Built site for AMR: 1.8.2.9004@0d8b098

2025-07-27 18:27:58 +02:00 · 2022-10-05 10:32:07 +00:00
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+++ b/articles/datasets.html
@ -24,7 +24,7 @@
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    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
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  <main id="main" class="col-md-9"><div class="page-header">
      <img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
            
-            <h4 data-toc-skip class="date">01 September 2022</h4>
+            <h4 data-toc-skip class="date">05 October 2022</h4>
      
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
      <div class="d-none name"><code>datasets.Rmd</code></div>
@ -172,41 +172,40 @@
 <p>All reference data (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are reliable, up-to-date and freely available. We continually export our data sets to formats for use in R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated text files that are machine-readable and suitable for input in any software program, such as laboratory information systems.</p>
 <p>On this page, we explain how to download them and how the structure of the data sets look like.</p>
 <div class="section level2">
-<h2 id="microorganisms-microbial-taxonomy-currently-accepted-names">
-<code>microorganisms</code>: Microbial Taxonomy (currently accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-microbial-taxonomy-currently-accepted-names"></a>
+<h2 id="microorganisms-full-microbial-taxonomy">
+<code>microorganisms</code>: Full Microbial Taxonomy<a class="anchor" aria-label="anchor" href="#microorganisms-full-microbial-taxonomy"></a>
 </h2>
-<p>A data set with 70,764 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
+<p>A data set with 48,787 rows and 22 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>source</em>, <em>lpsn</em>, <em>lpsn_parent</em>, <em>lpsn_renamed_to</em>, <em>gbif</em>, <em>gbif_parent</em>, <em>gbif_renamed_to</em>, <em>prevalence</em> and <em>snomed</em>.</p>
 <p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 1 September 2022 13:33:21 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
+<p>It was last updated on 5 October 2022 10:27:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">original R Data Structure (RDS) file</a> (1.3 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">original R Data Structure (RDS) file</a> (1.1 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">tab-separated text file</a> (13.1 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">tab-separated text file</a> (0.4 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Microsoft Excel workbook</a> (5.1 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Microsoft Excel workbook</a> (4.8 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.feather" class="external-link">Apache Feather file</a> (5.6 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.feather" class="external-link">Apache Feather file</a> (5.1 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.parquet" class="external-link">Apache Parquet file</a> (2.7 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.parquet" class="external-link">Apache Parquet file</a> (2.5 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS data file</a> (69.1 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS data file</a> (47.7 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">IBM SPSS Statistics data file</a> (20.8 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">IBM SPSS Statistics data file</a> (15.8 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata DTA file</a> (62.2 MB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata DTA file</a> (44.4 MB)</li>
 </ul>
 <p><strong>NOTE: The exported files for Excel, SAS, SPSS and Stata contain only the first 50 SNOMED codes per record, as their file size would otherwise exceed 100 MB; the file size limit of GitHub.</strong> Advice? Use R instead.</p>
 <div class="section level3">
 <h3 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a>
 </h3>
-<p>Our full taxonomy of microorganisms is based on the authoritative and comprehensive:</p>
+<p>This data set contains the full microbial taxonomy of five kingdoms from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF):</p>
 <ul>
-<li>
-<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (included version: 2019)</li>
-<li>
-<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
-<li>US Edition of SNOMED CT from 1 September 2020, retrieved from the <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)</a>, OID 2.16.840.1.114222.4.11.1009, version 12</li>
+<li>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong> International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; . Accessed from <a href="https://lpsn.dsmz.de" class="external-link uri">https://lpsn.dsmz.de</a> on 12 September, 2022.</li>
+<li>GBIF Secretariat (November 26, 2021). GBIF Backbone Taxonomy. Checklist dataset . Accessed from <a href="https://www.gbif.org" class="external-link uri">https://www.gbif.org</a> on 12 September, 2022.</li>
+<li>Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link uri">https://phinvads.cdc.gov</a>
+</li>
 </ul>
 </div>
 <div class="section level3">
@ -221,53 +220,60 @@
 <tbody>
 <tr class="odd">
 <td align="center">(unknown kingdom)</td>
-<td align="center">5</td>
+<td align="center">3</td>
 </tr>
 <tr class="even">
 <td align="center">Animalia</td>
-<td align="center">2,153</td>
+<td align="center">1,523</td>
 </tr>
 <tr class="odd">
 <td align="center">Archaea</td>
-<td align="center">694</td>
+<td align="center">1,237</td>
 </tr>
 <tr class="even">
 <td align="center">Bacteria</td>
-<td align="center">22,852</td>
+<td align="center">33,713</td>
 </tr>
 <tr class="odd">
-<td align="center">Chromista</td>
-<td align="center">32,167</td>
+<td align="center">Fungi</td>
+<td align="center">7,365</td>
 </tr>
 <tr class="even">
-<td align="center">Fungi</td>
-<td align="center">9,582</td>
+<td align="center">Protozoa</td>
+<td align="center">4,946</td>
 </tr>
 </tbody>
 </table>
 <p>Example rows when filtering on genus <em>Escherichia</em>:</p>
 <table style="width:100%;" class="table">
 <colgroup>
-<col width="5%">
-<col width="8%">
 <col width="3%">
-<col width="5%">
 <col width="7%">
-<col width="6%">
-<col width="7%">
-<col width="4%">
-<col width="4%">
-<col width="4%">
-<col width="3%">
-<col width="9%">
-<col width="4%">
+<col width="2%">
 <col width="2%">
 <col width="4%">
-<col width="16%">
+<col width="5%">
+<col width="5%">
+<col width="5%">
+<col width="3%">
+<col width="4%">
+<col width="3%">
+<col width="2%">
+<col width="7%">
+<col width="2%">
+<col width="2%">
+<col width="3%">
+<col width="4%">
+<col width="2%">
+<col width="3%">
+<col width="4%">
+<col width="3%">
+<col width="12%">
 </colgroup>
 <thead><tr class="header">
 <th align="center">mo</th>
 <th align="center">fullname</th>
+<th align="center">status</th>
 <th align="center">kingdom</th>
 <th align="center">phylum</th>
 <th align="center">class</th>
@ -278,8 +284,13 @@
 <th align="center">subspecies</th>
 <th align="center">rank</th>
 <th align="center">ref</th>
-<th align="center">species_id</th>
 <th align="center">source</th>
+<th align="center">lpsn</th>
+<th align="center">lpsn_parent</th>
+<th align="center">lpsn_renamed_to</th>
+<th align="center">gbif</th>
+<th align="center">gbif_parent</th>
+<th align="center">gbif_renamed_to</th>
 <th align="center">prevalence</th>
 <th align="center">snomed</th>
 </tr></thead>
@ -287,8 +298,9 @@
 <tr class="odd">
 <td align="center">B_ESCHR</td>
 <td align="center">Escherichia</td>
+<td align="center">accepted</td>
 <td align="center">Bacteria</td>
-<td align="center">Proteobacteria</td>
+<td align="center">Pseudomonadota</td>
 <td align="center">Gammaproteobacteria</td>
 <td align="center">Enterobacterales</td>
 <td align="center">Enterobacteriaceae</td>
@ -296,17 +308,47 @@
 <td align="center"></td>
 <td align="center"></td>
 <td align="center">genus</td>
-<td align="center"></td>
-<td align="center">515602</td>
+<td align="center">Castellani et al., 1919</td>
 <td align="center">LPSN</td>
+<td align="center">515602</td>
+<td align="center">482</td>
+<td align="center"></td>
+<td align="center">3221780</td>
+<td align="center">4899</td>
+<td align="center"></td>
 <td align="center">1</td>
-<td align="center">64735005</td>
+<td align="center">407310004, 407251000, 407281008, …</td>
 </tr>
 <tr class="even">
+<td align="center">B_ESCHR_ADCR</td>
+<td align="center">Escherichia adecarboxylata</td>
+<td align="center">synonym</td>
+<td align="center">Bacteria</td>
+<td align="center">Pseudomonadota</td>
+<td align="center">Gammaproteobacteria</td>
+<td align="center">Enterobacterales</td>
+<td align="center">Enterobacteriaceae</td>
+<td align="center">Escherichia</td>
+<td align="center">adecarboxylata</td>
+<td align="center"></td>
+<td align="center">species</td>
+<td align="center">Leclerc, 1962</td>
+<td align="center">LPSN</td>
+<td align="center">776052</td>
+<td align="center">515602</td>
+<td align="center">777447</td>
+<td align="center"></td>
+<td align="center"></td>
+<td align="center"></td>
+<td align="center">1</td>
+<td align="center"></td>
+</tr>
+<tr class="odd">
 <td align="center">B_ESCHR_ALBR</td>
 <td align="center">Escherichia albertii</td>
+<td align="center">accepted</td>
 <td align="center">Bacteria</td>
-<td align="center">Proteobacteria</td>
+<td align="center">Pseudomonadota</td>
 <td align="center">Gammaproteobacteria</td>
 <td align="center">Enterobacterales</td>
 <td align="center">Enterobacteriaceae</td>
@ -315,16 +357,46 @@
 <td align="center"></td>
 <td align="center">species</td>
 <td align="center">Huys et al., 2003</td>
-<td align="center">776053</td>
 <td align="center">LPSN</td>
+<td align="center">776053</td>
+<td align="center">515602</td>
+<td align="center"></td>
+<td align="center">5427575</td>
+<td align="center">3221780</td>
+<td align="center"></td>
 <td align="center">1</td>
 <td align="center">419388003</td>
 </tr>
+<tr class="even">
+<td align="center">B_ESCHR_BLTT</td>
+<td align="center">Escherichia blattae</td>
+<td align="center">synonym</td>
+<td align="center">Bacteria</td>
+<td align="center">Pseudomonadota</td>
+<td align="center">Gammaproteobacteria</td>
+<td align="center">Enterobacterales</td>
+<td align="center">Enterobacteriaceae</td>
+<td align="center">Escherichia</td>
+<td align="center">blattae</td>
+<td align="center"></td>
+<td align="center">species</td>
+<td align="center">Burgess et al., 1973</td>
+<td align="center">LPSN</td>
+<td align="center">776056</td>
+<td align="center">515602</td>
+<td align="center">788468</td>
+<td align="center"></td>
+<td align="center"></td>
+<td align="center"></td>
+<td align="center">1</td>
+<td align="center"></td>
+</tr>
 <tr class="odd">
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">Escherichia coli</td>
+<td align="center">accepted</td>
 <td align="center">Bacteria</td>
-<td align="center">Proteobacteria</td>
+<td align="center">Pseudomonadota</td>
 <td align="center">Gammaproteobacteria</td>
 <td align="center">Enterobacterales</td>
 <td align="center">Enterobacteriaceae</td>
@ -333,135 +405,39 @@
 <td align="center"></td>
 <td align="center">species</td>
 <td align="center">Castellani et al., 1919</td>
-<td align="center">776057</td>
 <td align="center">LPSN</td>
+<td align="center">776057</td>
+<td align="center">515602</td>
+<td align="center"></td>
+<td align="center">6110934</td>
+<td align="center">3221780</td>
+<td align="center"></td>
 <td align="center">1</td>
 <td align="center">1095001000112106, 715307006, 737528008, …</td>
 </tr>
 <tr class="even">
-<td align="center">B_ESCHR_FRGS</td>
-<td align="center">Escherichia fergusonii</td>
+<td align="center">B_ESCHR_DYSN</td>
+<td align="center">Escherichia dysenteriae</td>
+<td align="center">accepted</td>
 <td align="center">Bacteria</td>
-<td align="center">Proteobacteria</td>
+<td align="center">Pseudomonadota</td>
 <td align="center">Gammaproteobacteria</td>
 <td align="center">Enterobacterales</td>
 <td align="center">Enterobacteriaceae</td>
 <td align="center">Escherichia</td>
-<td align="center">fergusonii</td>
+<td align="center">dysenteriae</td>
 <td align="center"></td>
 <td align="center">species</td>
-<td align="center">Farmer et al., 1985</td>
-<td align="center">776059</td>
-<td align="center">LPSN</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">776060</td>
-<td align="center">LPSN</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">GBIF</td>
+<td align="center"></td>
+<td align="center"></td>
+<td align="center"></td>
+<td align="center">10862979</td>
+<td align="center">3221780</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">LPSN</td>
-<td align="center">1</td>
-<td align="center">14961000146107</td>
-</tr>
-</tbody>
-</table>
-</div>
-</div>
-<div class="section level2">
-<h2 id="microorganisms-old-microbial-taxonomy-previously-accepted-names">
-<code>microorganisms.old</code>: Microbial Taxonomy (previously accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-old-microbial-taxonomy-previously-accepted-names"></a>
-</h2>
-<p>A data set with 14,338 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>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>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 1 September 2022 13:33:21 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
-<p><strong>Direct download links:</strong></p>
-<ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">original R Data Structure (RDS) file</a> (0.2 MB)<br>
-</li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.txt" class="external-link">tab-separated text file</a> (1 MB)<br>
-</li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.xlsx" class="external-link">Microsoft Excel workbook</a> (0.5 MB)<br>
-</li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.feather" class="external-link">Apache Feather file</a> (0.6 MB)<br>
-</li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.parquet" class="external-link">Apache Parquet file</a> (0.4 MB)<br>
-</li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sas" class="external-link">SAS data file</a> (2.1 MB)<br>
-</li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sav" class="external-link">IBM SPSS Statistics data file</a> (1.3 MB)<br>
-</li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.dta" class="external-link">Stata DTA file</a> (2 MB)</li>
-</ul>
-<div class="section level3">
-<h3 id="source-1">Source<a class="anchor" aria-label="anchor" href="#source-1"></a>
-</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" class="external-link">Catalogue of Life</a> (included version: 2019)</li>
-<li>
-<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
-</ul>
-</div>
-<div class="section level3">
-<h3 id="example-content-1">Example content<a class="anchor" aria-label="anchor" href="#example-content-1"></a>
-</h3>
-<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>
+<td align="center"></td>
 </tr>
 </tbody>
 </table>
@ -473,7 +449,7 @@
 </h2>
 <p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
 <p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 1 September 2022 13:33:21 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
+<p>It was last updated on 5 October 2022 10:27:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">original R Data Structure (RDS) file</a> (36 kB)<br>
@ -493,7 +469,7 @@
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata DTA file</a> (0.3 MB)</li>
 </ul>
 <div class="section level3">
-<h3 id="source-2">Source<a class="anchor" aria-label="anchor" href="#source-2"></a>
+<h3 id="source-1">Source<a class="anchor" aria-label="anchor" href="#source-1"></a>
 </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>
@ -504,7 +480,7 @@
 </ul>
 </div>
 <div class="section level3">
-<h3 id="example-content-2">Example content<a class="anchor" aria-label="anchor" href="#example-content-2"></a>
+<h3 id="example-content-1">Example content<a class="anchor" aria-label="anchor" href="#example-content-1"></a>
 </h3>
 <table style="width:100%;" class="table">
 <colgroup>
@ -646,7 +622,7 @@
 </h2>
 <p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
 <p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 1 September 2022 13:33:21 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
+<p>It was last updated on 5 October 2022 10:27:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">original R Data Structure (RDS) file</a> (4 kB)<br>
@ -666,7 +642,7 @@
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata DTA file</a> (67 kB)</li>
 </ul>
 <div class="section level3">
-<h3 id="source-3">Source<a class="anchor" aria-label="anchor" href="#source-3"></a>
+<h3 id="source-2">Source<a class="anchor" aria-label="anchor" href="#source-2"></a>
 </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>
@ -676,7 +652,7 @@
 </ul>
 </div>
 <div class="section level3">
-<h3 id="example-content-3">Example content<a class="anchor" aria-label="anchor" href="#example-content-3"></a>
+<h3 id="example-content-2">Example content<a class="anchor" aria-label="anchor" href="#example-content-2"></a>
 </h3>
 <table class="table">
 <colgroup>
@ -778,7 +754,7 @@
 </h2>
 <p>A data set with 20,369 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
 <p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 1 September 2022 13:33:21 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
+<p>It was last updated on 5 October 2022 10:27:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">original R Data Structure (RDS) file</a> (49 kB)<br>
@ -798,12 +774,12 @@
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata DTA file</a> (3.8 MB)</li>
 </ul>
 <div class="section level3">
-<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
+<h3 id="source-3">Source<a class="anchor" aria-label="anchor" href="#source-3"></a>
 </h3>
 <p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2011-2022) and EUCAST (2011-2022).</p>
 </div>
 <div class="section level3">
-<h3 id="example-content-4">Example content<a class="anchor" aria-label="anchor" href="#example-content-4"></a>
+<h3 id="example-content-3">Example content<a class="anchor" aria-label="anchor" href="#example-content-3"></a>
 </h3>
 <table style="width:100%;" class="table">
 <colgroup>
@ -935,9 +911,9 @@
 <h2 id="intrinsic_resistant-intrinsic-bacterial-resistance">
 <code>intrinsic_resistant</code>: Intrinsic Bacterial Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intrinsic-bacterial-resistance"></a>
 </h2>
-<p>A data set with 134,956 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
+<p>A data set with 134,659 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
 <p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 1 September 2022 13:33:21 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
+<p>It was last updated on 5 October 2022 10:27:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">original R Data Structure (RDS) file</a> (78 kB)<br>
@ -950,19 +926,19 @@
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.parquet" class="external-link">Apache Parquet file</a> (0.2 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS data file</a> (10.4 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS data file</a> (9.8 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">IBM SPSS Statistics data file</a> (7.4 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata DTA file</a> (10.2 MB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata DTA file</a> (9.6 MB)</li>
 </ul>
 <div class="section level3">
-<h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></a>
+<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
 </h3>
 <p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes/" class="external-link">‘EUCAST Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ v3.3</a> (2021).</p>
 </div>
 <div class="section level3">
-<h3 id="example-content-5">Example content<a class="anchor" aria-label="anchor" href="#example-content-5"></a>
+<h3 id="example-content-4">Example content<a class="anchor" aria-label="anchor" href="#example-content-4"></a>
 </h3>
 <p>Example rows when filtering on <em>Enterobacter cloacae</em>:</p>
 <table class="table">
@ -1209,7 +1185,7 @@
 </h2>
 <p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
 <p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 1 September 2022 13:33:21 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
+<p>It was last updated on 5 October 2022 10:27:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">original R Data Structure (RDS) file</a> (3 kB)<br>
@ -1229,13 +1205,13 @@
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata DTA file</a> (44 kB)</li>
 </ul>
 <div class="section level3">
-<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
+<h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></a>
 </h3>
 <p>EUCAST breakpoints used in this package are based on the dosages in this data set.</p>
 <p>Currently included dosages in the data set are meant for: <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical Breakpoint Tables’ v11.0</a> (2021).</p>
 </div>
 <div class="section level3">
-<h3 id="example-content-6">Example content<a class="anchor" aria-label="anchor" href="#example-content-6"></a>
+<h3 id="example-content-5">Example content<a class="anchor" aria-label="anchor" href="#example-content-5"></a>
 </h3>
 <table class="table">
 <thead><tr class="header">
@ -1326,14 +1302,14 @@
 </h2>
 <p>A data set with 2,000 rows and 46 columns, containing the following column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>, <em>ward</em>, <em>mo</em>, <em>PEN</em>, <em>OXA</em>, <em>FLC</em>, <em>AMX</em>, <em>AMC</em>, <em>AMP</em>, <em>TZP</em>, <em>CZO</em>, <em>FEP</em>, <em>CXM</em>, <em>FOX</em>, <em>CTX</em>, <em>CAZ</em>, <em>CRO</em>, <em>GEN</em>, <em>TOB</em>, <em>AMK</em>, <em>KAN</em>, <em>TMP</em>, <em>SXT</em>, <em>NIT</em>, <em>FOS</em>, <em>LNZ</em>, <em>CIP</em>, <em>MFX</em>, <em>VAN</em>, <em>TEC</em>, <em>TCY</em>, <em>TGC</em>, <em>DOX</em>, <em>ERY</em>, <em>CLI</em>, <em>AZM</em>, <em>IPM</em>, <em>MEM</em>, <em>MTR</em>, <em>CHL</em>, <em>COL</em>, <em>MUP</em> and <em>RIF</em>.</p>
 <p>This data set is in R available as <code>example_isolates</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 1 September 2022 13:33:21 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
+<p>It was last updated on 5 October 2022 10:27:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
 <div class="section level3">
-<h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>
+<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
 </h3>
 <p>This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis.</p>
 </div>
 <div class="section level3">
-<h3 id="example-content-7">Example content<a class="anchor" aria-label="anchor" href="#example-content-7"></a>
+<h3 id="example-content-6">Example content<a class="anchor" aria-label="anchor" href="#example-content-6"></a>
 </h3>
 <table class="table">
 <colgroup>
@ -1731,14 +1707,14 @@
 </h2>
 <p>A data set with 3,000 rows and 8 columns, containing the following column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>, <em>bacteria</em>, <em>AMX</em>, <em>AMC</em>, <em>CIP</em> and <em>GEN</em>.</p>
 <p>This data set is in R available as <code>example_isolates_unclean</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 1 September 2022 13:33:21 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
+<p>It was last updated on 5 October 2022 10:27:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
 <div class="section level3">
-<h3 id="source-8">Source<a class="anchor" aria-label="anchor" href="#source-8"></a>
+<h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>
 </h3>
 <p>This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis.</p>
 </div>
 <div class="section level3">
-<h3 id="example-content-8">Example content<a class="anchor" aria-label="anchor" href="#example-content-8"></a>
+<h3 id="example-content-7">Example content<a class="anchor" aria-label="anchor" href="#example-content-7"></a>
 </h3>
 <table class="table">
 <thead><tr class="header">
@ -1829,7 +1805,7 @@

 <div class="pkgdown-footer-right">
  <p></p>
-<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 200px;"></a></p>
+<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a></p>
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