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(v0.7.1.9056) mo and ab subsetting

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dr. M.S. (Matthijs) Berends
2019-08-14 14:57:06 +02:00
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9056</span>
</span>
</div>
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<div id="microbial-taxonomic-reference-data" class="section level4">
<h4 class="hasAnchor">
<a href="#microbial-taxonomic-reference-data" class="anchor"></a>Microbial (taxonomic) reference data</h4>
<p><img src="reference/figures/logo_col.png"></p>
<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">www.catalogueoflife.org</a>). 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 id="antimicrobial-reference-data" class="section level4">
<h4 class="hasAnchor">
<a href="#antimicrobial-reference-data" class="anchor"></a>Antimicrobial reference data</h4>
<div>
<img src="reference/figures/logo_who.png" height="75px" class="logo_img"><p class="logo_txt">WHO Collaborating Centre for Drug Statistics Methodology</p>
</div>
<p>This package contains <strong>all ~450 antimicrobial 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="uri">https://www.whocc.no</a>) and the <a href="http://ec.europa.eu/health/documents/community-register/html/atc.htm">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="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>
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<div id="whonet-ears-net" class="section level4">
<h4 class="hasAnchor">
<a href="#whonet-ears-net" class="anchor"></a>WHONET / EARS-Net</h4>
<p><img src="./whonet.png"></p>
<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 <code>antibiotics</code></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>
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<li>
<a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1634-0010" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<li>
<a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0002-9213-6743" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<li>
<a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1241-1328" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<li><a href="authors.html">All authors...</a></li>
</ul>
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</div>
<footer><div class="copyright">
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">