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<div class="col-md-9 contents">
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<h1 data-toc-skip>Data sets for download</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
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<div class="hidden name"><code>datasets.Rmd</code></div>
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<p>This package contains a lot of reference data sets that are all reliable, up-to-date and free to download. You can even use them outside of R, for example to train your laboratory information system (LIS) about intrinsic resistance!</p>
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<p>We included them in our <code>AMR</code> package, but also automatically ‘mirror’ them to our public repository in different software formats. On this page, we explain how to download them and how the structure of the data sets look like. The tab separated files <strong>allow for machine reading taxonomic data and EUCAST and CLSI interpretation guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI.</p>
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<p><em>Note: Years and dates of updates mentioned on this page, are from on <code>AMR</code> package version 1.3.0.9004, online released on 16 August 2020. <strong>If you are reading this page from within R, please <a href="https://msberends.github.io/AMR/articles/datasets.html">visit our website</a> for the latest update.</strong></em></p>
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<div id="microorganisms" class="section level2">
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<h2 class="hasAnchor">
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<a href="#microorganisms" class="anchor"></a>Microorganisms</h2>
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<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
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<div id="source" class="section level4">
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<h4 class="hasAnchor">
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<a href="#source" class="anchor"></a>Source</h4>
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<p>Our full taxonomy of microorganisms is based on the authoritative and comprehensive:</p>
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<ul>
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<li>
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<a href="http://www.catalogueoflife.org">Catalogue of Life</a> (included version: 2019)</li>
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<li>
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<a href="https://lpsn.dsmz.de">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, included version: May 2020)</li>
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</ul>
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</div>
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<div id="structure" class="section level4">
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<h4 class="hasAnchor">
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<a href="#structure" class="anchor"></a>Structure</h4>
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<p>A data set with 67,151 rows and 16 columns, containing the following column names:</p>
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<p><em>mo, fullname, kingdom, phylum, class, order, family, genus, species, subspecies, rank, ref, species_id, source, prevalence, snomed</em>.</p>
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<p>Included per taxonomic kingdom:</p>
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<table class="table">
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<thead><tr class="header">
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<th align="center">Kingdom</th>
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<th align="center">Number of (sub)species</th>
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</tr></thead>
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<tbody>
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<tr class="odd">
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<td align="center">(unknown kingdom)</td>
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<td align="center">1</td>
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</tr>
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<tr class="even">
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<td align="center">Animalia</td>
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<td align="center">2,153</td>
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</tr>
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<tr class="odd">
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<td align="center">Archaea</td>
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<td align="center">697</td>
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</tr>
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<tr class="even">
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<td align="center">Bacteria</td>
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<td align="center">19,244</td>
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</tr>
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<tr class="odd">
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<td align="center">Chromista</td>
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<td align="center">32,164</td>
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</tr>
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<tr class="even">
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<td align="center">Fungi</td>
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<td align="center">9,582</td>
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</tr>
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</tbody>
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</table>
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</div>
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<div id="download" class="section level4">
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<h4 class="hasAnchor">
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<a href="#download" class="anchor"></a>Download</h4>
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<p>Download the data set preferably in the software you use, so the data file already has the correct data structure. Below files were updated on 28 July 2020 20:52:40 CEST.</p>
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<ul>
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<li><p>R file (.rds): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/microorganisms.rds">from GitLab</a> (file size: 2.7 MB)</p></li>
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<li><p>Excel workbook (.xlsx): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.xlsx">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/microorganisms.xlsx">from GitLab</a> (file size: 6.1 MB)</p></li>
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<li><p>SPSS file (.sav): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sav">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/microorganisms.sav">from GitLab</a> (file size: 28.2 MB)</p></li>
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<li><p>Stata file (.dta): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sav">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/microorganisms.sav">from GitLab</a> (file size: 28.2 MB)</p></li>
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<li><p>SAS file (.sas): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.dta">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/microorganisms.dta">from GitLab</a> (file size: 25.2 MB)</p></li>
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<li><p>Tab separated file (.txt): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.txt">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/microorganisms.txt">from GitLab</a> (file size: 13.3 MB)</p></li>
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</ul>
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</div>
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<div id="example" class="section level4">
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<h4 class="hasAnchor">
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<a href="#example" class="anchor"></a>Example</h4>
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<p>Example rows when filtering on genus <em>Escherichia</em>:</p>
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<table class="table">
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<colgroup>
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<col width="5%">
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<col width="9%">
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<col width="3%">
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<col width="6%">
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<col width="8%">
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<col width="6%">
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<col width="7%">
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<col width="5%">
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<col width="4%">
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<col width="4%">
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<col width="3%">
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<col width="9%">
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<col width="13%">
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<col width="3%">
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<col width="4%">
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<col width="4%">
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</colgroup>
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<thead><tr class="header">
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<th align="center">mo</th>
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<th align="center">fullname</th>
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<th align="center">kingdom</th>
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<th align="center">phylum</th>
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<th align="center">class</th>
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<th align="center">order</th>
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<th align="center">family</th>
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<th align="center">genus</th>
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<th align="center">species</th>
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<th align="center">subspecies</th>
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<th align="center">rank</th>
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<th align="center">ref</th>
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<th align="center">species_id</th>
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<th align="center">source</th>
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<th align="center">prevalence</th>
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<th align="center">snomed</th>
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</tr></thead>
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<tbody>
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<tr class="odd">
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<td align="center">B_ESCHR</td>
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<td align="center">Escherichia</td>
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<td align="center">Bacteria</td>
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<td align="center">Proteobacteria</td>
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<td align="center">Gammaproteobacteria</td>
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<td align="center">Enterobacterales</td>
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<td align="center">Enterobacteriaceae</td>
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<td align="center">Escherichia</td>
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<td align="center"></td>
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<td align="center"></td>
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<td align="center">genus</td>
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<td align="center"></td>
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<td align="center">bc4fdde6867d5ecfc728000b0bfb49a3</td>
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<td align="center">CoL</td>
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<td align="center">1</td>
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<td align="center">64735005</td>
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</tr>
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<tr class="even">
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<td align="center">B_ESCHR_ALBR</td>
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<td align="center">Escherichia albertii</td>
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<td align="center">Bacteria</td>
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<td align="center">Proteobacteria</td>
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<td align="center">Gammaproteobacteria</td>
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<td align="center">Enterobacterales</td>
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<td align="center">Enterobacteriaceae</td>
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<td align="center">Escherichia</td>
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<td align="center">albertii</td>
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<td align="center"></td>
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<td align="center">species</td>
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<td align="center">Huys et al., 2003</td>
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<td align="center">36618b1ed3b8b7e5a61f40eb9386e63c</td>
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<td align="center">CoL</td>
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<td align="center">1</td>
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<td align="center">419388003</td>
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</tr>
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<tr class="odd">
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<td align="center">B_ESCHR_COLI</td>
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<td align="center">Escherichia coli</td>
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<td align="center">Bacteria</td>
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<td align="center">Proteobacteria</td>
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<td align="center">Gammaproteobacteria</td>
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<td align="center">Enterobacterales</td>
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<td align="center">Enterobacteriaceae</td>
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<td align="center">Escherichia</td>
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<td align="center">coli</td>
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<td align="center"></td>
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<td align="center">species</td>
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<td align="center">Castellani et al., 1919</td>
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<td align="center">3254b3db31bf16fdde669ac57bf8c4fe</td>
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<td align="center">CoL</td>
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<td align="center">1</td>
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<td align="center">112283007</td>
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</tr>
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<tr class="even">
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<td align="center">B_ESCHR_FRGS</td>
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<td align="center">Escherichia fergusonii</td>
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<td align="center">Bacteria</td>
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<td align="center">Proteobacteria</td>
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<td align="center">Gammaproteobacteria</td>
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<td align="center">Enterobacterales</td>
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<td align="center">Enterobacteriaceae</td>
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<td align="center">Escherichia</td>
|
||
<td align="center">fergusonii</td>
|
||
<td align="center"></td>
|
||
<td align="center">species</td>
|
||
<td align="center">Farmer et al., 1985</td>
|
||
<td align="center">82d98b10c456ce5f4c8c515f4e1567e2</td>
|
||
<td align="center">CoL</td>
|
||
<td align="center">1</td>
|
||
<td align="center">72461005</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">B_ESCHR_HRMN</td>
|
||
<td align="center">Escherichia hermannii</td>
|
||
<td align="center">Bacteria</td>
|
||
<td align="center">Proteobacteria</td>
|
||
<td align="center">Gammaproteobacteria</td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center">Enterobacteriaceae</td>
|
||
<td align="center">Escherichia</td>
|
||
<td align="center">hermannii</td>
|
||
<td align="center"></td>
|
||
<td align="center">species</td>
|
||
<td align="center">Brenner et al., 1983</td>
|
||
<td align="center">b16086aee36e3b46b565510083ab4b65</td>
|
||
<td align="center">CoL</td>
|
||
<td align="center">1</td>
|
||
<td align="center">85786000</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">B_ESCHR_MRMT</td>
|
||
<td align="center">Escherichia marmotae</td>
|
||
<td align="center">Bacteria</td>
|
||
<td align="center">Proteobacteria</td>
|
||
<td align="center">Gammaproteobacteria</td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center">Enterobacteriaceae</td>
|
||
<td align="center">Escherichia</td>
|
||
<td align="center">marmotae</td>
|
||
<td align="center"></td>
|
||
<td align="center">species</td>
|
||
<td align="center">Liu et al., 2015</td>
|
||
<td align="center">792928</td>
|
||
<td align="center">DSMZ</td>
|
||
<td align="center">1</td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div id="antibiotic-agents" class="section level2">
|
||
<h2 class="hasAnchor">
|
||
<a href="#antibiotic-agents" class="anchor"></a>Antibiotic agents</h2>
|
||
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
|
||
<div id="source-1" class="section level4">
|
||
<h4 class="hasAnchor">
|
||
<a href="#source-1" class="anchor"></a>Source</h4>
|
||
<p>This data set contains all EARS-Net and ATC codes gathered from WHO and WHONET, and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
|
||
<ul>
|
||
<li>
|
||
<a href="https://www.whocc.no/atc_ddd_index/">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is frelly available from the WHO CC website for personal use)</li>
|
||
<li><a href="https://pubchem.ncbi.nlm.nih.gov">PubChem by the US National Library of Medicine</a></li>
|
||
<li><a href="https://whonet.org">WHONET software 2019</a></li>
|
||
</ul>
|
||
</div>
|
||
<div id="structure-1" class="section level4">
|
||
<h4 class="hasAnchor">
|
||
<a href="#structure-1" class="anchor"></a>Structure</h4>
|
||
<p>A data set with 456 rows and 14 columns, containing the following column names:</p>
|
||
<p><em>ab, atc, cid, name, group, atc_group1, atc_group2, abbreviations, synonyms, oral_ddd, oral_units, iv_ddd, iv_units, loinc</em>.</p>
|
||
</div>
|
||
<div id="download-1" class="section level4">
|
||
<h4 class="hasAnchor">
|
||
<a href="#download-1" class="anchor"></a>Download</h4>
|
||
<p>Download the data set preferably in the software you use, so the data file already has the correct data structure. Below files were updated on 31 July 2020 12:12:13 CEST.</p>
|
||
<ul>
|
||
<li><p>R file (.rds): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/antibiotics.rds">from GitLab</a> (file size: 37.3 kB)</p></li>
|
||
<li><p>Excel workbook (.xlsx): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.xlsx">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/antibiotics.xlsx">from GitLab</a> (file size: 64.5 kB)</p></li>
|
||
<li><p>SPSS file (.sav): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sav">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/antibiotics.sav">from GitLab</a> (file size: 1.3 MB)</p></li>
|
||
<li><p>Stata file (.dta): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sav">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/antibiotics.sav">from GitLab</a> (file size: 1.3 MB)</p></li>
|
||
<li><p>SAS file (.sas): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.dta">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/antibiotics.dta">from GitLab</a> (file size: 321.8 kB)</p></li>
|
||
<li><p>Tab separated file (.txt): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.txt">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/antibiotics.txt">from GitLab</a> (file size: 146.1 kB)</p></li>
|
||
</ul>
|
||
</div>
|
||
<div id="example-1" class="section level4">
|
||
<h4 class="hasAnchor">
|
||
<a href="#example-1" class="anchor"></a>Example</h4>
|
||
<p>Example rows:</p>
|
||
<table class="table">
|
||
<colgroup>
|
||
<col width="1%">
|
||
<col width="2%">
|
||
<col width="3%">
|
||
<col width="9%">
|
||
<col width="8%">
|
||
<col width="14%">
|
||
<col width="19%">
|
||
<col width="6%">
|
||
<col width="11%">
|
||
<col width="3%">
|
||
<col width="3%">
|
||
<col width="2%">
|
||
<col width="3%">
|
||
<col width="10%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="center">ab</th>
|
||
<th align="center">atc</th>
|
||
<th align="center">cid</th>
|
||
<th align="center">name</th>
|
||
<th align="center">group</th>
|
||
<th align="center">atc_group1</th>
|
||
<th align="center">atc_group2</th>
|
||
<th align="center">abbreviations</th>
|
||
<th align="center">synonyms</th>
|
||
<th align="center">oral_ddd</th>
|
||
<th align="center">oral_units</th>
|
||
<th align="center">iv_ddd</th>
|
||
<th align="center">iv_units</th>
|
||
<th align="center">loinc</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="center">AMK</td>
|
||
<td align="center">J01GB06</td>
|
||
<td align="center">37768</td>
|
||
<td align="center">Amikacin</td>
|
||
<td align="center">Aminoglycosides</td>
|
||
<td align="center">Aminoglycoside antibacterials</td>
|
||
<td align="center">Other aminoglycosides</td>
|
||
<td align="center">ak, ami, amik, …</td>
|
||
<td align="center">amicacin, amikacillin, amikacin, …</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">1.0</td>
|
||
<td align="center">g</td>
|
||
<td align="center">13546-7, 15098-7, 17798-0, …</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">AMX</td>
|
||
<td align="center">J01CA04</td>
|
||
<td align="center">33613</td>
|
||
<td align="center">Amoxicillin</td>
|
||
<td align="center">Beta-lactams/penicillins</td>
|
||
<td align="center">Beta-lactam antibacterials, penicillins</td>
|
||
<td align="center">Penicillins with extended spectrum</td>
|
||
<td align="center">ac, amox, amx</td>
|
||
<td align="center">actimoxi, amoclen, amolin, …</td>
|
||
<td align="center">1.0</td>
|
||
<td align="center">g</td>
|
||
<td align="center">1.0</td>
|
||
<td align="center">g</td>
|
||
<td align="center">16365-9, 25274-2, 3344-9, …</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">AMC</td>
|
||
<td align="center">J01CR02</td>
|
||
<td align="center">23665637</td>
|
||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||
<td align="center">Beta-lactams/penicillins</td>
|
||
<td align="center">Beta-lactam antibacterials, penicillins</td>
|
||
<td align="center">Combinations of penicillins, incl. beta-lactamase inhibitors</td>
|
||
<td align="center">a/c, amcl, aml, …</td>
|
||
<td align="center">amocla, amoclan, amoclav, …</td>
|
||
<td align="center">1.0</td>
|
||
<td align="center">g</td>
|
||
<td align="center">3.0</td>
|
||
<td align="center">g</td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">AMP</td>
|
||
<td align="center">J01CA01</td>
|
||
<td align="center">6249</td>
|
||
<td align="center">Ampicillin</td>
|
||
<td align="center">Beta-lactams/penicillins</td>
|
||
<td align="center">Beta-lactam antibacterials, penicillins</td>
|
||
<td align="center">Penicillins with extended spectrum</td>
|
||
<td align="center">am, amp, ampi</td>
|
||
<td align="center">acillin, adobacillin, amblosin, …</td>
|
||
<td align="center">2.0</td>
|
||
<td align="center">g</td>
|
||
<td align="center">2.0</td>
|
||
<td align="center">g</td>
|
||
<td align="center">21066-6, 3355-5, 33562-0, …</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">AZM</td>
|
||
<td align="center">J01FA10</td>
|
||
<td align="center">447043</td>
|
||
<td align="center">Azithromycin</td>
|
||
<td align="center">Macrolides/lincosamides</td>
|
||
<td align="center">Macrolides, lincosamides and streptogramins</td>
|
||
<td align="center">Macrolides</td>
|
||
<td align="center">az, azi, azit, …</td>
|
||
<td align="center">aritromicina, azasite, azenil, …</td>
|
||
<td align="center">0.3</td>
|
||
<td align="center">g</td>
|
||
<td align="center">0.5</td>
|
||
<td align="center">g</td>
|
||
<td align="center">16420-2, 25233-8</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">CZO</td>
|
||
<td align="center">J01DB04</td>
|
||
<td align="center">33255</td>
|
||
<td align="center">Cefazolin</td>
|
||
<td align="center">Cephalosporins (1st gen.)</td>
|
||
<td align="center">Other beta-lactam antibacterials</td>
|
||
<td align="center">First-generation cephalosporins</td>
|
||
<td align="center">cfz, cfzl, cz, …</td>
|
||
<td align="center">atirin, cefamezin, cefamezine, …</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">3.0</td>
|
||
<td align="center">g</td>
|
||
<td align="center">16566-2, 25235-3, 3442-1, …</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div id="antiviral-agents" class="section level2">
|
||
<h2 class="hasAnchor">
|
||
<a href="#antiviral-agents" class="anchor"></a>Antiviral agents</h2>
|
||
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
|
||
<div id="source-2" class="section level4">
|
||
<h4 class="hasAnchor">
|
||
<a href="#source-2" class="anchor"></a>Source</h4>
|
||
<p>This data set contains all ATC codes gathered from WHO and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
|
||
<ul>
|
||
<li>
|
||
<a href="https://www.whocc.no/atc_ddd_index/">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is frelly available from the WHO CC website for personal use)</li>
|
||
<li><a href="https://pubchem.ncbi.nlm.nih.gov">PubChem by the US National Library of Medicine</a></li>
|
||
</ul>
|
||
</div>
|
||
<div id="structure-2" class="section level4">
|
||
<h4 class="hasAnchor">
|
||
<a href="#structure-2" class="anchor"></a>Structure</h4>
|
||
<p>A data set with 102 rows and 9 columns, containing the following column names:</p>
|
||
<p><em>atc, cid, name, atc_group, synonyms, oral_ddd, oral_units, iv_ddd, iv_units</em>.</p>
|
||
</div>
|
||
<div id="download-2" class="section level4">
|
||
<h4 class="hasAnchor">
|
||
<a href="#download-2" class="anchor"></a>Download</h4>
|
||
<p>Download the data set preferably in the software you use, so the data file already has the correct data structure. Below files were updated on 23 November 2019 19:03:43 CET.</p>
|
||
<ul>
|
||
<li><p>R file (.rds): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.rds">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/antivirals.rds">from GitLab</a> (file size: 4.6 kB)</p></li>
|
||
<li><p>Excel workbook (.xlsx): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.xlsx">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/antivirals.xlsx">from GitLab</a> (file size: 13.6 kB)</p></li>
|
||
<li><p>SPSS file (.sav): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sav">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/antivirals.sav">from GitLab</a> (file size: 67.7 kB)</p></li>
|
||
<li><p>Stata file (.dta): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sav">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/antivirals.sav">from GitLab</a> (file size: 67.7 kB)</p></li>
|
||
<li><p>SAS file (.sas): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.dta">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/antivirals.dta">from GitLab</a> (file size: 67.2 kB)</p></li>
|
||
<li><p>Tab separated file (.txt): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.txt">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/antivirals.txt">from GitLab</a> (file size: 16.2 kB)</p></li>
|
||
</ul>
|
||
</div>
|
||
<div id="example-2" class="section level4">
|
||
<h4 class="hasAnchor">
|
||
<a href="#example-2" class="anchor"></a>Example</h4>
|
||
<p>Example rows:</p>
|
||
<table class="table">
|
||
<colgroup>
|
||
<col width="4%">
|
||
<col width="5%">
|
||
<col width="9%">
|
||
<col width="32%">
|
||
<col width="30%">
|
||
<col width="4%">
|
||
<col width="5%">
|
||
<col width="3%">
|
||
<col width="4%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="center">atc</th>
|
||
<th align="center">cid</th>
|
||
<th align="center">name</th>
|
||
<th align="center">atc_group</th>
|
||
<th align="center">synonyms</th>
|
||
<th align="center">oral_ddd</th>
|
||
<th align="center">oral_units</th>
|
||
<th align="center">iv_ddd</th>
|
||
<th align="center">iv_units</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="center">J05AF06</td>
|
||
<td align="center">441300</td>
|
||
<td align="center">abacavir</td>
|
||
<td align="center">Nucleoside and nucleotide reverse transcriptase inhibitors</td>
|
||
<td align="center">Abacavir, Abacavir sulfate, Ziagen</td>
|
||
<td align="center">0.6</td>
|
||
<td align="center">g</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">J05AB01</td>
|
||
<td align="center">135398513</td>
|
||
<td align="center">aciclovir</td>
|
||
<td align="center">Nucleosides and nucleotides excl. reverse transcriptase inhibitors</td>
|
||
<td align="center">Acicloftal, Aciclovier, Aciclovir, …</td>
|
||
<td align="center">4.0</td>
|
||
<td align="center">g</td>
|
||
<td align="center">4</td>
|
||
<td align="center">g</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">J05AF08</td>
|
||
<td align="center">60871</td>
|
||
<td align="center">adefovir dipivoxil</td>
|
||
<td align="center">Nucleoside and nucleotide reverse transcriptase inhibitors</td>
|
||
<td align="center">Adefovir di ester, Adefovir dipivoxil, Adefovir Dipivoxil, …</td>
|
||
<td align="center">10.0</td>
|
||
<td align="center">mg</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">J05AE05</td>
|
||
<td align="center">65016</td>
|
||
<td align="center">amprenavir</td>
|
||
<td align="center">Protease inhibitors</td>
|
||
<td align="center">Agenerase, Amprenavir, Amprenavirum, …</td>
|
||
<td align="center">1.2</td>
|
||
<td align="center">g</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">J05AP06</td>
|
||
<td align="center">16076883</td>
|
||
<td align="center">asunaprevir</td>
|
||
<td align="center">Antivirals for treatment of HCV infections</td>
|
||
<td align="center">Asunaprevir, Sunvepra</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">J05AE08</td>
|
||
<td align="center">148192</td>
|
||
<td align="center">atazanavir</td>
|
||
<td align="center">Protease inhibitors</td>
|
||
<td align="center">Atazanavir, Atazanavir Base, Latazanavir, …</td>
|
||
<td align="center">0.3</td>
|
||
<td align="center">g</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div id="intrinsic-bacterial-resistance" class="section level2">
|
||
<h2 class="hasAnchor">
|
||
<a href="#intrinsic-bacterial-resistance" class="anchor"></a>Intrinsic bacterial resistance</h2>
|
||
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
|
||
<div id="source-3" class="section level4">
|
||
<h4 class="hasAnchor">
|
||
<a href="#source-3" class="anchor"></a>Source</h4>
|
||
<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations.</p>
|
||
<p>The data set is based on ‘EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes’, version 3.1, 2016.</p>
|
||
</div>
|
||
<div id="structure-3" class="section level4">
|
||
<h4 class="hasAnchor">
|
||
<a href="#structure-3" class="anchor"></a>Structure</h4>
|
||
<p>A data set with 49,462 rows and 2 columns, containing the following column names:</p>
|
||
<p><em>microorganism, antibiotic</em>.</p>
|
||
</div>
|
||
<div id="download-3" class="section level4">
|
||
<h4 class="hasAnchor">
|
||
<a href="#download-3" class="anchor"></a>Download</h4>
|
||
<p>Download the data set preferably in the software you use, so the data file already has the correct data structure. Below files were updated on 14 August 2020 14:18:20 CEST.</p>
|
||
<ul>
|
||
<li><p>R file (.rds): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.rds">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/intrinsic_resistant.rds">from GitLab</a> (file size: 96.6 kB)</p></li>
|
||
<li><p>Excel workbook (.xlsx): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.xlsx">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/intrinsic_resistant.xlsx">from GitLab</a> (file size: 0.5 MB)</p></li>
|
||
<li><p>SPSS file (.sav): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sav">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/intrinsic_resistant.sav">from GitLab</a> (file size: 4.2 MB)</p></li>
|
||
<li><p>Stata file (.dta): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sav">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/intrinsic_resistant.sav">from GitLab</a> (file size: 4.2 MB)</p></li>
|
||
<li><p>SAS file (.sas): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.dta">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/intrinsic_resistant.dta">from GitLab</a> (file size: 3.7 MB)</p></li>
|
||
<li><p>Tab separated file (.txt): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.txt">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/intrinsic_resistant.txt">from GitLab</a> (file size: 1.8 MB)</p></li>
|
||
</ul>
|
||
</div>
|
||
<div id="example-3" class="section level4">
|
||
<h4 class="hasAnchor">
|
||
<a href="#example-3" class="anchor"></a>Example</h4>
|
||
<p>Example rows:</p>
|
||
<table class="table">
|
||
<thead><tr class="header">
|
||
<th align="center">microorganism</th>
|
||
<th align="center">antibiotic</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="center">Klebsiella</td>
|
||
<td align="center">Amoxicillin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Klebsiella</td>
|
||
<td align="center">Ampicillin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Klebsiella</td>
|
||
<td align="center">Azithromycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Klebsiella</td>
|
||
<td align="center">Clarithromycin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Klebsiella</td>
|
||
<td align="center">Daptomycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Klebsiella</td>
|
||
<td align="center">Erythromycin</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div id="interpretation-from-mic-values-disk-diameters-to-rsi" class="section level2">
|
||
<h2 class="hasAnchor">
|
||
<a href="#interpretation-from-mic-values-disk-diameters-to-rsi" class="anchor"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
|
||
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
|
||
<div id="source-4" class="section level4">
|
||
<h4 class="hasAnchor">
|
||
<a href="#source-4" class="anchor"></a>Source</h4>
|
||
<p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2019) and EUCAST (2011-2020).</p>
|
||
</div>
|
||
<div id="structure-4" class="section level4">
|
||
<h4 class="hasAnchor">
|
||
<a href="#structure-4" class="anchor"></a>Structure</h4>
|
||
<p>A data set with 18,650 rows and 10 columns, containing the following column names:</p>
|
||
<p><em>guideline, method, site, mo, ab, ref_tbl, disk_dose, breakpoint_S, breakpoint_R, uti</em>.</p>
|
||
</div>
|
||
<div id="download-4" class="section level4">
|
||
<h4 class="hasAnchor">
|
||
<a href="#download-4" class="anchor"></a>Download</h4>
|
||
<p>Download the data set preferably in the software you use, so the data file already has the correct data structure. Below files were updated on 29 July 2020 13:12:34 CEST.</p>
|
||
<ul>
|
||
<li><p>R file (.rds): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/rsi_translation.rds">from GitLab</a> (file size: 55.1 kB)</p></li>
|
||
<li><p>Excel workbook (.xlsx): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.xlsx">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/rsi_translation.xlsx">from GitLab</a> (file size: 0.6 MB)</p></li>
|
||
<li><p>SPSS file (.sav): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sav">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/rsi_translation.sav">from GitLab</a> (file size: 3.4 MB)</p></li>
|
||
<li><p>Stata file (.dta): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sav">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/rsi_translation.sav">from GitLab</a> (file size: 3.4 MB)</p></li>
|
||
<li><p>SAS file (.sas): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.dta">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/rsi_translation.dta">from GitLab</a> (file size: 3 MB)</p></li>
|
||
<li><p>Tab separated file (.txt): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.txt">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/rsi_translation.txt">from GitLab</a> (file size: 1.5 MB)</p></li>
|
||
</ul>
|
||
</div>
|
||
<div id="example-4" class="section level4">
|
||
<h4 class="hasAnchor">
|
||
<a href="#example-4" class="anchor"></a>Example</h4>
|
||
<p>Example rows:</p>
|
||
<table class="table">
|
||
<colgroup>
|
||
<col width="8%">
|
||
<col width="5%">
|
||
<col width="4%">
|
||
<col width="12%">
|
||
<col width="20%">
|
||
<col width="17%">
|
||
<col width="7%">
|
||
<col width="9%">
|
||
<col width="9%">
|
||
<col width="4%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="center">guideline</th>
|
||
<th align="center">method</th>
|
||
<th align="center">site</th>
|
||
<th align="center">mo</th>
|
||
<th align="center">ab</th>
|
||
<th align="center">ref_tbl</th>
|
||
<th align="center">disk_dose</th>
|
||
<th align="center">breakpoint_S</th>
|
||
<th align="center">breakpoint_R</th>
|
||
<th align="center">uti</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="center">EUCAST 2020</td>
|
||
<td align="center">DISK</td>
|
||
<td align="center"></td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center">20-10ug</td>
|
||
<td align="center">19</td>
|
||
<td align="center">19</td>
|
||
<td align="center">FALSE</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">EUCAST 2020</td>
|
||
<td align="center">DISK</td>
|
||
<td align="center">UTI</td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center">20-10ug</td>
|
||
<td align="center">16</td>
|
||
<td align="center">16</td>
|
||
<td align="center">TRUE</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">EUCAST 2020</td>
|
||
<td align="center">MIC</td>
|
||
<td align="center"></td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center"></td>
|
||
<td align="center">8</td>
|
||
<td align="center">8</td>
|
||
<td align="center">FALSE</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">EUCAST 2020</td>
|
||
<td align="center">MIC</td>
|
||
<td align="center">UTI</td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center"></td>
|
||
<td align="center">32</td>
|
||
<td align="center">32</td>
|
||
<td align="center">TRUE</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">EUCAST 2020</td>
|
||
<td align="center">MIC</td>
|
||
<td align="center"></td>
|
||
<td align="center">Actinomyces</td>
|
||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||
<td align="center">Anaerobes, Grampositive</td>
|
||
<td align="center"></td>
|
||
<td align="center">4</td>
|
||
<td align="center">8</td>
|
||
<td align="center">FALSE</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">EUCAST 2020</td>
|
||
<td align="center">MIC</td>
|
||
<td align="center"></td>
|
||
<td align="center">Bacteroides</td>
|
||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||
<td align="center">Anaerobes, Gramnegative</td>
|
||
<td align="center"></td>
|
||
<td align="center">4</td>
|
||
<td align="center">8</td>
|
||
<td align="center">FALSE</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||
|
||
<nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2>
|
||
</nav>
|
||
</div>
|
||
|
||
</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/">Alexander 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">
|
||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||
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|
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