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<a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</small>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</small>
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website update since they are based on randomly created values and the website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was Markdown</a>. However, the methodology remains unchanged. This page was
generated on 12 May 2025.</p> generated on 13 May 2025.</p>
<div class="section level2"> <div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a> <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2> </h2>
@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">2025-05-12</td> <td align="center">2025-05-13</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2025-05-12</td> <td align="center">2025-05-13</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">2025-05-12</td> <td align="center">2025-05-13</td>
<td align="center">efgh</td> <td align="center">efgh</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">R</td> <td align="center">R</td>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</small>
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@ -80,7 +80,7 @@
<main id="main" class="col-md-9"><div class="page-header"> <main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1> <img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
<h4 data-toc-skip class="date">12 May 2025</h4> <h4 data-toc-skip class="date">13 May 2025</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small> <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div> <div class="d-none name"><code>datasets.Rmd</code></div>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</small>
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</small>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</small>
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@ -49,11 +49,11 @@
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9274" id="amr-2119274">AMR 2.1.1.9274<a class="anchor" aria-label="anchor" href="#amr-2119274"></a></h2> <h2 class="pkg-version" data-toc-text="2.1.1.9275" id="amr-2119275">AMR 2.1.1.9275<a class="anchor" aria-label="anchor" href="#amr-2119275"></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><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> <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"> <div class="section level3">
<h3 id="tldr-2-1-1-9274">tl;dr<a class="anchor" aria-label="anchor" href="#tldr-2-1-1-9274"></a></h3> <h3 id="tldr-2-1-1-9275">tl;dr<a class="anchor" aria-label="anchor" href="#tldr-2-1-1-9275"></a></h3>
<ul><li>Scope Expansion: One Health support (Human + Veterinary + Environmental microbiology).</li> <ul><li>Scope Expansion: One Health support (Human + Veterinary + Environmental microbiology).</li>
<li>Data Updates: <li>Data Updates:
<ul><li> <ul><li>
@ -103,15 +103,15 @@
</ul></li> </ul></li>
</ul></div> </ul></div>
<div class="section level3"> <div class="section level3">
<h3 id="full-changelog-2-1-1-9274">Full Changelog<a class="anchor" aria-label="anchor" href="#full-changelog-2-1-1-9274"></a></h3> <h3 id="full-changelog-2-1-1-9275">Full Changelog<a class="anchor" aria-label="anchor" href="#full-changelog-2-1-1-9275"></a></h3>
<div class="section level4"> <div class="section level4">
<h4 id="breaking-2-1-1-9274">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9274"></a></h4> <h4 id="breaking-2-1-1-9275">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9275"></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> <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>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> <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> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="new-2-1-1-9274">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9274"></a></h4> <h4 id="new-2-1-1-9275">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9275"></a></h4>
<ul><li> <ul><li>
<strong>One Health implementation</strong> <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> <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></li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="changed-2-1-1-9274">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9274"></a></h4> <h4 id="changed-2-1-1-9275">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9275"></a></h4>
<ul><li>SIR interpretation <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> <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> <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>
@ -249,11 +249,12 @@
<li>MDRO determination (using <code><a href="../reference/mdro.html">mdro()</a></code>) <li>MDRO determination (using <code><a href="../reference/mdro.html">mdro()</a></code>)
<ul><li>Implemented the new Dutch national MDRO guideline (SRI-richtlijn BRMO, Nov 2024)</li> <ul><li>Implemented the new Dutch national MDRO guideline (SRI-richtlijn BRMO, Nov 2024)</li>
<li>Added arguments <code>esbl</code>, <code>carbapenemase</code>, <code>mecA</code>, <code>mecC</code>, <code>vanA</code>, <code>vanB</code> to denote column names or logical values indicating presence of these genes (or production of their proteins)</li> <li>Added arguments <code>esbl</code>, <code>carbapenemase</code>, <code>mecA</code>, <code>mecC</code>, <code>vanA</code>, <code>vanB</code> to denote column names or logical values indicating presence of these genes (or production of their proteins)</li>
<li>The Verbose Mode (<code>verbose = TRUE</code>) now includes the guideline name</li>
</ul></li> </ul></li>
<li>Added console colours support of <code>sir</code> class for Positron</li> <li>Added console colours support of <code>sir</code> class for Positron</li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="other-2-1-1-9274">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9274"></a></h4> <h4 id="other-2-1-1-9275">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9275"></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> <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 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>Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations</li>
@ -264,7 +265,7 @@
</ul></div> </ul></div>
</div> </div>
<div class="section level3"> <div class="section level3">
<h3 id="older-versions-2-1-1-9274">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9274"></a></h3> <h3 id="older-versions-2-1-1-9275">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9275"></a></h3>
<p>This changelog only contains changes from AMR v3.0 (March 2025) and later.</p> <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> <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> <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>

2
pkgdown.yml
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@ -11,7 +11,7 @@ articles:
PCA: PCA.html PCA: PCA.html
WHONET: WHONET.html WHONET: WHONET.html
WISCA: WISCA.html WISCA: WISCA.html
last_built: 2025-05-12T10:39Z last_built: 2025-05-13T17:01Z
urls: urls:
reference: https://amr-for-r.org/reference reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles article: https://amr-for-r.org/articles

2
reference/AMR-deprecated.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/AMR-options.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</small>
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2
reference/AMR.html
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@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/WHOCC.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</small>
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2
reference/WHONET.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</small>
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2
reference/ab_from_text.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</small>
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2
reference/ab_property.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</small>
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2
reference/add_custom_antimicrobials.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/add_custom_microorganisms.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

22
reference/age.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -112,16 +112,16 @@
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span> <span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span> <span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 25 25.86575 0</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 25 25.86849 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 57 57.28219 31</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 57 57.28493 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 59 59.43288 34</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 59 59.43562 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 45 45.19726 19</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 45 45.20000 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 75 75.52603 50</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 75 75.52877 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 78 78.23836 52</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 78 78.24110 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 85 85.22466 59</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 85 85.22740 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 37 37.33425 11</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 37 37.33699 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 27 27.70685 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 27 27.70959 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 47 47.29041 21</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 47 47.29315 21</span>
</code></pre></div> </code></pre></div>
</div> </div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

2
reference/age_groups.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/antibiogram.html
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@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</small>
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2
reference/antimicrobial_selectors.html
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@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/antimicrobials.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/as.ab.html
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@ -7,7 +7,7 @@
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2
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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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> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/as.mic.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</small>
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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> <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="">2.1.1.9274</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</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,
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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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> <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> 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: #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> 2025-05-12 <span style="color: #949494;">10:40:00</span> 1 MIC amoxicillin Escherich… human 8 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2025-05-13 <span style="color: #949494;">17:02:01</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> 2025-05-12 <span style="color: #949494;">10:40:00</span> 1 MIC cipro Escherich… human 0.256 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2025-05-13 <span style="color: #949494;">17:02:01</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> 2025-05-12 <span style="color: #949494;">10:40:00</span> 1 DISK tobra Escherich… human 16 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2025-05-13 <span style="color: #949494;">17:02:01</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> 2025-05-12 <span style="color: #949494;">10:40:01</span> 1 DISK genta Escherich… human 18 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2025-05-13 <span style="color: #949494;">17:02:02</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;"># 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;"># 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> <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> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/av_from_text.html
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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reference/availability.html
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@ -7,7 +7,7 @@
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reference/bug_drug_combinations.html
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@ -7,7 +7,7 @@
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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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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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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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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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reference/example_isolates.html
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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reference/first_isolate.html
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@ -9,7 +9,7 @@
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@ -7,7 +7,7 @@
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reference/get_episode.html
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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reference/ggplot_sir.html
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@ -7,7 +7,7 @@
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reference/guess_ab_col.html
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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reference/kurtosis.html
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@ -7,7 +7,7 @@
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reference/like.html
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@ -7,7 +7,7 @@
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reference/mdro.html
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@ -7,7 +7,7 @@
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@ -149,14 +149,16 @@
<div class="section level2"> <div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<ul><li><p>CMI 2012 paper - function <code>mdr_cmi2012()</code> or <code>mdro()</code>:<br> <ul><li><p>If <code>verbose</code> is set to <code>TRUE</code>:<br>
A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing columns <code>row_number</code>, <code>microorganism</code>, <code>MDRO</code>, <code>reason</code>, <code>all_nonsusceptible_columns</code>, <code>guideline</code></p></li>
<li><p>CMI 2012 paper - function <code>mdr_cmi2012()</code> or <code>mdro()</code>:<br>
Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with levels <code>Negative</code> &lt; <code>Multi-drug-resistant (MDR)</code> &lt; <code>Extensively drug-resistant (XDR)</code> &lt; <code>Pandrug-resistant (PDR)</code></p></li> Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with levels <code>Negative</code> &lt; <code>Multi-drug-resistant (MDR)</code> &lt; <code>Extensively drug-resistant (XDR)</code> &lt; <code>Pandrug-resistant (PDR)</code></p></li>
<li><p>TB guideline - function <code>mdr_tb()</code> or <code>mdro(..., guideline = "TB")</code>:<br> <li><p>TB guideline - function <code>mdr_tb()</code> or <code>mdro(..., guideline = "TB")</code>:<br>
Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with levels <code>Negative</code> &lt; <code>Mono-resistant</code> &lt; <code>Poly-resistant</code> &lt; <code>Multi-drug-resistant</code> &lt; <code>Extensively drug-resistant</code></p></li> Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with levels <code>Negative</code> &lt; <code>Mono-resistant</code> &lt; <code>Poly-resistant</code> &lt; <code>Multi-drug-resistant</code> &lt; <code>Extensively drug-resistant</code></p></li>
<li><p>German guideline - function <code>mrgn()</code> or <code>mdro(..., guideline = "MRGN")</code>:<br> <li><p>German guideline - function <code>mrgn()</code> or <code>mdro(..., guideline = "MRGN")</code>:<br>
Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with levels <code>Negative</code> &lt; <code>3MRGN</code> &lt; <code>4MRGN</code></p></li> Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with levels <code>Negative</code> &lt; <code>3MRGN</code> &lt; <code>4MRGN</code></p></li>
<li><p>Everything else, except for custom guidelines:<br> <li><p>Everything else, except for custom guidelines:<br>
Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with levels <code>Negative</code> &lt; <code>Positive, unconfirmed</code> &lt; <code>Positive</code>. The value <code>"Positive, unconfirmed"</code> means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. molecular) tests</p></li> Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with levels <code>Negative</code> &lt; <code>Positive, unconfirmed</code> &lt; <code>Positive</code>. The value <code>"Positive, unconfirmed"</code> means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. genotypic) tests</p></li>
</ul></div> </ul></div>
<div class="section level2"> <div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>

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reference/microorganisms.codes.html
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reference/microorganisms.html
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@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
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reference/mo_matching_score.html
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reference/mo_property.html
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@ -7,7 +7,7 @@
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reference/mo_source.html
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@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@ -7,7 +7,7 @@
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reference/plot.html
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@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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reference/proportion.html
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@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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reference/random.html
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@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
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@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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