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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
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Conduct AMR analysis
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Conduct principal component analysis for AMR
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Apply EUCAST rules
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Get properties of a microorganism
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Get properties of an antibiotic
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Other: benchmarks
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<div class="contents col-md-9">
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<div class="section level1">
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<div class="page-header"><h1 id="amr-for-r-">
|
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<code>AMR</code> (for R) <img src="./logo.svg" align="right"><a class="anchor" aria-label="anchor" href="#amr-for-r-"></a>
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</h1></div>
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<blockquote>
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<p>Update: The latest <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST
|
||
guideline for intrinsic resistance</a> (v3.3, October 2021) is now
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||
supported, the CLSI 2021 interpretation guideline is now supported, and
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||
our taxonomy tables have been updated as well (LPSN, 5 October
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2021).</p>
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</blockquote>
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<div class="section level3">
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<h3 id="what-is-amr-for-r">What is <code>AMR</code> (for R)?<a class="anchor" aria-label="anchor" href="#what-is-amr-for-r"></a>
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</h3>
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<p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org" class="external-link">R package</a> (see <a href="#copyright">Copyright</a>) to simplify the analysis and prediction
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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
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treatment evaluation in any setting.</p>
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||
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~71,000 distinct
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microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~570 antibiotic, antimycotic
|
||
and antiviral drugs</strong></a> by name and code (including ATC,
|
||
WHONET/EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about
|
||
valid R/SI and MIC values. It supports any data format, including
|
||
WHONET/EARS-Net data.</p>
|
||
<p>The <code>AMR</code> package is available in
|
||
<img src="lang_da.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||
Danish,
|
||
<img src="lang_nl.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||
Dutch,
|
||
<img src="lang_en.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||
English,
|
||
<img src="lang_fr.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||
French,
|
||
<img src="lang_de.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||
German,
|
||
<img src="lang_it.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||
Italian,
|
||
<img src="lang_pt.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||
Portuguese,
|
||
<img src="lang_ru.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||
Russian,
|
||
<img src="lang_es.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||
Spanish and
|
||
<img src="lang_sv.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||
Swedish. Antimicrobial drug (group) names and colloquial microorganism
|
||
names are provided in these languages.</p>
|
||
<p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">fully independent
|
||
of any other R package</a> and works on Windows, macOS and Linux with
|
||
all versions of R since R-3.0 (April 2013). <strong>It was designed to
|
||
work in any setting, including those with very limited
|
||
resources</strong>. It 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>. This
|
||
R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI
|
||
10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI
|
||
10.33612/diss.192486375</a>) but is <a href="./news">actively and
|
||
durably maintained</a> by two public healthcare organisations in the
|
||
Netherlands.</p>
|
||
<div class="main-content" style="display: inline-block;">
|
||
<p>
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||
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a>
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||
<strong>Used in 175 countries</strong><br> Since its first public
|
||
release in early 2018, this R package has been used in almost all
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||
countries in the world. Click the map to enlarge and to see the country
|
||
names.
|
||
</p>
|
||
</div>
|
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<div class="section level5">
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<h5 id="with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side">With <code>AMR</code> (for R), there’s always a knowledgeable
|
||
microbiologist by your side!<a class="anchor" aria-label="anchor" href="#with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side"></a>
|
||
</h5>
|
||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span class="co"># AMR works great with dplyr, but it's not required or neccesary</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>
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||
<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>
|
||
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||
<span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
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||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>bacteria <span class="op">=</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span>,
|
||
<span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>,
|
||
<span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,
|
||
<span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||
<p>With only having defined a row filter on Gram-negative bacteria with
|
||
intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code>
|
||
and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on
|
||
two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and
|
||
<code><a href="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the
|
||
<code>AMR</code> package make sure you get what you meant:</p>
|
||
<table class="table">
|
||
<thead><tr class="header">
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||
<th align="left">bacteria</th>
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||
<th align="center">GEN</th>
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||
<th align="center">TOB</th>
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||
<th align="center">AMK</th>
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||
<th align="center">KAN</th>
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||
<th align="center">IPM</th>
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||
<th align="center">MEM</th>
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||
</tr></thead>
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||
<tbody>
|
||
<tr class="odd">
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||
<td align="left"><em>Pseudomonas aeruginosa</em></td>
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||
<td align="center">I</td>
|
||
<td align="center">S</td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center">S</td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left"><em>Pseudomonas aeruginosa</em></td>
|
||
<td align="center">I</td>
|
||
<td align="center">S</td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center">S</td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left"><em>Pseudomonas aeruginosa</em></td>
|
||
<td align="center">I</td>
|
||
<td align="center">S</td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center">S</td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left"><em>Pseudomonas aeruginosa</em></td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center">S</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left"><em>Pseudomonas aeruginosa</em></td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">R</td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left"><em>Pseudomonas aeruginosa</em></td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">R</td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left"><em>Stenotrophomonas maltophilia</em></td>
|
||
<td align="center">R</td>
|
||
<td align="center">R</td>
|
||
<td align="center">R</td>
|
||
<td align="center">R</td>
|
||
<td align="center">R</td>
|
||
<td align="center">R</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left"><em>Pseudomonas aeruginosa</em></td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center">S</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left"><em>Pseudomonas aeruginosa</em></td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center">S</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left"><em>Pseudomonas aeruginosa</em></td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">R</td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p>A base R equivalent would be, giving the exact same results:</p>
|
||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span class="va">example_isolates</span><span class="op">$</span><span class="va">bacteria</span> <span class="op"><-</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">mo</span><span class="op">)</span>
|
||
<span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&</span>
|
||
<span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</span><span class="op">)</span>,
|
||
<span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"bacteria"</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></code></pre></div>
|
||
</div>
|
||
<div class="section level4">
|
||
<h4 id="partners">Partners<a class="anchor" aria-label="anchor" href="#partners"></a>
|
||
</h4>
|
||
<p>The development of this package is part of, related to, or made
|
||
possible by:</p>
|
||
<div align="center">
|
||
<p><a href="https://www.rug.nl" title="University of Groningen" class="external-link"><img src="./logo_rug.png" class="partner_logo"></a>
|
||
<a href="https://www.umcg.nl" title="University Medical Center Groningen" class="external-link"><img src="./logo_umcg.png" class="partner_logo"></a>
|
||
<a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation" class="external-link"><img src="./logo_certe.png" class="partner_logo"></a>
|
||
<a href="https://www.deutschland-nederland.eu" title="EurHealth-1-Health" class="external-link"><img src="./logo_eh1h.png" class="partner_logo"></a>
|
||
<a href="https://www.deutschland-nederland.eu" title="INTERREG" class="external-link"><img src="./logo_interreg.png" class="partner_logo"></a></p>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="section level3">
|
||
<h3 id="what-can-you-do-with-this-package">What can you do with this package?<a class="anchor" aria-label="anchor" href="#what-can-you-do-with-this-package"></a>
|
||
</h3>
|
||
<p>This package can be used for:</p>
|
||
<ul>
|
||
<li>Reference for the taxonomy of microorganisms, since the package
|
||
contains all microbial (sub)species from the <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> and <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in
|
||
Nomenclature</a> (<a href="./reference/mo_property.html">manual</a>)</li>
|
||
<li>Interpreting raw MIC and disk diffusion values, based on the latest
|
||
CLSI or EUCAST guidelines (<a href="./reference/as.rsi.html">manual</a>)</li>
|
||
<li>Retrieving antimicrobial drug names, doses and forms of
|
||
administration from clinical health care records (<a href="./reference/ab_from_text.html">manual</a>)</li>
|
||
<li>Determining first isolates to be used for AMR data analysis (<a href="./reference/first_isolate.html">manual</a>)</li>
|
||
<li>Calculating antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
|
||
<li>Determining multi-drug resistance (MDR) / multi-drug resistant
|
||
organisms (MDRO) (<a href="./articles/MDR.html">tutorial</a>)</li>
|
||
<li>Calculating (empirical) susceptibility of both mono therapy and
|
||
combination therapies (<a href="./articles/AMR.html">tutorial</a>)</li>
|
||
<li>Predicting future antimicrobial resistance using regression models
|
||
(<a href="./articles/resistance_predict.html">tutorial</a>)</li>
|
||
<li>Getting properties for any microorganism (like Gram stain, species,
|
||
genus or family) (<a href="./reference/mo_property.html">manual</a>)</li>
|
||
<li>Getting properties for any antibiotic (like name, code of
|
||
EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) (<a href="./reference/ab_property.html">manual</a>)</li>
|
||
<li>Plotting antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
|
||
<li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li>
|
||
<li>Getting SNOMED codes of a microorganism, or getting properties of a
|
||
microorganism based on a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li>
|
||
<li>Getting LOINC codes of an antibiotic, or getting properties of an
|
||
antibiotic based on a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
|
||
<li>Machine reading the EUCAST and CLSI guidelines from 2011-2021 to
|
||
translate MIC values and disk diffusion diameters to R/SI (<a href="./articles/datasets.html">link</a>)</li>
|
||
<li>Principal component analysis for AMR (<a href="./articles/PCA.html">tutorial</a>)</li>
|
||
</ul>
|
||
</div>
|
||
<div class="section level3">
|
||
<h3 id="get-this-package">Get this package<a class="anchor" aria-label="anchor" href="#get-this-package"></a>
|
||
</h3>
|
||
<div class="section level4">
|
||
<h4 id="latest-released-version">Latest released version<a class="anchor" aria-label="anchor" href="#latest-released-version"></a>
|
||
</h4>
|
||
<p><a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://www.r-pkg.org/badges/version-ago/AMR" alt="CRAN"></a> <a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt="CRANlogs"></a></p>
|
||
<p>This package is available <a href="https://cran.r-project.org/package=AMR" class="external-link">here on the official R
|
||
network (CRAN)</a>. Install this package in R from CRAN by using the
|
||
command:</p>
|
||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></code></pre></div>
|
||
<p>It will be downloaded and installed automatically. For RStudio, click
|
||
on the menu <em>Tools</em> > <em>Install Packages…</em> and then type
|
||
in “AMR” and press <kbd>Install</kbd>.</p>
|
||
<p><strong>Note:</strong> Not all functions on this website may be
|
||
available in this latest release. To use all functions and data sets
|
||
mentioned on this website, install the latest development version.</p>
|
||
</div>
|
||
<div class="section level4">
|
||
<h4 id="latest-development-version">Latest development version<a class="anchor" aria-label="anchor" href="#latest-development-version"></a>
|
||
</h4>
|
||
<p><a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=main" alt="R-code-check"></a> <a href="https://www.codefactor.io/repository/github/msberends/amr" class="external-link"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://codecov.io/gh/msberends/AMR/branch/main/graph/badge.svg" alt="Codecov"></a></p>
|
||
<p>The latest and unpublished development version can be installed from
|
||
GitHub in two ways:</p>
|
||
<ol style="list-style-type: decimal">
|
||
<li>
|
||
<p>Manually, using:</p>
|
||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span>
|
||
<span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></code></pre></div>
|
||
</li>
|
||
<li>
|
||
<p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe
|
||
platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our
|
||
R-universe address</a> to your list of repositories (‘repos’):</p>
|
||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>,
|
||
msberends <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||
<p>After this, you can install and update this <code>AMR</code> package
|
||
like any official release (e.g., using
|
||
<code>install.packages("AMR")</code> or in RStudio via <em>Tools</em>
|
||
> <em>Check for Package Updates…</em>).</p>
|
||
</li>
|
||
</ol>
|
||
<p>You can also download the latest build from our repository: <a href="https://github.com/msberends/AMR/raw/main/data-raw/AMR_latest.tar.gz" class="external-link uri">https://github.com/msberends/AMR/raw/main/data-raw/AMR_latest.tar.gz</a></p>
|
||
</div>
|
||
</div>
|
||
<div class="section level3">
|
||
<h3 id="get-started">Get started<a class="anchor" aria-label="anchor" href="#get-started"></a>
|
||
</h3>
|
||
<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or
|
||
click a link in the <a href="https://msberends.github.io/AMR/articles/">‘How to’ menu</a>.</p>
|
||
</div>
|
||
<div class="section level3">
|
||
<h3 id="short-introduction">Short introduction<a class="anchor" aria-label="anchor" href="#short-introduction"></a>
|
||
</h3>
|
||
<div class="section level4">
|
||
<h4 id="microbial-taxonomic-reference-data">Microbial (taxonomic) reference data<a class="anchor" aria-label="anchor" href="#microbial-taxonomic-reference-data"></a>
|
||
</h4>
|
||
<p>This package contains the complete taxonomic tree of almost all
|
||
~70,000 microorganisms from the authoritative and comprehensive
|
||
Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">www.catalogueoflife.org</a>),
|
||
supplemented by data from the List of Prokaryotic names with Standing in
|
||
Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>).
|
||
This supplementation is needed until the <a href="https://github.com/Sp2000/colplus" class="external-link">CoL+ project</a> is finished,
|
||
which we await. With <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be
|
||
checked which version of the CoL is included in this package.</p>
|
||
<p>Read more about which data from the Catalogue of Life <a href="./reference/catalogue_of_life.html">in our manual</a>.</p>
|
||
</div>
|
||
<div class="section level4">
|
||
<h4 id="antimicrobial-reference-data">Antimicrobial reference data<a class="anchor" aria-label="anchor" href="#antimicrobial-reference-data"></a>
|
||
</h4>
|
||
<p>This package contains <strong>all ~550 antibiotic, antimycotic and
|
||
antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC)
|
||
codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the
|
||
World Health Organization Collaborating Centre for Drug Statistics
|
||
Methodology (WHOCC, <a href="https://www.whocc.no" class="external-link uri">https://www.whocc.no</a>) and the <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">Pharmaceuticals
|
||
Community Register of the European Commission</a>.</p>
|
||
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial
|
||
purposes, unlike any other info from this package. See <a href="https://www.whocc.no/copyright_disclaimer/" class="external-link uri">https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
|
||
<p>Read more about the data from WHOCC <a href="./reference/WHOCC.html">in our manual</a>.</p>
|
||
</div>
|
||
<div class="section level4">
|
||
<h4 id="whonet--ears-net">WHONET / EARS-Net<a class="anchor" aria-label="anchor" href="#whonet--ears-net"></a>
|
||
</h4>
|
||
<p>We support WHONET and EARS-Net data. Exported files from WHONET can
|
||
be imported into R and can be analysed easily using this package. For
|
||
education purposes, we created an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a>
|
||
with the exact same structure as a WHONET export file. Furthermore, this
|
||
package also contains a <a href="./reference/antibiotics.html">data set
|
||
antibiotics</a> with all EARS-Net antibiotic abbreviations, and knows
|
||
almost all WHONET abbreviations for microorganisms. When using WHONET
|
||
data as input for analysis, all input parameters will be set
|
||
automatically.</p>
|
||
<p>Read our tutorial about <a href="./articles/WHONET.html">how to work
|
||
with WHONET data here</a>.</p>
|
||
</div>
|
||
<div class="section level4">
|
||
<h4 id="overview-of-functions">Overview of functions<a class="anchor" aria-label="anchor" href="#overview-of-functions"></a>
|
||
</h4>
|
||
<p>The <code>AMR</code> package basically does four important
|
||
things:</p>
|
||
<ol style="list-style-type: decimal">
|
||
<li>
|
||
<p>It <strong>cleanses existing data</strong> by providing new
|
||
<em>classes</em> for microoganisms, antibiotics and antimicrobial
|
||
results (both S/I/R and MIC). By installing this package, you teach R
|
||
everything about microbiology that is needed for analysis. These
|
||
functions all use intelligent rules to guess results that you would
|
||
expect:</p>
|
||
<ul>
|
||
<li>Use <code><a href="reference/as.mo.html">as.mo()</a></code> to get a microbial ID. The IDs are human
|
||
readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em>
|
||
is “B_KLBSL_PNMN” (B stands for Bacteria) and the ID of <em>S.
|
||
aureus</em> is “B_STPHY_AURS”. The function takes almost any text as
|
||
input that looks like the name or code of a microorganism like “E.
|
||
coli”, “esco” or “esccol” and tries to find expected results using
|
||
intelligent rules combined with the included Catalogue of Life data set.
|
||
It only takes milliseconds to find results, please see our <a href="./articles/benchmarks.html">benchmarks</a>. Moreover, it can group
|
||
<em>Staphylococci</em> into coagulase negative and positive (CoNS and
|
||
CoPS, see <a href="./reference/as.mo.html#source">source</a>) and can
|
||
categorise <em>Streptococci</em> into Lancefield groups (like
|
||
beta-haemolytic <em>Streptococcus</em> Group B, <a href="./reference/as.mo.html#source">source</a>).</li>
|
||
<li>Use <code><a href="reference/as.ab.html">as.ab()</a></code> to get an antibiotic ID. Like microbial
|
||
IDs, these IDs are also human readable based on those used by EARS-Net.
|
||
For example, the ID of amoxicillin is <code>AMX</code> and the ID of
|
||
gentamicin is <code>GEN</code>. The <code><a href="reference/as.ab.html">as.ab()</a></code> function also
|
||
uses intelligent rules to find results like accepting misspelling, trade
|
||
names and abbrevations used in many laboratory systems. For instance,
|
||
the values “Furabid”, “Furadantin”, “nitro” all return the ID of
|
||
Nitrofurantoine. To accomplish this, the package contains a database
|
||
with most LIS codes, official names, trade names, ATC codes, defined
|
||
daily doses (DDD) and drug categories of antibiotics.</li>
|
||
<li>Use <code><a href="reference/as.rsi.html">as.rsi()</a></code> to get antibiotic interpretations based on
|
||
raw MIC values (in mg/L) or disk diffusion values (in mm), or transform
|
||
existing values to valid antimicrobial results. It produces just S, I or
|
||
R based on your input and warns about invalid values. Even values like
|
||
“<=0.002; S” (combined MIC/RSI) will result in “S”.</li>
|
||
<li>Use <code><a href="reference/as.mic.html">as.mic()</a></code> to cleanse your MIC values. It produces a
|
||
so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values
|
||
as levels. A value like “<=0.002; S” (combined MIC/RSI) will result
|
||
in “<=0.002”.</li>
|
||
</ul>
|
||
</li>
|
||
<li>
|
||
<p>It <strong>enhances existing data</strong> and <strong>adds new
|
||
data</strong> from data sets included in this package.</p>
|
||
<ul>
|
||
<li>Use <code><a href="reference/eucast_rules.html">eucast_rules()</a></code> to apply <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST
|
||
expert rules to isolates</a> (not the translation from MIC to R/SI
|
||
values, use <code><a href="reference/as.rsi.html">as.rsi()</a></code> for that).</li>
|
||
<li>Use <code><a href="reference/first_isolate.html">first_isolate()</a></code> to identify the first isolates of
|
||
every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">using
|
||
guidelines from the CLSI</a> (Clinical and Laboratory Standards
|
||
Institute).
|
||
<ul>
|
||
<li>You can also identify first <em>weighted</em> isolates of every
|
||
patient, an adjusted version of the CLSI guideline. This takes into
|
||
account key antibiotics of every strain and compares them.</li>
|
||
</ul>
|
||
</li>
|
||
<li>Use <code><a href="reference/mdro.html">mdro()</a></code> to determine which micro-organisms are
|
||
multi-drug resistant organisms (MDRO). It supports a variety of
|
||
international guidelines, such as the MDR-paper by Magiorakos <em>et
|
||
al.</em> (2012, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=21793988" class="external-link">PMID
|
||
21793988</a>), the exceptional phenotype definitions of EUCAST and the
|
||
WHO guideline on multi-drug resistant TB. It also supports the national
|
||
guidelines of the Netherlands and Germany.</li>
|
||
<li>The <a href="./reference/microorganisms.html">data set
|
||
microorganisms</a> contains the complete taxonomic tree of ~70,000
|
||
microorganisms. Furthermore, some colloquial names and all Gram stains
|
||
are available, which enables resistance analysis of e.g. different
|
||
antibiotics per Gram stain. The package also contains functions to look
|
||
up values in this data set like <code><a href="reference/mo_property.html">mo_genus()</a></code>,
|
||
<code><a href="reference/mo_property.html">mo_family()</a></code>, <code><a href="reference/mo_property.html">mo_gramstain()</a></code> or even
|
||
<code><a href="reference/mo_property.html">mo_phylum()</a></code>. Use <code><a href="reference/mo_property.html">mo_snomed()</a></code> to look up any
|
||
SNOMED CT code associated with a microorganism. As all these function
|
||
use <code><a href="reference/as.mo.html">as.mo()</a></code> internally, they also use the same intelligent
|
||
rules for determination. For example, <code>mo_genus("MRSA")</code> and
|
||
<code>mo_genus("S. aureus")</code> will both return
|
||
<code>"Staphylococcus"</code>. They also come with support for German,
|
||
Danish, Dutch, Spanish, Italian, French and Portuguese. These functions
|
||
can be used to add new variables to your data.</li>
|
||
<li>The <a href="./reference/antibiotics.html">data set antibiotics</a>
|
||
contains ~450 antimicrobial drugs with their EARS-Net code, ATC code,
|
||
PubChem compound ID, LOINC code, official name, common LIS codes and
|
||
DDDs of both oral and parenteral administration. It also contains all
|
||
(thousands of) trade names found in PubChem. Use functions like
|
||
<code><a href="reference/ab_property.html">ab_name()</a></code>, <code><a href="reference/ab_property.html">ab_group()</a></code>, <code><a href="reference/ab_property.html">ab_atc()</a></code>,
|
||
<code><a href="reference/ab_property.html">ab_loinc()</a></code> and <code><a href="reference/ab_property.html">ab_tradenames()</a></code> to look up
|
||
values. The <code>ab_*</code> functions use <code><a href="reference/as.ab.html">as.ab()</a></code>
|
||
internally so they support the same intelligent rules to guess the most
|
||
probable result. For example, <code>ab_name("Fluclox")</code>,
|
||
<code>ab_name("Floxapen")</code> and <code>ab_name("J01CF05")</code>
|
||
will all return <code>"Flucloxacillin"</code>. These functions can again
|
||
be used to add new variables to your data.</li>
|
||
</ul>
|
||
</li>
|
||
<li>
|
||
<p>It <strong>analyses the data</strong> with convenient functions
|
||
that use well-known methods.</p>
|
||
<ul>
|
||
<li>Calculate the microbial susceptibility or resistance (and even
|
||
co-resistance) with the <code><a href="reference/proportion.html">susceptibility()</a></code> and
|
||
<code><a href="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the
|
||
<code><a href="reference/proportion.html">proportion_R()</a></code>, <code><a href="reference/proportion.html">proportion_IR()</a></code>,
|
||
<code><a href="reference/proportion.html">proportion_I()</a></code>, <code><a href="reference/proportion.html">proportion_SI()</a></code> and
|
||
<code><a href="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of
|
||
isolates can be determined with the <code><a href="reference/count.html">count_resistant()</a></code>,
|
||
<code><a href="reference/count.html">count_susceptible()</a></code> and <code><a href="reference/count.html">count_all()</a></code> functions.
|
||
All these functions can be used with the <code>dplyr</code> package
|
||
(e.g. in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>)</li>
|
||
<li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for
|
||
the <code>ggplot2</code> package</li>
|
||
<li>Predict antimicrobial resistance for the nextcoming years using
|
||
logistic regression models with the <code><a href="reference/resistance_predict.html">resistance_predict()</a></code>
|
||
function</li>
|
||
</ul>
|
||
</li>
|
||
<li>
|
||
<p>It <strong>teaches the user</strong> how to use all the above
|
||
actions.</p>
|
||
<ul>
|
||
<li>Aside from this website with many tutorials, the package itself
|
||
contains extensive help pages with many examples for all functions.</li>
|
||
<li>The package also contains example data sets:
|
||
<ul>
|
||
<li>The <a href="./reference/example_isolates.html"><code>example_isolates</code>
|
||
data set</a>. This data set contains 2,000 microbial isolates with their
|
||
full antibiograms. It reflects reality and can be used to practice AMR
|
||
data analysis.</li>
|
||
<li>The <a href="./reference/WHONET.html"><code>WHONET</code> data
|
||
set</a>. This data set only contains fake data, but with the exact same
|
||
structure as files exported by WHONET. Read more about WHONET <a href="./articles/WHONET.html">on its tutorial page</a>.</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
</li>
|
||
</ol>
|
||
</div>
|
||
</div>
|
||
<div class="section level3">
|
||
<h3 id="copyright">Copyright<a class="anchor" aria-label="anchor" href="#copyright"></a>
|
||
</h3>
|
||
<p>This R package is free, open-source software and licensed under the
|
||
<a href="./LICENSE-text.html">GNU General Public License v2.0
|
||
(GPL-2)</a>. In a nutshell, this means that this package:</p>
|
||
<ul>
|
||
<li><p>May be used for commercial purposes</p></li>
|
||
<li><p>May be used for private purposes</p></li>
|
||
<li><p>May <strong>not</strong> be used for patent purposes</p></li>
|
||
<li>
|
||
<p>May be modified, although:</p>
|
||
<ul>
|
||
<li>Modifications <strong>must</strong> be released under the same
|
||
license when distributing the package</li>
|
||
<li>Changes made to the code <strong>must</strong> be documented</li>
|
||
</ul>
|
||
</li>
|
||
<li>
|
||
<p>May be distributed, although:</p>
|
||
<ul>
|
||
<li>Source code <strong>must</strong> be made available when the package
|
||
is distributed</li>
|
||
<li>A copy of the license and copyright notice <strong>must</strong> be
|
||
included with the package.</li>
|
||
</ul>
|
||
</li>
|
||
<li><p>Comes with a LIMITATION of liability</p></li>
|
||
<li><p>Comes with NO warranty</p></li>
|
||
</ul>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||
<div class="links">
|
||
<h2 data-toc-skip>Links</h2>
|
||
<ul class="list-unstyled">
|
||
<li><a href="https://cloud.r-project.org/package=AMR" class="external-link">View on CRAN</a></li>
|
||
<li><a href="https://github.com/msberends/AMR/" class="external-link">Browse source code</a></li>
|
||
<li><a href="https://github.com/msberends/AMR/issues" class="external-link">Report a bug</a></li>
|
||
</ul>
|
||
</div>
|
||
|
||
<div class="license">
|
||
<h2 data-toc-skip>License</h2>
|
||
<ul class="list-unstyled">
|
||
<li>
|
||
<a href="https://www.r-project.org/Licenses/GPL-2" class="external-link">GPL-2</a> | file <a href="LICENSE-text.html">LICENSE</a>
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
|
||
|
||
<div class="citation">
|
||
<h2 data-toc-skip>Citation</h2>
|
||
<ul class="list-unstyled">
|
||
<li><a href="authors.html#citation">Citing AMR</a></li>
|
||
</ul>
|
||
</div>
|
||
|
||
<div class="developers">
|
||
<h2 data-toc-skip>Developers</h2>
|
||
<ul class="list-unstyled">
|
||
<li>Matthijs S. Berends <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-7620-1800" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||
<li>Christian F. Luz <br><small class="roles"> Author, contributor </small> <a href="https://orcid.org/0000-0001-5809-5995" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||
<li>Dennis Souverein <br><small class="roles"> Author, contributor </small> <a href="https://orcid.org/0000-0003-0455-0336" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||
<li>Erwin E. A. Hassing <br><small class="roles"> Author, contributor </small> </li>
|
||
<li><a href="authors.html">More about authors...</a></li>
|
||
</ul>
|
||
</div>
|
||
|
||
|
||
|
||
</div>
|
||
</div>
|
||
|
||
|
||
<footer><div class="copyright">
|
||
<p></p>
|
||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||
Erwin E. A. Hassing.</p>
|
||
</div>
|
||
|
||
<div class="pkgdown">
|
||
<p></p>
|
||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||
2.0.2.</p>
|
||
</div>
|
||
|
||
</footer>
|
||
</div>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
</body>
|
||
</html>
|