div class="section level4">
<h4 id="new-2-1-1-9276">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9276"></a></h4>
<h4 id="new-2-1-1-9277">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9277"></a></h4>
<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>
@ -170,7 +170,7 @@
</ul></li>
</ul></div>
<div class="section level4">
<h4 id="changed-2-1-1-9276">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9276"></a></h4>
<h4 id="changed-2-1-1-9277">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9277"></a></h4>
<ul><li>SIR interpretation
<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>
<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>
@ -255,7 +255,7 @@
<li>Added console colours support of <code>sir</code> class for Positron</li>
</ul></div>
<div class="section level4">
<h4 id="other-2-1-1-9276">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9276"></a></h4>
<h4 id="other-2-1-1-9277">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9277"></a></h4>
<ul><li>New website domain: <a href="https://amr-for-r.org" class="uri">https://amr-for-r.org</a>! The old domain will remain to work.</li>
<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>
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</ul></div>
</div>
<div class="section level3">
<h3 id="older-versions-2-1-1-9276">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9276"></a></h3>
<h3 id="older-versions-2-1-1-9277">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9277"></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>

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pkgdown.yml
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PCA: PCA.html
WHONET: WHONET.html
WISCA: WISCA.html
last_built: 2025-05-15T08:45Z
last_built: 2025-05-15T11:11Z
urls:
reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles

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reference/AMR-deprecated.html
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@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
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@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
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@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
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2
reference/as.ab.html
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@ -7,7 +7,7 @@
<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="">2.1.1.9276</small>
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2
reference/as.av.html
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@ -7,7 +7,7 @@
<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="">2.1.1.9276</small>
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2
reference/as.disk.html
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@ -7,7 +7,7 @@
<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="">2.1.1.9276</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9277</small>
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2
reference/as.mic.html
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@ -7,7 +7,7 @@
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2
reference/as.mo.html
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@ -7,7 +7,7 @@
<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="">2.1.1.9276</small>
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10
reference/as.sir.html
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@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9276</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9277</small>
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@ -414,10 +414,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2025-05-15 <span style="color: #949494;">08:46:28</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2025-05-15 <span style="color: #949494;">08:46:28</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2025-05-15 <span style="color: #949494;">08:46:28</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2025-05-15 <span style="color: #949494;">08:46:28</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2025-05-15 <span style="color: #949494;">11:12:05</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2025-05-15 <span style="color: #949494;">11:12:05</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2025-05-15 <span style="color: #949494;">11:12:06</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2025-05-15 <span style="color: #949494;">11:12:06</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>

2
reference/atc_online.html
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@ -7,7 +7,7 @@
<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="">2.1.1.9276</small>
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reference/av_from_text.html
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@ -7,7 +7,7 @@
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2
reference/av_property.html
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@ -7,7 +7,7 @@
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2
reference/availability.html
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@ -7,7 +7,7 @@
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2
reference/bug_drug_combinations.html
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@ -7,7 +7,7 @@
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2
reference/clinical_breakpoints.html
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@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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2
reference/count.html
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@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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2
reference/custom_eucast_rules.html
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@ -7,7 +7,7 @@
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2
reference/dosage.html
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@ -7,7 +7,7 @@
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2
reference/eucast_rules.html
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@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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2
reference/example_isolates.html
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@ -7,7 +7,7 @@
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reference/example_isolates_unclean.html
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@ -7,7 +7,7 @@
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2
reference/export_ncbi_biosample.html
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@ -7,7 +7,7 @@
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2
reference/first_isolate.html
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@ -9,7 +9,7 @@
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2
reference/g.test.html
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@ -7,7 +7,7 @@
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2
reference/get_episode.html
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@ -7,7 +7,7 @@
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2
reference/ggplot_pca.html
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@ -7,7 +7,7 @@
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2
reference/ggplot_sir.html
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@ -7,7 +7,7 @@
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2
reference/guess_ab_col.html
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@ -7,7 +7,7 @@
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2
reference/index.html
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@ -7,7 +7,7 @@
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2
reference/intrinsic_resistant.html
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@ -7,7 +7,7 @@
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2
reference/italicise_taxonomy.html
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@ -7,7 +7,7 @@
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2
reference/join.html
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@ -7,7 +7,7 @@
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2
reference/key_antimicrobials.html
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@ -7,7 +7,7 @@
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2
reference/kurtosis.html
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@ -7,7 +7,7 @@
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2
reference/like.html
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@ -7,7 +7,7 @@
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4
reference/mdro.html
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@ -7,7 +7,7 @@
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@ -185,7 +185,7 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
<p>The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (<a href="https://www.who.int/publications/i/item/9789241548809" class="external-link">link</a>)</p></li>
<li><p><code>guideline = "MRGN"</code></p>
<p>The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7; <a href="https://doi.org/10.1186/s13756-015-0047-6" class="external-link">doi:10.1186/s13756-015-0047-6</a></p></li>
<li><p><code>guideline = "BRMO"</code></p>
<li><p><code>guideline = "BRMO 2024"</code> (or simply <code>guideline = "BRMO"</code>)</p>
<p>The Dutch national guideline - Samenwerkingverband Richtlijnen Infectiepreventie (SRI) (2024) "Bijzonder Resistente Micro-Organismen (BRMO)" (<a href="https://www.sri-richtlijnen.nl/brmo" class="external-link">link</a>)</p>
<p>Also:</p><ul><li><p><code>guideline = "BRMO 2017"</code></p>
<p>The former Dutch national guideline - Werkgroep Infectiepreventie (WIP), RIVM, last revision as of 2017: "Bijzonder Resistente Micro-Organismen (BRMO)"</p></li>

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@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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