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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="">2.1.1.9234</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</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 07 April 2025.</p>
generated on 08 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">2025-04-07</td>
<td align="center">2025-04-08</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">2025-04-07</td>
<td align="center">2025-04-08</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">2025-04-07</td>
<td align="center">2025-04-08</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://msberends.github.io/AMR/">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://www.amr-for-r.org/" class="external-link">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>

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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="">2.1.1.9234</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</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="">2.1.1.9234</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</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">
@ -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://msberends.github.io/AMR/">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://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://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://msberends.github.io/AMR/">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://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://tidymodels.tidymodels.org" class="external-link">tidymodels</a></span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Transform dataset</span></span>

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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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9234</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</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="">2.1.1.9234</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</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">

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="">2.1.1.9234</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</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://msberends.github.io/AMR/">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://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://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>

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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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9234</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</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">
@ -101,8 +101,8 @@ correctly.</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://readxl.tidyverse.org" class="external-link">readxl</a></span><span class="op">)</span></span>
<span><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://readxl.tidyverse.org/reference/read_excel.html" class="external-link">read_excel</a></span><span class="op">(</span>path <span class="op">=</span> <span class="st">"path/to/your/file.xlsx"</span><span class="op">)</span></span></code></pre></div>
<p>This package comes with an <a href="https://msberends.github.io/AMR/reference/WHONET.html">example
data set <code>WHONET</code></a>. We will use it for this analysis.</p>
<p>This package comes with an <a href="https://amr-for-r.org/reference/WHONET.html">example data set
<code>WHONET</code></a>. We will use it for this analysis.</p>
</div>
<div class="section level3">
<h3 id="preparation">Preparation<a class="anchor" aria-label="anchor" href="#preparation"></a>
@ -113,14 +113,14 @@ 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://msberends.github.io/AMR/">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://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://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>
<ul>
<li>Microorganisms should be transformed to our own microorganism codes
(called an <code>mo</code>) using <a href="https://msberends.github.io/AMR/reference/catalogue_of_life">our
Catalogue of Life reference data set</a>, which contains all ~70,000
(called an <code>mo</code>) using <a href="https://amr-for-r.org/reference/catalogue_of_life">our Catalogue
of Life reference data set</a>, which contains all ~70,000
microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa.
We do the tranformation with <code><a href="../reference/as.mo.html">as.mo()</a></code>. This function also
recognises almost all WHONET abbreviations of microorganisms.</li>

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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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9234</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</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">07 April 2025</h4>
<h4 data-toc-skip class="date">08 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>
@ -97,9 +97,9 @@ Parquet, SPSS, and Stata. We also provide tab-separated text files that
are machine-readable and suitable for input in any software program,
such as laboratory information systems.</p>
<blockquote>
<p>If you are working in Python, be sure to use our <a href="https://msberends.github.io/AMR/articles/AMR_for_Python.html">AMR
for Python</a> package. It allows all relevant AMR data sets to be
natively available in Python.</p>
<p>If you are working in Python, be sure to use our <a href="https://amr-for-r.org/articles/AMR_for_Python.html">AMR for
Python</a> package. It allows all relevant AMR data sets to be natively
available in Python.</p>
</blockquote>
<div class="section level2">
<h2 id="microorganisms-full-microbial-taxonomy">
@ -117,8 +117,8 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
<p>This data set is in R available as <code>microorganisms</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 26 March 2025 16:19:17 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://msberends.github.io/AMR/reference/microorganisms.html">data
set here</a>.</p>
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/microorganisms.html">data set
here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.rds" class="external-link">original
@ -425,8 +425,8 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
<p>This data set is in R available as <code>antimicrobials</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 19 March 2025 15:05:24 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://msberends.github.io/AMR/reference/antimicrobials.html">data
set here</a>.</p>
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.rds" class="external-link">original
@ -602,7 +602,7 @@ column names:<br><em>guideline</em>, <em>type</em>, <em>host</em>, <em>method</e
<p>This data set is in R available as <code>clinical_breakpoints</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 13 March 2025 14:38:39 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://msberends.github.io/AMR/reference/clinical_breakpoints.html">data
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/clinical_breakpoints.html">data
set here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -789,7 +789,7 @@ column names:<br><em>mo_group</em>, <em>mo</em>, <em>mo_group_name</em>, and
<code>microorganisms.groups</code>, after you load the <code>AMR</code>
package.</p>
<p>It was last updated on 26 March 2025 16:19:17 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://msberends.github.io/AMR/reference/microorganisms.groups.html">data
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/microorganisms.groups.html">data
set here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -878,8 +878,8 @@ column names:<br><em>mo</em> and <em>ab</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 28 March 2025 10:17:49 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">data
set here</a>.</p>
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/intrinsic_resistant.html">data set
here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.rds" class="external-link">original
@ -1153,7 +1153,7 @@ column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>,
<p>This data set is in R available as <code>dosage</code>, after you
load the <code>AMR</code> package.</p>
<p>It was last updated on 22 June 2023 13:10:59 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://msberends.github.io/AMR/reference/dosage.html">data set
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/dosage.html">data set
here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -1290,8 +1290,8 @@ column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>,
<p>This data set is in R available as <code>example_isolates</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 15 June 2024 13:33:49 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://msberends.github.io/AMR/reference/example_isolates.html">data
set here</a>.</p>
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/example_isolates.html">data set
here</a>.</p>
<p><strong>Example content</strong></p>
<table class="table">
<colgroup>
@ -1695,7 +1695,7 @@ column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>,
<code>example_isolates_unclean</code>, after you load the
<code>AMR</code> package.</p>
<p>It was last updated on 27 August 2022 18:49:37 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">data
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/example_isolates_unclean.html">data
set here</a>.</p>
<p><strong>Example content</strong></p>
<table style="width:100%;" class="table">
@ -1792,7 +1792,7 @@ column names:<br><em>code</em> and <em>mo</em>.</p>
<p>This data set is in R available as <code>microorganisms.codes</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 September 2024 20:17:56 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://msberends.github.io/AMR/reference/microorganisms.codes.html">data
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/microorganisms.codes.html">data
set here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -1863,8 +1863,8 @@ column names:<br><em>av</em>, <em>name</em>, <em>atc</em>, <em>cid</em>,
<p>This data set is in R available as <code>antivirals</code>, after you
load the <code>AMR</code> package.</p>
<p>It was last updated on 20 October 2023 12:51:48 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://msberends.github.io/AMR/reference/antimicrobials.html">data
set here</a>.</p>
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antivirals.rds" class="external-link">original

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<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://msberends.github.io/AMR/articles/" class="uri">https://msberends.github.io/AMR/articles/</a>.</p>
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>
<hr>
<p>The <code>AMR</code> package is a <a href="https://msberends.github.io/AMR/#copyright">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://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
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://msberends.github.io/AMR/authors.html">Many different
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>
<p>This work was published in the Journal of Statistical Software
@ -165,25 +165,25 @@ 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://msberends.github.io/AMR/articles/datasets.html">all
download links on our website</a>, which is automatically updated with
every code change.</p>
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
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://msberends.github.io/AMR/news/">actively and
durably maintained</a> by two public healthcare organisations in the
is being <a href="https://www.amr-for-r.org/news/" class="external-link">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://msberends.github.io/AMR/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>
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>
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