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<meta charset="utf-8">
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<title>Data sets for download • AMR (for R)</title>
<title>Data sets for download / own use • AMR (for R)</title>
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<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">1.3.0.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9005</span>
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</div>
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<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our free data sets
Download our reference data sets for own use
</a>
</li>
<li>
@ -190,7 +190,7 @@
</header><script src="datasets_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download</h1>
<h1 data-toc-skip>Data sets for download / own use</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
@ -200,16 +200,18 @@
<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>
<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>
<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>
<div id="microorganisms" class="section level2">
<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 teach your laboratory information system (LIS) about intrinsic resistance!</p>
<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. We also offer all data sets in formats for R, SPSS, SAS, Stata and Excel.</p>
<p><em>Note: Years and dates of updates mentioned on this page, are from on <code>AMR</code> package version 1.3.0.9005, online released on 17 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>
<div id="microorganisms-currently-accepted-names" class="section level2">
<h2 class="hasAnchor">
<a href="#microorganisms" class="anchor"></a>Microorganisms</h2>
<a href="#microorganisms-currently-accepted-names" class="anchor"></a>Microorganisms (currently accepted names)</h2>
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
<div id="source" class="section level4">
<h4 class="hasAnchor">
<a href="#source" class="anchor"></a>Source</h4>
<p>It was last updated on 28 July 2020 20:52:40 CEST.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds">R file (.rds)</a>, 2.7 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.xlsx">Excel workbook (.xlsx)</a>, 6.1 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sav">SPSS file (.sav)</a>, 28.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sav">Stata file (.dta)</a>, 28.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.dta">SAS file (.sas)</a>, 25.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.txt">Tab separated file (.txt)</a>, 13.3 MB.</p>
<div id="source" class="section level3">
<h3 class="hasAnchor">
<a href="#source" class="anchor"></a>Source</h3>
<p>Our full taxonomy of microorganisms is based on the authoritative and comprehensive:</p>
<ul>
<li>
@ -218,12 +220,11 @@
<a href="https://lpsn.dsmz.de">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, included version: May 2020)</li>
</ul>
</div>
<div id="structure" class="section level4">
<h4 class="hasAnchor">
<a href="#structure" class="anchor"></a>Structure</h4>
<p>A data set with 67,151 rows and 16 columns, containing the following column names:</p>
<p><em>mo, fullname, kingdom, phylum, class, order, family, genus, species, subspecies, rank, ref, species_id, source, prevalence, snomed</em>.</p>
<p>Included per taxonomic kingdom:</p>
<div id="structure" class="section level3">
<h3 class="hasAnchor">
<a href="#structure" class="anchor"></a>Structure</h3>
<p>A data set with 67,151 rows and 16 columns, containing the following column names:<br><em>mo, fullname, kingdom, phylum, class, order, family, genus, species, subspecies, rank, ref, species_id, source, prevalence, snomed</em>.</p>
<p>Included (sub)species per taxonomic kingdom:</p>
<table class="table">
<thead><tr class="header">
<th align="center">Kingdom</th>
@ -256,23 +257,6 @@
</tr>
</tbody>
</table>
</div>
<div id="download" class="section level4">
<h4 class="hasAnchor">
<a href="#download" 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 28 July 2020 20:52:40 CEST.</p>
<ul>
<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>
<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>
<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>
<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>
<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>
<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>
</ul>
</div>
<div id="example" class="section level4">
<h4 class="hasAnchor">
<a href="#example" class="anchor"></a>Example</h4>
<p>Example rows when filtering on genus <em>Escherichia</em>:</p>
<table class="table">
<colgroup>
@ -424,13 +408,68 @@
</table>
</div>
</div>
<div id="microorganisms-previously-accepted-names" class="section level2">
<h2 class="hasAnchor">
<a href="#microorganisms-previously-accepted-names" class="anchor"></a>Microorganisms (previously accepted names)</h2>
<p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 28 May 2020 11:17:56 CEST.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.rds">R file (.rds)</a>, 0.3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.xlsx">Excel workbook (.xlsx)</a>, 0.4 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sav">SPSS file (.sav)</a>, 1.9 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sav">Stata file (.dta)</a>, 1.9 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.dta">SAS file (.sas)</a>, 1.8 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.txt">Tab separated file (.txt)</a>, 0.8 MB.</p>
<div id="source-1" class="section level3">
<h3 class="hasAnchor">
<a href="#source-1" class="anchor"></a>Source</h3>
<p>This data set contains old, previously accepted taxonomic names. The data sources are the same as the <code>microorganisms</code> data set:</p>
<ul>
<li>
<a href="http://www.catalogueoflife.org">Catalogue of Life</a> (included version: 2019)</li>
<li>
<a href="https://lpsn.dsmz.de">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, included version: May 2020)</li>
</ul>
</div>
<div id="structure-1" class="section level3">
<h3 class="hasAnchor">
<a href="#structure-1" class="anchor"></a>Structure</h3>
<p>A data set with 12,708 rows and 4 columns, containing the following column names:<br><em>fullname, fullname_new, ref, prevalence</em>.</p>
<p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>fullname</em>. For the scientific reference of the new names, i.e. of column <em>fullname_new</em>, see the <code>microorganisms</code> data set.</p>
<p>Example rows when filtering on <em>Escherichia</em>:</p>
<table class="table">
<thead><tr class="header">
<th align="center">fullname</th>
<th align="center">fullname_new</th>
<th align="center">ref</th>
<th align="center">prevalence</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">Escherichia adecarboxylata</td>
<td align="center">Leclercia adecarboxylata</td>
<td align="center">Leclerc, 1962</td>
<td align="center">1</td>
</tr>
<tr class="even">
<td align="center">Escherichia blattae</td>
<td align="center">Shimwellia blattae</td>
<td align="center">Burgess et al., 1973</td>
<td align="center">1</td>
</tr>
<tr class="odd">
<td align="center">Escherichia vulneris</td>
<td align="center">Pseudescherichia vulneris</td>
<td align="center">Brenner et al., 1983</td>
<td align="center">1</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>It was last updated on 31 July 2020 12:12:13 CEST.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds">R file (.rds)</a>, 37 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.xlsx">Excel workbook (.xlsx)</a>, 65 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sav">SPSS file (.sav)</a>, 1.3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sav">Stata file (.dta)</a>, 1.3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.dta">SAS file (.sas)</a>, 0.3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.txt">Tab separated file (.txt)</a>, 0.1 MB.</p>
<div id="source-2" class="section level3">
<h3 class="hasAnchor">
<a href="#source-2" class="anchor"></a>Source</h3>
<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>
@ -439,28 +478,10 @@
<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>
<div id="structure-2" class="section level3">
<h3 class="hasAnchor">
<a href="#structure-2" class="anchor"></a>Structure</h3>
<p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>ab, atc, cid, name, group, atc_group1, atc_group2, abbreviations, synonyms, oral_ddd, oral_units, iv_ddd, iv_units, loinc</em>.</p>
<p>Example rows:</p>
<table class="table">
<colgroup>
@ -600,9 +621,11 @@
<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>It was last updated on 23 November 2019 19:03:43 CET.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.rds">R file (.rds)</a>, 5 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.xlsx">Excel workbook (.xlsx)</a>, 14 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sav">SPSS file (.sav)</a>, 68 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sav">Stata file (.dta)</a>, 68 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.dta">SAS file (.sas)</a>, 67 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.txt">Tab separated file (.txt)</a>, 16 kB.</p>
<div id="source-3" class="section level3">
<h3 class="hasAnchor">
<a href="#source-3" class="anchor"></a>Source</h3>
<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>
@ -610,28 +633,10 @@
<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>
<div id="structure-3" class="section level3">
<h3 class="hasAnchor">
<a href="#structure-3" class="anchor"></a>Structure</h3>
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc, cid, name, atc_group, synonyms, oral_ddd, oral_units, iv_ddd, iv_units</em>.</p>
<p>Example rows:</p>
<table class="table">
<colgroup>
@ -731,35 +736,19 @@
<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>It was last updated on 14 August 2020 14:18:20 CEST.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.rds">R file (.rds)</a>, 97 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.xlsx">Excel workbook (.xlsx)</a>, 0.5 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sav">SPSS file (.sav)</a>, 4.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sav">Stata file (.dta)</a>, 4.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.dta">SAS file (.sas)</a>, 3.7 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.txt">Tab separated file (.txt)</a>, 1.8 MB.</p>
<div id="source-4" class="section level3">
<h3 class="hasAnchor">
<a href="#source-4" class="anchor"></a>Source</h3>
<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>
<div id="structure-4" class="section level3">
<h3 class="hasAnchor">
<a href="#structure-4" class="anchor"></a>Structure</h3>
<p>A data set with 49,462 rows and 2 columns, containing the following column names:<br><em>microorganism, antibiotic</em>.</p>
<p>Example rows when filtering on <em>Klebsiella</em>:</p>
<table class="table">
<thead><tr class="header">
<th align="center">microorganism</th>
@ -798,33 +787,17 @@
<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>It was last updated on 29 July 2020 13:12:34 CEST.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds">R file (.rds)</a>, 55 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.xlsx">Excel workbook (.xlsx)</a>, 0.6 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sav">SPSS file (.sav)</a>, 3.4 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sav">Stata file (.dta)</a>, 3.4 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.dta">SAS file (.sas)</a>, 3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.txt">Tab separated file (.txt)</a>, 1.5 MB.</p>
<div id="source-5" class="section level3">
<h3 class="hasAnchor">
<a href="#source-5" class="anchor"></a>Source</h3>
<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>
<div id="structure-5" class="section level3">
<h3 class="hasAnchor">
<a href="#structure-5" class="anchor"></a>Structure</h3>
<p>A data set with 18,650 rows and 10 columns, containing the following column names:<br><em>guideline, method, site, mo, ab, ref_tbl, disk_dose, breakpoint_S, breakpoint_R, uti</em>.</p>
<p>Example rows:</p>
<table class="table">
<colgroup>