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12
articles/AMR.html
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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</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">
@ -92,7 +92,7 @@
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
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 08 April 2025.</p>
generated on 12 April 2025.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -148,21 +148,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2025-04-08</td>
<td align="center">2025-04-12</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2025-04-08</td>
<td align="center">2025-04-12</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2025-04-08</td>
<td align="center">2025-04-12</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -183,7 +183,7 @@ for cleaning data and creating frequency tables.</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://www.amr-for-r.org/" class="external-link">AMR</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
<span></span>
<span><span class="co"># (if not yet installed, install with:)</span></span>
<span><span class="co"># install.packages(c("dplyr", "ggplot2", "AMR"))</span></span></code></pre></div>

2
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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</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">

6
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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</small>
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@ -133,7 +133,7 @@ train, and evaluate the model.</li>
package.</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Load required libraries</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://www.amr-for-r.org/" class="external-link">AMR</a></span><span class="op">)</span> <span class="co"># For AMR data analysis</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span> <span class="co"># For AMR data analysis</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://tidymodels.tidymodels.org" class="external-link">tidymodels</a></span><span class="op">)</span> <span class="co"># For machine learning workflows, and data manipulation (dplyr, tidyr, ...)</span></span></code></pre></div>
<p>Prepare the data:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
@ -455,7 +455,7 @@ model.</li>
into a structured time-series format.</p>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Load required libraries</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://www.amr-for-r.org/" class="external-link">AMR</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://tidymodels.tidymodels.org" class="external-link">tidymodels</a></span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Transform dataset</span></span>

2
articles/EUCAST.html
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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</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">

2
articles/MDR.html
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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</small>
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4
articles/PCA.html
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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</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">
@ -100,7 +100,7 @@ is currently being developed.</strong></p>
<p>For PCA, we need to transform our AMR data first. This is what the
<code>example_isolates</code> data set in this package looks like:</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://www.amr-for-r.org/" class="external-link">AMR</a></span><span class="op">)</span></span>
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
<span><span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span>
<span><span class="co">#&gt; Rows: 2,000</span></span>

4
articles/WHONET.html
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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</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">
@ -113,7 +113,7 @@ yet, I suggest you read about it on their website: <a href="https://www.tidyvers
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span> <span class="co"># part of tidyverse</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span> <span class="co"># part of tidyverse</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://www.amr-for-r.org/" class="external-link">AMR</a></span><span class="op">)</span> <span class="co"># this package</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span> <span class="co"># this package</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/cleaner/" class="external-link">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></span></code></pre></div>
<p>We will have to transform some variables to simplify and automate the
analysis:</p>

4
articles/datasets.html
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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</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">
@ -81,7 +81,7 @@
<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>
<h4 data-toc-skip class="date">08 April 2025</h4>
<h4 data-toc-skip class="date">12 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>
<div class="d-none name"><code>datasets.Rmd</code></div>

2
articles/index.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</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">

33
articles/welcome_to_AMR.html
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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</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">
@ -91,19 +91,18 @@
<p>Note: to keep the package size as small as possible, we only include
this vignette on CRAN. You can read more vignettes on our website about
how to conduct AMR data analysis, determine MDROs, find explanation of
EUCAST and CLSI breakpoints, and much more: <a href="https://www.amr-for-r.org/articles/" class="external-link uri">https://www.amr-for-r.org/articles/</a>.</p>
EUCAST and CLSI breakpoints, and much more: <a href="https://amr-for-r.org/articles/" class="uri">https://amr-for-r.org/articles/</a>.</p>
<hr>
<p>The <code>AMR</code> package is a <a href="https://www.amr-for-r.org/" class="external-link">free and open-source</a> R package
with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero
<p>The <code>AMR</code> package is a <a href="https://amr-for-r.org/">free and open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero
dependencies</a> to simplify the analysis and prediction of
Antimicrobial Resistance (AMR) and to work with microbial and
antimicrobial data and properties, by using evidence-based methods.
<strong>Our aim is to provide a standard</strong> for clean and
reproducible AMR data analysis, that can therefore empower
epidemiological analyses to continuously enable surveillance and
treatment evaluation in any setting. <a href="https://www.amr-for-r.org/authors.html" class="external-link">Many different
researchers</a> from around the globe are continually helping us to make
this a successful and durable project!</p>
treatment evaluation in any setting. <a href="https://amr-for-r.org/authors.html">Many different researchers</a>
from around the globe are continually helping us to make this a
successful and durable project!</p>
<p>This work was published in the Journal of Statistical Software
(Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">DOI
10.18637/jss.v104.i03</a>) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI
@ -165,25 +164,25 @@ interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are
publicly and freely available. We continually export our data sets to
formats for use in R, SPSS, Stata and Excel. We also supply flat files
that are machine-readable and suitable for input in any software
program, such as laboratory information systems. Please find <a href="https://www.amr-for-r.org/articles/datasets.html" class="external-link">all download
links on our website</a>, which is automatically updated with every code
program, such as laboratory information systems. Please find <a href="https://amr-for-r.org/articles/datasets.html">all download links
on our website</a>, which is automatically updated with every code
change.</p>
<p>This R package was created for both routine data analysis and
academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration
with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe
Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>, and
is being <a href="https://www.amr-for-r.org/news/" class="external-link">actively and durably
is being <a href="https://amr-for-r.org/news/">actively and durably
maintained</a> by two public healthcare organisations in the
Netherlands.</p>
<hr>
<p><small> This AMR package for R is free, open-source software and
licensed under the <a href="https://www.amr-for-r.org/LICENSE-text.html" class="external-link">GNU General Public
License v2.0 (GPL-2)</a>. These requirements are consequently legally
binding: modifications must be released under the same license when
distributing the package, changes made to the code must be documented,
source code must be made available when the package is distributed, and
a copy of the license and copyright notice must be included with the
package. </small></p>
licensed under the <a href="https://amr-for-r.org/LICENSE-text.html">GNU
General Public License v2.0 (GPL-2)</a>. These requirements are
consequently legally binding: modifications must be released under the
same license when distributing the package, changes made to the code
must be documented, source code must be made available when the package
is distributed, and a copy of the license and copyright notice must be
included with the package. </small></p>
</main>
</div>