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Data sets for download / own use
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Other: benchmarks
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</header><div class="row">
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<div class="col-md-9 contents">
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<div class="page-header toc-ignore">
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<h1 data-toc-skip>Data sets for download / own use</h1>
|
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|
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<h4 data-toc-skip class="date">09 May 2022</h4>
|
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<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>
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<div class="hidden name"><code>datasets.Rmd</code></div>
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</div>
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<p>All reference data (about microorganisms, antibiotics, R/SI
|
||
interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are
|
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reliable, up-to-date and freely available. We continually export our
|
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data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also
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supply tab separated files that are machine-readable and suitable for
|
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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>
|
||
<p class="dataset-within-r">
|
||
If you are reading this page from within R, please
|
||
<a href="https://msberends.github.io/AMR/articles/datasets.html">visit
|
||
our website</a>, which is automatically updated with every code change.
|
||
</p>
|
||
<div class="section level2">
|
||
<h2 id="microorganisms-currently-accepted-names">Microorganisms (currently accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-currently-accepted-names"></a>
|
||
</h2>
|
||
<p>A data set with 70,760 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>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 29 November 2021 11:38:23 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">R
|
||
file</a> (1.3 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Excel
|
||
file</a> (6.4 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">plain
|
||
text file</a> (13.1 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
|
||
file</a> (30.7 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">SPSS
|
||
file</a> (16.3 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
|
||
file</a> (27.5 MB)</li>
|
||
</ul>
|
||
<p><strong>NOTE: The exported files for SAS, SPSS and Stata do not
|
||
contain SNOMED codes, as their file size would 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>
|
||
<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>
|
||
</ul>
|
||
</div>
|
||
<div class="section level3">
|
||
<h3 id="example-content">Example content<a class="anchor" aria-label="anchor" href="#example-content"></a>
|
||
</h3>
|
||
<p>Included (sub)species per taxonomic kingdom:</p>
|
||
<table class="table">
|
||
<thead><tr class="header">
|
||
<th align="center">Kingdom</th>
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||
<th align="center">Number of (sub)species</th>
|
||
</tr></thead>
|
||
<tbody>
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||
<tr class="odd">
|
||
<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>
|
||
<td align="center">2,153</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Archaea</td>
|
||
<td align="center">694</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Bacteria</td>
|
||
<td align="center">22,852</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Chromista</td>
|
||
<td align="center">32,167</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Fungi</td>
|
||
<td align="center">9,582</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="4%">
|
||
<col width="16%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="center">mo</th>
|
||
<th align="center">fullname</th>
|
||
<th align="center">kingdom</th>
|
||
<th align="center">phylum</th>
|
||
<th align="center">class</th>
|
||
<th align="center">order</th>
|
||
<th align="center">family</th>
|
||
<th align="center">genus</th>
|
||
<th align="center">species</th>
|
||
<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">prevalence</th>
|
||
<th align="center">snomed</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="center">B_ESCHR</td>
|
||
<td align="center">Escherichia</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"></td>
|
||
<td align="center"></td>
|
||
<td align="center">genus</td>
|
||
<td align="center"></td>
|
||
<td align="center">515602</td>
|
||
<td align="center">LPSN</td>
|
||
<td align="center">1</td>
|
||
<td align="center">64735005</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">B_ESCHR_ALBR</td>
|
||
<td align="center">Escherichia albertii</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">albertii</td>
|
||
<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">1</td>
|
||
<td align="center">419388003</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">B_ESCHR_COLI</td>
|
||
<td align="center">Escherichia coli</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">coli</td>
|
||
<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">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">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">fergusonii</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"></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-previously-accepted-names">Microorganisms (previously accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-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 6 October 2021 14:38:29 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">R
|
||
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.xlsx" class="external-link">Excel
|
||
file</a> (0.5 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">plain
|
||
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.sas" class="external-link">SAS
|
||
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">SPSS
|
||
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
|
||
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 style="width:100%;" class="table">
|
||
<colgroup>
|
||
<col width="31%">
|
||
<col width="30%">
|
||
<col width="24%">
|
||
<col width="13%">
|
||
</colgroup>
|
||
<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 class="section level2">
|
||
<h2 id="antibiotic-agents">Antibiotic agents<a class="anchor" aria-label="anchor" href="#antibiotic-agents"></a>
|
||
</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 14 December 2021 21:59:33 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">R
|
||
file</a> (33 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Excel
|
||
file</a> (65 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">plain
|
||
text file</a> (0.1 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas" class="external-link">SAS
|
||
file</a> (1.8 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">SPSS
|
||
file</a> (0.3 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata
|
||
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>
|
||
<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/" class="external-link">ATC/DDD index from WHO
|
||
Collaborating Centre for Drug Statistics Methodology</a> (note: this may
|
||
not be used for commercial purposes, but is freely available from the
|
||
WHO CC website for personal use)</li>
|
||
<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US
|
||
National Library of Medicine</a></li>
|
||
<li><a href="https://whonet.org" class="external-link">WHONET software 2019</a></li>
|
||
</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>
|
||
<table style="width:100%;" class="table">
|
||
<colgroup>
|
||
<col width="1%">
|
||
<col width="2%">
|
||
<col width="8%">
|
||
<col width="7%">
|
||
<col width="7%">
|
||
<col width="13%">
|
||
<col width="17%">
|
||
<col width="6%">
|
||
<col width="13%">
|
||
<col width="2%">
|
||
<col width="3%">
|
||
<col width="2%">
|
||
<col width="2%">
|
||
<col width="9%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="center">ab</th>
|
||
<th align="center">cid</th>
|
||
<th align="center">name</th>
|
||
<th align="center">group</th>
|
||
<th align="center">atc</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">37768</td>
|
||
<td align="center">Amikacin</td>
|
||
<td align="center">Aminoglycosides</td>
|
||
<td align="center">D06AX12, J01GB06, S01AA21</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">33613</td>
|
||
<td align="center">Amoxicillin</td>
|
||
<td align="center">Beta-lactams/penicillins</td>
|
||
<td align="center">J01CA04</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">1.5</td>
|
||
<td align="center">g</td>
|
||
<td align="center">3.0</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">23665637</td>
|
||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||
<td align="center">Beta-lactams/penicillins</td>
|
||
<td align="center">J01CR02</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">1.5</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">6249</td>
|
||
<td align="center">Ampicillin</td>
|
||
<td align="center">Beta-lactams/penicillins</td>
|
||
<td align="center">J01CA01, S01AA19</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">6.0</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">447043</td>
|
||
<td align="center">Azithromycin</td>
|
||
<td align="center">Macrolides/lincosamides</td>
|
||
<td align="center">J01FA10, S01AA26</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">PEN</td>
|
||
<td align="center">5904</td>
|
||
<td align="center">Benzylpenicillin</td>
|
||
<td align="center">Beta-lactams/penicillins</td>
|
||
<td align="center">J01CE01, S01AA14</td>
|
||
<td align="center">Combinations of antibacterials</td>
|
||
<td align="center">Combinations of antibacterials</td>
|
||
<td align="center">bepe, pen, peni, …</td>
|
||
<td align="center">abbocillin, ayercillin, bencilpenicilina, …</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">3.6</td>
|
||
<td align="center">g</td>
|
||
<td align="center">3913-1</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="antiviral-agents">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents"></a>
|
||
</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 29 August 2020 19:53:07 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">R
|
||
file</a> (5 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class="external-link">Excel
|
||
file</a> (14 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt" class="external-link">plain
|
||
text file</a> (16 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas" class="external-link">SAS
|
||
file</a> (80 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">SPSS
|
||
file</a> (68 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata
|
||
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>
|
||
<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/" class="external-link">ATC/DDD index from WHO
|
||
Collaborating Centre for Drug Statistics Methodology</a> (note: this may
|
||
not be used for commercial purposes, but is freely available from the
|
||
WHO CC website for personal use)</li>
|
||
<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US
|
||
National Library of Medicine</a></li>
|
||
</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>
|
||
<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 class="section level2">
|
||
<h2 id="intrinsic-bacterial-resistance">Intrinsic bacterial resistance<a class="anchor" aria-label="anchor" href="#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>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 14 December 2021 21:59:33 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">R
|
||
file</a> (78 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Excel
|
||
file</a> (0.9 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">plain
|
||
text file</a> (5.1 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
|
||
file</a> (10.4 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">SPSS
|
||
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
|
||
file</a> (10.2 MB)</li>
|
||
</ul>
|
||
<div class="section level3">
|
||
<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-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">
|
||
<thead><tr class="header">
|
||
<th align="center">microorganism</th>
|
||
<th align="center">antibiotic</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Acetylmidecamycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Ampicillin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Amoxicillin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Acetylspiramycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Avoparcin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Azithromycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Cadazolid</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Cephalothin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Cefadroxil</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Clindamycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Clarithromycin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Cycloserine</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Cefazolin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Dalbavancin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Dirithromycin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Erythromycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Flurithromycin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Cefoxitin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Fusidic acid</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Gamithromycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Josamycin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Kitasamycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Cephalexin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Lincomycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Linezolid</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Miocamycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Meleumycin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Midecamycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Norvancomycin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Oleandomycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Oritavancin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Benzylpenicillin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Pristinamycin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Pirlimycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Primycin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Quinupristin/dalfopristin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Ramoplanin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Rifampicin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Rokitamycin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Roxithromycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Ampicillin/sulbactam</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Solithromycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Spiramycin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Teicoplanin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Thiacetazone</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Tilmicosin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Tildipirosin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Telithromycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Telavancin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Troleandomycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Tulathromycin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Tylosin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Tylvalosin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Tedizolid</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Vancomycin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Nafithromycin</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="interpretation-from-mic-values-disk-diameters-to-rsi">Interpretation from MIC values / disk diameters to R/SI<a class="anchor" aria-label="anchor" href="#interpretation-from-mic-values-disk-diameters-to-rsi"></a>
|
||
</h2>
|
||
<p>A data set with 20,318 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 14 December 2021 21:59:33 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">R
|
||
file</a> (39 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Excel
|
||
file</a> (0.7 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain
|
||
text file</a> (1.7 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS
|
||
file</a> (3.6 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS
|
||
file</a> (2.2 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata
|
||
file</a> (3.4 MB)</li>
|
||
</ul>
|
||
<div class="section level3">
|
||
<h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></a>
|
||
</h3>
|
||
<p>This data set contains interpretation rules for MIC values and disk
|
||
diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
|
||
(2011-2021).</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>
|
||
<table class="table">
|
||
<colgroup>
|
||
<col width="9%">
|
||
<col width="5%">
|
||
<col width="4%">
|
||
<col width="16%">
|
||
<col width="8%">
|
||
<col width="11%">
|
||
<col width="9%">
|
||
<col width="8%">
|
||
<col width="10%">
|
||
<col width="10%">
|
||
<col width="5%">
|
||
</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">rank_index</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 2021</td>
|
||
<td align="center">MIC</td>
|
||
<td align="center"></td>
|
||
<td align="center">Aspergillus fumigatus</td>
|
||
<td align="center">2</td>
|
||
<td align="center">Amphotericin B</td>
|
||
<td align="center">Aspergillus</td>
|
||
<td align="center"></td>
|
||
<td align="center">1</td>
|
||
<td align="center">4</td>
|
||
<td align="center">FALSE</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">EUCAST 2021</td>
|
||
<td align="center">MIC</td>
|
||
<td align="center"></td>
|
||
<td align="center">Aspergillus niger</td>
|
||
<td align="center">2</td>
|
||
<td align="center">Amphotericin B</td>
|
||
<td align="center">Aspergillus</td>
|
||
<td align="center"></td>
|
||
<td align="center">1</td>
|
||
<td align="center">4</td>
|
||
<td align="center">FALSE</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">EUCAST 2021</td>
|
||
<td align="center">MIC</td>
|
||
<td align="center"></td>
|
||
<td align="center">Candida</td>
|
||
<td align="center">3</td>
|
||
<td align="center">Amphotericin B</td>
|
||
<td align="center">Candida</td>
|
||
<td align="center"></td>
|
||
<td align="center">1</td>
|
||
<td align="center">2</td>
|
||
<td align="center">FALSE</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">EUCAST 2021</td>
|
||
<td align="center">MIC</td>
|
||
<td align="center"></td>
|
||
<td align="center">Candida albicans</td>
|
||
<td align="center">2</td>
|
||
<td align="center">Amphotericin B</td>
|
||
<td align="center">Candida</td>
|
||
<td align="center"></td>
|
||
<td align="center">1</td>
|
||
<td align="center">2</td>
|
||
<td align="center">FALSE</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">EUCAST 2021</td>
|
||
<td align="center">MIC</td>
|
||
<td align="center"></td>
|
||
<td align="center">Candida krusei</td>
|
||
<td align="center">2</td>
|
||
<td align="center">Amphotericin B</td>
|
||
<td align="center">Candida</td>
|
||
<td align="center"></td>
|
||
<td align="center">1</td>
|
||
<td align="center">2</td>
|
||
<td align="center">FALSE</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">EUCAST 2021</td>
|
||
<td align="center">MIC</td>
|
||
<td align="center"></td>
|
||
<td align="center">Candida parapsilosis</td>
|
||
<td align="center">2</td>
|
||
<td align="center">Amphotericin B</td>
|
||
<td align="center">Candida</td>
|
||
<td align="center"></td>
|
||
<td align="center">1</td>
|
||
<td align="center">2</td>
|
||
<td align="center">FALSE</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="dosage-guidelines-from-eucast">Dosage guidelines from EUCAST<a class="anchor" aria-label="anchor" href="#dosage-guidelines-from-eucast"></a>
|
||
</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 25 January 2021 20:58:20 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">R
|
||
file</a> (3 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class="external-link">Excel
|
||
file</a> (14 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt" class="external-link">plain
|
||
text file</a> (15 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class="external-link">SAS
|
||
file</a> (52 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">SPSS
|
||
file</a> (45 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata
|
||
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>
|
||
<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>
|
||
<table class="table">
|
||
<colgroup>
|
||
<col width="4%">
|
||
<col width="10%">
|
||
<col width="15%">
|
||
<col width="10%">
|
||
<col width="9%">
|
||
<col width="13%">
|
||
<col width="5%">
|
||
<col width="16%">
|
||
<col width="13%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="center">ab</th>
|
||
<th align="center">name</th>
|
||
<th align="center">type</th>
|
||
<th align="center">dose</th>
|
||
<th align="center">dose_times</th>
|
||
<th align="center">administration</th>
|
||
<th align="center">notes</th>
|
||
<th align="center">original_txt</th>
|
||
<th align="center">eucast_version</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="center">AMK</td>
|
||
<td align="center">Amikacin</td>
|
||
<td align="center">standard_dosage</td>
|
||
<td align="center">25-30 mg/kg</td>
|
||
<td align="center">1</td>
|
||
<td align="center">iv</td>
|
||
<td align="center"></td>
|
||
<td align="center">25-30 mg/kg x 1 iv</td>
|
||
<td align="center">11</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">AMX</td>
|
||
<td align="center">Amoxicillin</td>
|
||
<td align="center">high_dosage</td>
|
||
<td align="center">2 g</td>
|
||
<td align="center">6</td>
|
||
<td align="center">iv</td>
|
||
<td align="center"></td>
|
||
<td align="center">2 g x 6 iv</td>
|
||
<td align="center">11</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">AMX</td>
|
||
<td align="center">Amoxicillin</td>
|
||
<td align="center">standard_dosage</td>
|
||
<td align="center">1 g</td>
|
||
<td align="center">3</td>
|
||
<td align="center">iv</td>
|
||
<td align="center"></td>
|
||
<td align="center">1 g x 3-4 iv</td>
|
||
<td align="center">11</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">AMX</td>
|
||
<td align="center">Amoxicillin</td>
|
||
<td align="center">high_dosage</td>
|
||
<td align="center">0.75-1 g</td>
|
||
<td align="center">3</td>
|
||
<td align="center">oral</td>
|
||
<td align="center"></td>
|
||
<td align="center">0.75-1 g x 3 oral</td>
|
||
<td align="center">11</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">AMX</td>
|
||
<td align="center">Amoxicillin</td>
|
||
<td align="center">standard_dosage</td>
|
||
<td align="center">0.5 g</td>
|
||
<td align="center">3</td>
|
||
<td align="center">oral</td>
|
||
<td align="center"></td>
|
||
<td align="center">0.5 g x 3 oral</td>
|
||
<td align="center">11</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">AMX</td>
|
||
<td align="center">Amoxicillin</td>
|
||
<td align="center">uncomplicated_uti</td>
|
||
<td align="center">0.5 g</td>
|
||
<td align="center">3</td>
|
||
<td align="center">oral</td>
|
||
<td align="center"></td>
|
||
<td align="center">0.5 g x 3 oral</td>
|
||
<td align="center">11</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></p>
|
||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||
</div>
|
||
|
||
<div class="pkgdown">
|
||
<p></p>
|
||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||
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|
||
|
||
</footer>
|
||
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|
||
|
||
|
||
|
||
|
||
|
||
|
||
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|
||
</html>
|