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@@ -32,7 +32,7 @@
<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>
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@@ -91,7 +91,7 @@ Content not found. Please use links in the navbar.
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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="">2.1.1.9236</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9237</small>
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@@ -306,7 +306,7 @@ END OF TERMS AND CONDITIONS
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articles/AMR.html
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@@ -31,7 +31,7 @@
<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="">2.1.1.9236</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9237</small>
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@@ -92,7 +92,7 @@
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 April 2025.</p> generated on 13 April 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>
@@ -148,21 +148,21 @@ 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">2025-04-12</td> <td align="center">2025-04-13</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">2025-04-12</td> <td align="center">2025-04-13</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">2025-04-12</td> <td align="center">2025-04-13</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>
@@ -1384,7 +1384,7 @@ values:</p>
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articles/AMR_for_Python.html
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@@ -31,7 +31,7 @@
<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="">2.1.1.9236</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9237</small>
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@@ -647,7 +647,7 @@ Python.</p>
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<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_umcg.svg" style="max-width: 150px;"></a></p> <p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://amr-for-r.org/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://amr-for-r.org/logo_umcg.svg" style="max-width: 150px;"></a></p>
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articles/AMR_with_tidymodels.html
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@@ -31,7 +31,7 @@
<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="">2.1.1.9236</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9237</small>
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@@ -89,9 +89,9 @@
<blockquote> <blockquote>
<p>This page was entirely written by our <a href="https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant" class="external-link">AMR for R <p>This page was entirely written by our <a href="https://chat.amr-for-r.org" class="external-link">AMR for R Assistant</a>, a ChatGPT
Assistant</a>, a ChatGPT manually-trained model able to answer any manually-trained model able to answer any question about the AMR
question about the AMR package.</p> package.</p>
</blockquote> </blockquote>
<p>Antimicrobial resistance (AMR) is a global health crisis, and <p>Antimicrobial resistance (AMR) is a global health crisis, and
understanding resistance patterns is crucial for managing effective understanding resistance patterns is crucial for managing effective
@@ -693,7 +693,7 @@ settings.</p>
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<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_umcg.svg" style="max-width: 150px;"></a></p> <p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://amr-for-r.org/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://amr-for-r.org/logo_umcg.svg" style="max-width: 150px;"></a></p>
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articles/EUCAST.html
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@@ -31,7 +31,7 @@
<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="">2.1.1.9236</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9237</small>
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@@ -324,7 +324,7 @@ reading</em>, and is basically a form of imputation:</p>
</div> </div>
<div class="pkgdown-footer-right"> <div class="pkgdown-footer-right">
<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_umcg.svg" style="max-width: 150px;"></a></p> <p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://amr-for-r.org/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://amr-for-r.org/logo_umcg.svg" style="max-width: 150px;"></a></p>
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articles/MDR.html
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@@ -31,7 +31,7 @@
<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="">2.1.1.9236</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9237</small>
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@@ -393,7 +393,7 @@ Unique: 5</p>
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<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_umcg.svg" style="max-width: 150px;"></a></p> <p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://amr-for-r.org/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://amr-for-r.org/logo_umcg.svg" style="max-width: 150px;"></a></p>
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articles/PCA.html
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@@ -31,7 +31,7 @@
<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="">2.1.1.9236</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9237</small>
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@@ -235,7 +235,7 @@ automatically adds the right labels and even groups:</p>
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<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_umcg.svg" style="max-width: 150px;"></a></p> <p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://amr-for-r.org/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://amr-for-r.org/logo_umcg.svg" style="max-width: 150px;"></a></p>
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articles/WHONET.html
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@@ -31,7 +31,7 @@
<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="">2.1.1.9236</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9237</small>
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@@ -325,7 +325,7 @@ using the included <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a>
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articles/datasets.html
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@@ -31,7 +31,7 @@
<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="">2.1.1.9236</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9237</small>
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@@ -81,7 +81,7 @@
<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>Data sets for download / own use</h1> <img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">12 April 2025</h4> <h4 data-toc-skip class="date">13 April 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>
@@ -2015,7 +2015,7 @@ inhibitors</td>
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articles/index.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="">2.1.1.9236</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9237</small>
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@@ -78,7 +78,7 @@
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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="">2.1.1.9236</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9237</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">
@@ -193,7 +193,7 @@ included with the package. </small></p>
</div> </div>
<div class="pkgdown-footer-right"> <div class="pkgdown-footer-right">
<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_umcg.svg" style="max-width: 150px;"></a></p> <p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://amr-for-r.org/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://amr-for-r.org/logo_umcg.svg" style="max-width: 150px;"></a></p>
</div> </div>
</footer> </footer>

4
authors.html
View File

@@ -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="">2.1.1.9236</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9237</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">
@@ -202,7 +202,7 @@
</div> </div>
<div class="pkgdown-footer-right"> <div class="pkgdown-footer-right">
<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_umcg.svg" style="max-width: 150px;"></a></p> <p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://amr-for-r.org/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://amr-for-r.org/logo_umcg.svg" style="max-width: 150px;"></a></p>
</div> </div>
</footer></div> </footer></div>

4
extra.css
View File

@@ -131,9 +131,13 @@ input[type="search"] {
width: 150px; width: 150px;
} }
blockquote { blockquote {
font-style: italic;
padding: 1.25rem 1.25rem; padding: 1.25rem 1.25rem;
border-left: 1rem solid var(--amr-green-dark); border-left: 1rem solid var(--amr-green-dark);
} }
p {
text-align: justify;
}
/* /*
this shows on top of every sidebar to the right this shows on top of every sidebar to the right

4
extra.js
View File

@@ -31,7 +31,7 @@
$(document).ready(function() { $(document).ready(function() {
// add GPT assistant info // add GPT assistant info
$('aside').prepend('<div class="amr-gpt-assistant"><a target="_blank" href="https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/AMRforRGPT.svg"></a></div>'); $('aside').prepend('<div class="amr-gpt-assistant"><a target="_blank" href="https://chat.amr-for-r.org"><img src="https://amr-for-r.org/AMRforRGPT.svg"></a></div>');
// replace 'Developers' with 'Maintainers' on the main page, and "Contributors" on the Authors page // replace 'Developers' with 'Maintainers' on the main page, and "Contributors" on the Authors page
$(".developers h2").text("Maintainers"); $(".developers h2").text("Maintainers");
@@ -62,7 +62,7 @@ $(document).ready(function() {
if (window.location.href.includes('AMR_for_Python')) { if (window.location.href.includes('AMR_for_Python')) {
$('body').addClass('amr-for-python'); /* to set colours in CSS */ $('body').addClass('amr-for-python'); /* to set colours in CSS */
$('img[src="../logo.svg"]').attr('src', '../logo_python.svg'); /* replace base logo */ $('img[src="../logo.svg"]').attr('src', '../logo_python.svg'); /* replace base logo */
$('img[src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/AMRforRGPT.svg"]').attr('src', 'https://github.com/msberends/AMR/raw/main/pkgdown/assets/AMRforRGPT_python.svg'); /* replace GPT logo */ $('img[src="https://amr-for-r.org/AMRforRGPT.svg"]').attr('src', 'https://amr-for-r.org/AMRforRGPT_python.svg'); /* replace GPT logo */
} }
// add country flags // add country flags

6
index.html
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@@ -34,7 +34,7 @@
<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="">2.1.1.9236</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9237</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">
@@ -466,7 +466,7 @@
<span> <span class="co"># NEW scale function: write out S/I/R in any of the 20 supported languages</span></span> <span> <span class="co"># NEW scale function: write out S/I/R in any of the 20 supported languages</span></span>
<span> <span class="co"># and set colourblind-friendly colours</span></span> <span> <span class="co"># and set colourblind-friendly colours</span></span>
<span> <span class="fu"><a href="reference/plot.html">scale_colour_sir</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> <span> <span class="fu"><a href="reference/plot.html">scale_colour_sir</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p><a href="./reference/plotting.html" title="Plotting Helpers for AMR Data Analysis"> <img src="./plot_readme.png" style="width: 600px; max-width: 100%;"></a></p> <p><a href="./reference/plotting.html" title="Plotting Helpers for AMR Data Analysis"> <img src="./plot_readme.png" style="width: 1400px; max-width: 100%;"></a></p>
</div> </div>
<div class="section level4"> <div class="section level4">
<h4 id="calculating-resistance-per-group">Calculating resistance per group<a class="anchor" aria-label="anchor" href="#calculating-resistance-per-group"></a> <h4 id="calculating-resistance-per-group">Calculating resistance per group<a class="anchor" aria-label="anchor" href="#calculating-resistance-per-group"></a>
@@ -772,7 +772,7 @@
</div> </div>
<div class="pkgdown-footer-right"> <div class="pkgdown-footer-right">
<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_umcg.svg" style="max-width: 150px;"></a></p> <p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://amr-for-r.org/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://amr-for-r.org/logo_umcg.svg" style="max-width: 150px;"></a></p>
</div> </div>
</footer> </footer>

24
news/index.html
View File

@@ -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="">2.1.1.9236</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9237</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">
@@ -49,20 +49,20 @@
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9236" id="amr-2119236">AMR 2.1.1.9236<a class="anchor" aria-label="anchor" href="#amr-2119236"></a></h2> <h2 class="pkg-version" data-toc-text="2.1.1.9237" id="amr-2119237">AMR 2.1.1.9237<a class="anchor" aria-label="anchor" href="#amr-2119237"></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>
<div class="section level5"> <div class="section level5">
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9236">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-2-1-1-9236"></a></h5> <h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9237">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-2-1-1-9237"></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> <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>
<div class="section level3"> <div class="section level3">
<h3 id="breaking-2-1-1-9236">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9236"></a></h3> <h3 id="breaking-2-1-1-9237">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9237"></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> <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>Function <code><a href="../reference/resistance_predict.html">resistance_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> <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>
</ul></div> </ul></div>
<div class="section level3"> <div class="section level3">
<h3 id="new-2-1-1-9236">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9236"></a></h3> <h3 id="new-2-1-1-9237">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9237"></a></h3>
<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>
@@ -116,11 +116,12 @@
</ul></li> </ul></li>
</ul></div> </ul></div>
<div class="section level3"> <div class="section level3">
<h3 id="changed-2-1-1-9236">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9236"></a></h3> <h3 id="changed-2-1-1-9237">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9237"></a></h3>
<ul><li>SIR interpretation <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> <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> <li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
<li>To get quantitative values, <code><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double()</a></code> on a <code>sir</code> object will return 1 for S, 2 for SDD/I, and 3 for R (NI will become <code>NA</code>). Other functions using <code>sir</code> classes (e.g., <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code>) are updated to reflect the change to contain NI and SDD.</li> <li>To get quantitative values, <code><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double()</a></code> on a <code>sir</code> object will return 1 for S, 2 for SDD/I, and 3 for R (NI will become <code>NA</code>). Other functions using <code>sir</code> classes (e.g., <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code>) are updated to reflect the change to contain NI and SDD.</li>
<li>Following CLSI interpretation rules, values outside the log2-dilution range will be rounded upwards to the nearest log2-level before interpretation. Only if using a CLSI guideline.</li>
<li>Combined MIC values (e.g., from CLSI) are now supported</li> <li>Combined MIC values (e.g., from CLSI) are now supported</li>
<li>The argument <code>conserve_capped_values</code> in <code><a href="../reference/as.sir.html">as.sir()</a></code> has been replaced with <code>capped_mic_handling</code>, which allows greater flexibility in handling capped MIC values (<code>&lt;</code>, <code>&lt;=</code>, <code>&gt;</code>, <code>&gt;=</code>). The four available options (<code>"standard"</code>, <code>"strict"</code>, <code>"relaxed"</code>, <code>"inverse"</code>) provide full control over whether these values should be interpreted conservatively or ignored. Using <code>conserve_capped_values</code> is now deprecated and returns a warning.</li> <li>The argument <code>conserve_capped_values</code> in <code><a href="../reference/as.sir.html">as.sir()</a></code> has been replaced with <code>capped_mic_handling</code>, which allows greater flexibility in handling capped MIC values (<code>&lt;</code>, <code>&lt;=</code>, <code>&gt;</code>, <code>&gt;=</code>). The four available options (<code>"standard"</code>, <code>"strict"</code>, <code>"relaxed"</code>, <code>"inverse"</code>) provide full control over whether these values should be interpreted conservatively or ignored. Using <code>conserve_capped_values</code> is now deprecated and returns a warning.</li>
<li>Added argument <code>info</code> so silence all console messages</li> <li>Added argument <code>info</code> so silence all console messages</li>
@@ -195,8 +196,9 @@
<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 level3"> <div class="section level3">
<h3 id="other-2-1-1-9236">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9236"></a></h3> <h3 id="other-2-1-1-9237">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9237"></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> <ul><li>New website domain: <a href="https://amr-for-r.org" class="uri">https://amr-for-r.org</a>! The old links (all based on <a href="http://amr-for-r.org" class="external-link uri">http://amr-for-r.org</a>) 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> <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 Prof. Kat Holt, Dr. Jane Hawkey, and Dr. Natacha Couto as contributors for their many suggestions, ideas and bugfixes</li> <li>Added Prof. Kat Holt, Dr. Jane Hawkey, and Dr. Natacha Couto as contributors for their many suggestions, ideas and bugfixes</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>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>
@@ -204,7 +206,7 @@
<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> <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> </ul></div>
<div class="section level3"> <div class="section level3">
<h3 id="older-versions-2-1-1-9236">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9236"></a></h3> <h3 id="older-versions-2-1-1-9237">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9237"></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>
@@ -219,7 +221,7 @@
</div> </div>
<div class="pkgdown-footer-right"> <div class="pkgdown-footer-right">
<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_umcg.svg" style="max-width: 150px;"></a></p> <p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://amr-for-r.org/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://amr-for-r.org/logo_umcg.svg" style="max-width: 150px;"></a></p>
</div> </div>
</footer></div> </footer></div>

2
pkgdown.yml
View File

@@ -11,7 +11,7 @@ articles:
PCA: PCA.html PCA: PCA.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
WHONET: WHONET.html WHONET: WHONET.html
last_built: 2025-04-12T15:54Z last_built: 2025-04-13T08:06Z
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

8
reference/AMR-deprecated.html
View File

@@ -1,5 +1,5 @@
<!DOCTYPE html> <!DOCTYPE html>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9237</small>
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@@ -21,7 +21,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
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@@ -7,7 +7,7 @@
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@@ -7,7 +7,7 @@
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@@ -130,7 +130,7 @@
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@@ -201,7 +201,7 @@
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@@ -7,7 +7,7 @@
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@@ -442,7 +442,7 @@
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@@ -7,7 +7,7 @@
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@@ -213,7 +213,7 @@
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@@ -7,7 +7,7 @@
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@@ -244,7 +244,7 @@
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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="">2.1.1.9236</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9237</small>
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@@ -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 25.78356 0</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 25 25.78630 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 57 57.20000 31</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 57 57.20274 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 59 59.35068 34</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 59 59.35342 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 45 45.11507 19</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 45 45.11781 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 75 75.44384 50</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 75 75.44658 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 78 78.15616 52</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 78 78.15890 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 85 85.14247 59</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 85 85.14521 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 37 37.25205 11</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 37 37.25479 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 27 27.62466 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 27 27.62740 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 47 47.20822 21</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 47 47.21096 21</span>
</code></pre></div> </code></pre></div>
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@@ -133,7 +133,7 @@
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reference/age_groups.html
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@@ -7,7 +7,7 @@
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@@ -160,7 +160,7 @@ The default is to split on young children (0-11), youth (12-24), young adults (2
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4
reference/antibiogram.html
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@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
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@@ -659,7 +659,7 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
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reference/antimicrobial_selectors.html
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@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
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@@ -843,7 +843,7 @@ my_data_with_all_these_columns %&amp;gt;%
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4
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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9237</small>
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@@ -180,7 +180,7 @@
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4
reference/as.ab.html
View File

@@ -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="">2.1.1.9236</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9237</small>
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@@ -220,7 +220,7 @@
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4
reference/as.av.html
View File

@@ -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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@@ -178,7 +178,7 @@
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4
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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@@ -168,7 +168,7 @@
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4
reference/as.mic.html
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@@ -7,7 +7,7 @@
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@@ -233,7 +233,7 @@
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4
reference/as.mo.html
View File

@@ -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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@@ -333,7 +333,7 @@
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22
reference/as.sir.html
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@@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
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@@ -842,16 +842,16 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 65 × 17</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 65 × 17</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> 2025-04-12 <span style="color: #949494;">15:55:26</span> 1 DISK ampicillin Strep pneu human 18 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2025-04-13 <span style="color: #949494;">08:06:49</span> 1 DISK ampicillin Strep pneu human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-04-12 <span style="color: #949494;">15:55:26</span> 1 DISK AMP Escherich… human 20 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-04-13 <span style="color: #949494;">08:06:49</span> 1 DISK AMP Escherich… human 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2025-04-12 <span style="color: #949494;">15:55:26</span> 1 DISK AMP Escherich… human 20 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2025-04-13 <span style="color: #949494;">08:06:49</span> 1 DISK AMP Escherich… human 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-04-12 <span style="color: #949494;">15:55:27</span> 1 DISK GEN Escherich… human 18 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-04-13 <span style="color: #949494;">08:06:50</span> 1 DISK GEN Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-04-12 <span style="color: #949494;">15:55:27</span> 1 DISK TOB Escherich… human 16 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-04-13 <span style="color: #949494;">08:06:50</span> 1 DISK TOB Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-04-12 <span style="color: #949494;">15:55:27</span> 1 MIC AMX B_STRPT_P… human 2 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-04-13 <span style="color: #949494;">08:06:51</span> 1 MIC AMX B_STRPT_P… human 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-04-12 <span style="color: #949494;">15:55:28</span> 1 MIC AMX B_STRPT_P… human 0.01 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-04-13 <span style="color: #949494;">08:06:51</span> 1 MIC AMX B_STRPT_P… human 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-04-12 <span style="color: #949494;">15:55:28</span> 2 MIC AMX B_STRPT_P… human 2 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-04-13 <span style="color: #949494;">08:06:51</span> 2 MIC AMX B_STRPT_P… human 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-04-12 <span style="color: #949494;">15:55:28</span> 3 MIC AMX B_STRPT_P… human 4 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-04-13 <span style="color: #949494;">08:06:51</span> 3 MIC AMX B_STRPT_P… human 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 55 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 55 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 10 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 10 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>
@@ -959,7 +959,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
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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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@@ -170,7 +170,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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@@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -272,7 +272,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -7,7 +7,7 @@
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@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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@@ -302,7 +302,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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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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@@ -9,7 +9,7 @@
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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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@@ -7,7 +7,7 @@
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@@ -529,9 +529,9 @@
</dt> </dt>
<dd>Skewness of the Sample</dd> <dd>Skewness of the Sample</dd>
</dl></div><div class="section level2"> </dl></div><div class="section level2">
<h2 id="other-deprecated-functions">Other: deprecated functions<a class="anchor" aria-label="anchor" href="#other-deprecated-functions"></a></h2> <h2 id="other-deprecated-functions-arguments-datasets">Other: deprecated functions/arguments/datasets<a class="anchor" aria-label="anchor" href="#other-deprecated-functions-arguments-datasets"></a></h2>
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@@ -544,7 +544,7 @@
<code><a href="AMR-deprecated.html">ab_class()</a></code> <code><a href="AMR-deprecated.html">ab_selector()</a></code> <code><a href="AMR-deprecated.html">ab_class()</a></code> <code><a href="AMR-deprecated.html">ab_selector()</a></code>
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@@ -7,7 +7,7 @@
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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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@@ -181,7 +181,7 @@ Public Health Information Network Vocabulary Access and Distribution System (PHI
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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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@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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@@ -479,7 +479,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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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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@@ -7,7 +7,7 @@
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reference/resistance_predict.html
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@@ -1,5 +1,7 @@
<!DOCTYPE html> <!DOCTYPE html>
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Standard errors (SE) will be returned as columns se_min and se_max. See Examples for a real live example.
NOTE: These functions are deprecated and will be removed in a future version. Use the AMR package combined with the tidymodels framework instead, for which we have written a basic and short introduction on our website."><meta property="og:description" content="Create a prediction model to predict antimicrobial resistance for the next years. Standard errors (SE) will be returned as columns se_min and se_max. See Examples for a real live example.
NOTE: These functions are deprecated and will be removed in a future version. Use the AMR package combined with the tidymodels framework instead, for which we have written a basic and short introduction on our website."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
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<p>Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns <code>se_min</code> and <code>se_max</code>. See <em>Examples</em> for a real live example.</p> <p>Create a prediction model to predict antimicrobial resistance for the next years. Standard errors (SE) will be returned as columns <code>se_min</code> and <code>se_max</code>. See <em>Examples</em> for a real live example.</p>
<p><strong>NOTE:</strong> These functions are <a href="AMR-deprecated.html">deprecated</a> and will be removed in a future version. Use the AMR package combined with the tidymodels framework instead, for which we have written a <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">basic and short introduction on our website</a>.</p>
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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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@@ -7,7 +7,7 @@
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