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<main id="main" class="col-md-9"><div class="page-header">
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<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
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<h4 data-toc-skip class="date">03 March 2024</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="d-none name"><code>datasets.Rmd</code></div>
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<p>All reference data (about microorganisms, antibiotics, SIR
|
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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, MS Excel, Apache Feather, Apache
|
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Parquet, SPSS, SAS, and Stata. We also provide tab-separated text files
|
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that are machine-readable and suitable for input in any software
|
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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-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 52 171 rows and 23 columns, containing the following
|
||
column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>,
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||
<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>oxygen_tolerance</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
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||
you load the <code>AMR</code> package.</p>
|
||
<p>It was last updated on 14 July 2023 08:49:06 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> (1.2 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> (11.7 MB)<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> (5.2 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> (5.5 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> (2.6 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xpt" class="external-link">SAS
|
||
transport (XPT) file</a> (48.6 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> (17.8 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> (48.6 MB)</li>
|
||
</ul>
|
||
<p><strong>NOTE: The exported files for 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> Their file
|
||
structures and compression techniques are very inefficient. Advice? Use
|
||
R instead. It’s free and much better in many ways.</p>
|
||
<p>The tab-separated text file and Microsoft Excel workbook both contain
|
||
all SNOMED codes as comma separated values.</p>
|
||
<div class="section level3">
|
||
<h3 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a>
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||
</h3>
|
||
<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>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 December 11th, 2022.</li>
|
||
<li>GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset .
|
||
Accessed from <a href="https://www.gbif.org" class="external-link uri">https://www.gbif.org</a> on January 8th, 2024.</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 ‘Microorganism’, 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">
|
||
<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">
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||
<thead><tr class="header">
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||
<th align="center">Kingdom</th>
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||
<th align="center">Number of (sub)species</th>
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||
</tr></thead>
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<tbody>
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<tr class="odd">
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<td align="center">(unknown kingdom)</td>
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<td align="center">1</td>
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</tr>
|
||
<tr class="even">
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<td align="center">Animalia</td>
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||
<td align="center">1 379</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Archaea</td>
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||
<td align="center">1 314</td>
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||
</tr>
|
||
<tr class="even">
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||
<td align="center">Bacteria</td>
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||
<td align="center">36 501</td>
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||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Fungi</td>
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||
<td align="center">7 905</td>
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||
</tr>
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||
<tr class="even">
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||
<td align="center">Protozoa</td>
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||
<td align="center">5 071</td>
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||
</tr>
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||
</tbody>
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||
</table>
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<p>Example rows when filtering on genus <em>Escherichia</em>:</p>
|
||
<table class="table">
|
||
<colgroup>
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||
<col width="3%">
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||
<col width="7%">
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<col width="2%">
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<col width="2%">
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<col width="4%">
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<col width="5%">
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<col width="4%">
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<col width="5%">
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<col width="3%">
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<col width="4%">
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<col width="3%">
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<col width="2%">
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||
<col width="6%">
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<col width="7%">
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<col width="2%">
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<col width="2%">
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<col width="3%">
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<col width="4%">
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<col width="2%">
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<col width="3%">
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<col width="4%">
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<col width="3%">
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<col width="11%">
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||
</colgroup>
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||
<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>
|
||
<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">oxygen_tolerance</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>
|
||
<tbody>
|
||
<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">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"></td>
|
||
<td align="center"></td>
|
||
<td align="center">genus</td>
|
||
<td align="center">Castellani et al., 1919</td>
|
||
<td align="center">facultative anaerobe</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">11158430</td>
|
||
<td align="center"></td>
|
||
<td align="center">1.0</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">aerobe</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">1.0</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">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">albertii</td>
|
||
<td align="center"></td>
|
||
<td align="center">species</td>
|
||
<td align="center">Huys et al., 2003</td>
|
||
<td align="center">aerobe</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">1.0</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">likely facultative anaerobe</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">1.5</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">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">coli</td>
|
||
<td align="center"></td>
|
||
<td align="center">species</td>
|
||
<td align="center">Castellani et al., 1919</td>
|
||
<td align="center">facultative anaerobe</td>
|
||
<td align="center">LPSN</td>
|
||
<td align="center">776057</td>
|
||
<td align="center">515602</td>
|
||
<td align="center"></td>
|
||
<td align="center">11286021</td>
|
||
<td align="center">3221780</td>
|
||
<td align="center"></td>
|
||
<td align="center">1.0</td>
|
||
<td align="center">1095001000112106, 715307006, 737528008, …</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<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">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">dysenteriae</td>
|
||
<td align="center"></td>
|
||
<td align="center">species</td>
|
||
<td align="center"></td>
|
||
<td align="center">likely facultative anaerobe</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">1.5</td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="antibiotics-antibiotic-antifungal-drugs">
|
||
<code>antibiotics</code>: Antibiotic (+Antifungal) Drugs<a class="anchor" aria-label="anchor" href="#antibiotics-antibiotic-antifungal-drugs"></a>
|
||
</h2>
|
||
<p>A data set with 483 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 24 February 2024 14:16:52 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> (44 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">tab-separated
|
||
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.xlsx" class="external-link">Microsoft
|
||
Excel workbook</a> (73 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.feather" class="external-link">Apache
|
||
Feather file</a> (0.1 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.parquet" class="external-link">Apache
|
||
Parquet file</a> (0.1 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xpt" class="external-link">SAS
|
||
transport (XPT) file</a> (1.5 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">IBM
|
||
SPSS Statistics data file</a> (0.4 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
|
||
DTA file</a> (0.5 MB)</li>
|
||
</ul>
|
||
<p>The tab-separated text file and Microsoft Excel workbook, and SAS,
|
||
SPSS and Stata files all contain the ATC codes, common abbreviations,
|
||
trade names and LOINC codes as comma separated values.</p>
|
||
<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 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>
|
||
<li><a href="https://loinc.org" class="external-link">LOINC (Logical Observation Identifiers
|
||
Names and Codes)</a></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>
|
||
<table class="table">
|
||
<colgroup>
|
||
<col width="1%">
|
||
<col width="2%">
|
||
<col width="8%">
|
||
<col width="7%">
|
||
<col width="7%">
|
||
<col width="12%">
|
||
<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">101493-5, 11-7, 12-5, …</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">101498-4, 15-8, 16-6, …</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">101477-8, 101478-6, 18864-9, …</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, aruzilina, azasite, …</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">100043-9, 16420-2, 16421-0, …</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"></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="antivirals-antiviral-drugs">
|
||
<code>antivirals</code>: Antiviral Drugs<a class="anchor" aria-label="anchor" href="#antivirals-antiviral-drugs"></a>
|
||
</h2>
|
||
<p>A data set with 120 rows and 11 columns, containing the following
|
||
column names:<br><em>av</em>, <em>name</em>, <em>atc</em>, <em>cid</em>,
|
||
<em>atc_group</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>antivirals</code>, after you
|
||
load the <code>AMR</code> package.</p>
|
||
<p>It was last updated on 20 October 2023 12:51:48 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> (6 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt" class="external-link">tab-separated
|
||
text file</a> (17 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class="external-link">Microsoft
|
||
Excel workbook</a> (16 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.feather" class="external-link">Apache
|
||
Feather file</a> (16 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.parquet" class="external-link">Apache
|
||
Parquet file</a> (13 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xpt" class="external-link">SAS
|
||
transport (XPT) file</a> (73 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">IBM
|
||
SPSS Statistics data file</a> (32 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
|
||
DTA file</a> (78 kB)</li>
|
||
</ul>
|
||
<p>The tab-separated text file and Microsoft Excel workbook, and SAS,
|
||
SPSS and Stata files all contain the trade names and LOINC codes as
|
||
comma separated values.</p>
|
||
<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 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>
|
||
<li><a href="https://loinc.org" class="external-link">LOINC (Logical Observation Identifiers
|
||
Names and Codes)</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 class="table">
|
||
<colgroup>
|
||
<col width="2%">
|
||
<col width="8%">
|
||
<col width="3%">
|
||
<col width="4%">
|
||
<col width="28%">
|
||
<col width="23%">
|
||
<col width="4%">
|
||
<col width="4%">
|
||
<col width="3%">
|
||
<col width="4%">
|
||
<col width="13%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="center">av</th>
|
||
<th align="center">name</th>
|
||
<th align="center">atc</th>
|
||
<th align="center">cid</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>
|
||
<th align="center">loinc</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="center">ABA</td>
|
||
<td align="center">Abacavir</td>
|
||
<td align="center">J05AF06</td>
|
||
<td align="center">441300</td>
|
||
<td align="center">Nucleoside and nucleotide reverse transcriptase
|
||
inhibitors</td>
|
||
<td align="center">abacavir sulfate, avacavir, ziagen</td>
|
||
<td align="center">0.6</td>
|
||
<td align="center">g</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">29113-8, 30273-7, 30287-7, …</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">ACI</td>
|
||
<td align="center">Aciclovir</td>
|
||
<td align="center">J05AB01</td>
|
||
<td align="center">135398513</td>
|
||
<td align="center">Nucleosides and nucleotides excl. reverse
|
||
transcriptase inhibitors</td>
|
||
<td align="center">acicloftal, aciclovier, aciclovirum, …</td>
|
||
<td align="center">4.0</td>
|
||
<td align="center">g</td>
|
||
<td align="center">4</td>
|
||
<td align="center">g</td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">ADD</td>
|
||
<td align="center">Adefovir dipivoxil</td>
|
||
<td align="center">J05AF08</td>
|
||
<td align="center">60871</td>
|
||
<td align="center">Nucleoside and nucleotide reverse transcriptase
|
||
inhibitors</td>
|
||
<td align="center">adefovir di, adefovir di ester, adefovir dipivoxyl,
|
||
…</td>
|
||
<td align="center">10.0</td>
|
||
<td align="center">mg</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">AME</td>
|
||
<td align="center">Amenamevir</td>
|
||
<td align="center">J05AX26</td>
|
||
<td align="center">11397521</td>
|
||
<td align="center">Other antivirals</td>
|
||
<td align="center">amenalief</td>
|
||
<td align="center">0.4</td>
|
||
<td align="center">g</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">AMP</td>
|
||
<td align="center">Amprenavir</td>
|
||
<td align="center">J05AE05</td>
|
||
<td align="center">65016</td>
|
||
<td align="center">Protease inhibitors</td>
|
||
<td align="center">agenerase, carbamate, prozei</td>
|
||
<td align="center">1.2</td>
|
||
<td align="center">g</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">29114-6, 30296-8, 30297-6, …</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">ASU</td>
|
||
<td align="center">Asunaprevir</td>
|
||
<td align="center">J05AP06</td>
|
||
<td align="center">16076883</td>
|
||
<td align="center">Antivirals for treatment of HCV infections</td>
|
||
<td align="center">sunvepra, sunvepratrade</td>
|
||
<td align="center">0.2</td>
|
||
<td align="center">g</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir">
|
||
<code>clinical_breakpoints</code>: Interpretation from MIC values
|
||
& disk diameters to SIR<a class="anchor" aria-label="anchor" href="#clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir"></a>
|
||
</h2>
|
||
<p>A data set with 29 883 rows and 13 columns, containing the following
|
||
column names:<br><em>guideline</em>, <em>type</em>, <em>host</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>clinical_breakpoints</code>,
|
||
after you load the <code>AMR</code> package.</p>
|
||
<p>It was last updated on 24 February 2024 14:16:52 UTC. Find more info
|
||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/clinical_breakpoints.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/clinical_breakpoints.rds" class="external-link">original
|
||
R Data Structure (RDS) file</a> (61 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.txt" class="external-link">tab-separated
|
||
text file</a> (2.5 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xlsx" class="external-link">Microsoft
|
||
Excel workbook</a> (1.4 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.feather" class="external-link">Apache
|
||
Feather file</a> (1.3 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.parquet" class="external-link">Apache
|
||
Parquet file</a> (91 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xpt" class="external-link">SAS
|
||
transport (XPT) file</a> (8.2 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.sav" class="external-link">IBM
|
||
SPSS Statistics data file</a> (4.9 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.dta" class="external-link">Stata
|
||
DTA file</a> (8.1 MB)</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 interpretation rules for MIC values and disk
|
||
diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST
|
||
(2011-2023).</p>
|
||
<p>Clinical breakpoints in this package were validated through and
|
||
imported from <a href="https://whonet.org" class="external-link">WHONET</a>, a free desktop
|
||
Windows application developed and supported by the WHO Collaborating
|
||
Centre for Surveillance of Antimicrobial Resistance. More can be read on
|
||
<a href="https://whonet.org" class="external-link">their website</a>. The developers of WHONET
|
||
and this <code>AMR</code> package have been in contact about sharing
|
||
their work. We highly appreciate their development on the WHONET
|
||
software.</p>
|
||
<p>The CEO of CLSI and the chairman of EUCAST have endorsed the work and
|
||
public use of this <code>AMR</code> package (and consequently the use of
|
||
their breakpoints) in June 2023, when future development of distributing
|
||
clinical breakpoints was discussed in a meeting between CLSI, EUCAST,
|
||
the WHO, and developers of WHONET and the <code>AMR</code> package.</p>
|
||
<p><strong>NOTE:</strong> this <code>AMR</code> package (and the WHONET
|
||
software as well) contains internal methods to apply the guidelines,
|
||
which is rather complex. For example, some breakpoints must be applied
|
||
on certain species groups (which are in case of this package available
|
||
through the <code>microorganisms.groups</code> data set). It is
|
||
important that this is considered when using the breakpoints for own
|
||
use.</p>
|
||
</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="6%">
|
||
<col width="3%">
|
||
<col width="3%">
|
||
<col width="4%">
|
||
<col width="3%">
|
||
<col width="7%">
|
||
<col width="14%">
|
||
<col width="6%">
|
||
<col width="2%">
|
||
<col width="15%">
|
||
<col width="8%">
|
||
<col width="8%">
|
||
<col width="7%">
|
||
<col width="7%">
|
||
<col width="3%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="center">guideline</th>
|
||
<th align="center">type</th>
|
||
<th align="center">host</th>
|
||
<th align="center">method</th>
|
||
<th align="center">site</th>
|
||
<th align="center">mo</th>
|
||
<th align="center">mo_name</th>
|
||
<th align="center">rank_index</th>
|
||
<th align="center">ab</th>
|
||
<th align="center">ab_name</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 2023</td>
|
||
<td align="center">human</td>
|
||
<td align="center">human</td>
|
||
<td align="center">DISK</td>
|
||
<td align="center"></td>
|
||
<td align="center">B_ACHRMB_XYLS</td>
|
||
<td align="center">Achromobacter xylosoxidans</td>
|
||
<td align="center">2</td>
|
||
<td align="center">MEM</td>
|
||
<td align="center">Meropenem</td>
|
||
<td align="center">A. xylosoxidans</td>
|
||
<td align="center">10ug</td>
|
||
<td align="center">26.000</td>
|
||
<td align="center">20.000</td>
|
||
<td align="center">FALSE</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">EUCAST 2023</td>
|
||
<td align="center">human</td>
|
||
<td align="center">human</td>
|
||
<td align="center">MIC</td>
|
||
<td align="center"></td>
|
||
<td align="center">B_ACHRMB_XYLS</td>
|
||
<td align="center">Achromobacter xylosoxidans</td>
|
||
<td align="center">2</td>
|
||
<td align="center">MEM</td>
|
||
<td align="center">Meropenem</td>
|
||
<td align="center">A. xylosoxidans</td>
|
||
<td align="center"></td>
|
||
<td align="center">1.000</td>
|
||
<td align="center">4.000</td>
|
||
<td align="center">FALSE</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">EUCAST 2023</td>
|
||
<td align="center">human</td>
|
||
<td align="center">human</td>
|
||
<td align="center">DISK</td>
|
||
<td align="center"></td>
|
||
<td align="center">B_ACHRMB_XYLS</td>
|
||
<td align="center">Achromobacter xylosoxidans</td>
|
||
<td align="center">2</td>
|
||
<td align="center">SXT</td>
|
||
<td align="center">Trimethoprim/sulfamethoxazole</td>
|
||
<td align="center">A. xylosoxidans</td>
|
||
<td align="center">1.25ug/23.75ug</td>
|
||
<td align="center">26.000</td>
|
||
<td align="center">26.000</td>
|
||
<td align="center">FALSE</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">EUCAST 2023</td>
|
||
<td align="center">human</td>
|
||
<td align="center">human</td>
|
||
<td align="center">MIC</td>
|
||
<td align="center"></td>
|
||
<td align="center">B_ACHRMB_XYLS</td>
|
||
<td align="center">Achromobacter xylosoxidans</td>
|
||
<td align="center">2</td>
|
||
<td align="center">SXT</td>
|
||
<td align="center">Trimethoprim/sulfamethoxazole</td>
|
||
<td align="center">A. xylosoxidans</td>
|
||
<td align="center"></td>
|
||
<td align="center">0.125</td>
|
||
<td align="center">0.125</td>
|
||
<td align="center">FALSE</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">EUCAST 2023</td>
|
||
<td align="center">human</td>
|
||
<td align="center">human</td>
|
||
<td align="center">DISK</td>
|
||
<td align="center"></td>
|
||
<td align="center">B_ACHRMB_XYLS</td>
|
||
<td align="center">Achromobacter xylosoxidans</td>
|
||
<td align="center">2</td>
|
||
<td align="center">TZP</td>
|
||
<td align="center">Piperacillin/tazobactam</td>
|
||
<td align="center">A. xylosoxidans</td>
|
||
<td align="center">30ug/6ug</td>
|
||
<td align="center">26.000</td>
|
||
<td align="center">26.000</td>
|
||
<td align="center">FALSE</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">EUCAST 2023</td>
|
||
<td align="center">human</td>
|
||
<td align="center">human</td>
|
||
<td align="center">MIC</td>
|
||
<td align="center"></td>
|
||
<td align="center">B_ACHRMB_XYLS</td>
|
||
<td align="center">Achromobacter xylosoxidans</td>
|
||
<td align="center">2</td>
|
||
<td align="center">TZP</td>
|
||
<td align="center">Piperacillin/tazobactam</td>
|
||
<td align="center">A. xylosoxidans</td>
|
||
<td align="center"></td>
|
||
<td align="center">4.000</td>
|
||
<td align="center">4.000</td>
|
||
<td align="center">FALSE</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div class="section level2">
|
||
<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 134 634 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 16 December 2022 15:10:43 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>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">tab-separated
|
||
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.xlsx" class="external-link">Microsoft
|
||
Excel workbook</a> (1.3 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.feather" class="external-link">Apache
|
||
Feather file</a> (1.2 MB)<br>
|
||
</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.xpt" class="external-link">SAS
|
||
transport (XPT) file</a> (9.5 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> (9.5 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">Acetylspiramycin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Amoxicillin</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">Ampicillin/sulbactam</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Avoparcin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Azithromycin</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">Cadazolid</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Cefadroxil</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Cefalexin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Cefalotin</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">Cefoxitin</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">Clindamycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Cycloserine</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">Fusidic acid</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Gamithromycin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Josamycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Kitasamycin</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">Meleumycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Midecamycin</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">Nafithromycin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Norvancomycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Oleandomycin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Oritavancin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Pirlimycin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Primycin</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">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">Solithromycin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Spiramycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Tedizolid</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">Telavancin</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">Thiacetazone</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Tildipirosin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Enterobacter cloacae</td>
|
||
<td align="center">Tilmicosin</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">Vancomycin</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="dosage-dosage-guidelines-from-eucast">
|
||
<code>dosage</code>: Dosage Guidelines from EUCAST<a class="anchor" aria-label="anchor" href="#dosage-dosage-guidelines-from-eucast"></a>
|
||
</h2>
|
||
<p>A data set with 503 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 22 June 2023 13:10:59 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>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt" class="external-link">tab-separated
|
||
text file</a> (43 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class="external-link">Microsoft
|
||
Excel workbook</a> (25 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.feather" class="external-link">Apache
|
||
Feather file</a> (21 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.parquet" class="external-link">Apache
|
||
Parquet file</a> (9 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xpt" class="external-link">SAS
|
||
transport (XPT) file</a> (0.1 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">IBM
|
||
SPSS Statistics data file</a> (64 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
|
||
DTA file</a> (0.1 MB)</li>
|
||
</ul>
|
||
<div class="section level3">
|
||
<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=""></a> (), <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
|
||
Breakpoint Tables’ v11.0</a> (2021), and <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
|
||
Breakpoint Tables’ v12.0</a> (2022).</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="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">13</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">13</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">13</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">13</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">13</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">13</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="example_isolates-example-data-for-practice">
|
||
<code>example_isolates</code>: Example Data for Practice<a class="anchor" aria-label="anchor" href="#example_isolates-example-data-for-practice"></a>
|
||
</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 21 January 2023 22:47:20 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-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-6">Example content<a class="anchor" aria-label="anchor" href="#example-content-6"></a>
|
||
</h3>
|
||
<table class="table">
|
||
<colgroup>
|
||
<col width="4%">
|
||
<col width="3%">
|
||
<col width="1%">
|
||
<col width="3%">
|
||
<col width="3%">
|
||
<col width="5%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
<col width="1%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="center">date</th>
|
||
<th align="center">patient</th>
|
||
<th align="center">age</th>
|
||
<th align="center">gender</th>
|
||
<th align="center">ward</th>
|
||
<th align="center">mo</th>
|
||
<th align="center">PEN</th>
|
||
<th align="center">OXA</th>
|
||
<th align="center">FLC</th>
|
||
<th align="center">AMX</th>
|
||
<th align="center">AMC</th>
|
||
<th align="center">AMP</th>
|
||
<th align="center">TZP</th>
|
||
<th align="center">CZO</th>
|
||
<th align="center">FEP</th>
|
||
<th align="center">CXM</th>
|
||
<th align="center">FOX</th>
|
||
<th align="center">CTX</th>
|
||
<th align="center">CAZ</th>
|
||
<th align="center">CRO</th>
|
||
<th align="center">GEN</th>
|
||
<th align="center">TOB</th>
|
||
<th align="center">AMK</th>
|
||
<th align="center">KAN</th>
|
||
<th align="center">TMP</th>
|
||
<th align="center">SXT</th>
|
||
<th align="center">NIT</th>
|
||
<th align="center">FOS</th>
|
||
<th align="center">LNZ</th>
|
||
<th align="center">CIP</th>
|
||
<th align="center">MFX</th>
|
||
<th align="center">VAN</th>
|
||
<th align="center">TEC</th>
|
||
<th align="center">TCY</th>
|
||
<th align="center">TGC</th>
|
||
<th align="center">DOX</th>
|
||
<th align="center">ERY</th>
|
||
<th align="center">CLI</th>
|
||
<th align="center">AZM</th>
|
||
<th align="center">IPM</th>
|
||
<th align="center">MEM</th>
|
||
<th align="center">MTR</th>
|
||
<th align="center">CHL</th>
|
||
<th align="center">COL</th>
|
||
<th align="center">MUP</th>
|
||
<th align="center">RIF</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="center">2002-01-02</td>
|
||
<td align="center">A77334</td>
|
||
<td align="center">65</td>
|
||
<td align="center">F</td>
|
||
<td align="center">Clinical</td>
|
||
<td align="center">B_ESCHR_COLI</td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">I</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">I</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center">R</td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center">R</td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">2002-01-03</td>
|
||
<td align="center">A77334</td>
|
||
<td align="center">65</td>
|
||
<td align="center">F</td>
|
||
<td align="center">Clinical</td>
|
||
<td align="center">B_ESCHR_COLI</td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">I</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">I</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center">R</td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center">R</td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">2002-01-07</td>
|
||
<td align="center">067927</td>
|
||
<td align="center">45</td>
|
||
<td align="center">F</td>
|
||
<td align="center">ICU</td>
|
||
<td align="center">B_STPHY_EPDR</td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">S</td>
|
||
<td align="center"></td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">2002-01-07</td>
|
||
<td align="center">067927</td>
|
||
<td align="center">45</td>
|
||
<td align="center">F</td>
|
||
<td align="center">ICU</td>
|
||
<td align="center">B_STPHY_EPDR</td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">S</td>
|
||
<td align="center"></td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">2002-01-13</td>
|
||
<td align="center">067927</td>
|
||
<td align="center">45</td>
|
||
<td align="center">F</td>
|
||
<td align="center">ICU</td>
|
||
<td align="center">B_STPHY_EPDR</td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">S</td>
|
||
<td align="center"></td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">2002-01-13</td>
|
||
<td align="center">067927</td>
|
||
<td align="center">45</td>
|
||
<td align="center">F</td>
|
||
<td align="center">ICU</td>
|
||
<td align="center">B_STPHY_EPDR</td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">S</td>
|
||
<td align="center"></td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">R</td>
|
||
<td align="center">R</td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">R</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="example_isolates_unclean-example-data-for-practice">
|
||
<code>example_isolates_unclean</code>: Example Data for
|
||
Practice<a class="anchor" aria-label="anchor" href="#example_isolates_unclean-example-data-for-practice"></a>
|
||
</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 27 August 2022 18:49:37 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-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-7">Example content<a class="anchor" aria-label="anchor" href="#example-content-7"></a>
|
||
</h3>
|
||
<table style="width:100%;" class="table">
|
||
<colgroup>
|
||
<col width="17%">
|
||
<col width="14%">
|
||
<col width="17%">
|
||
<col width="21%">
|
||
<col width="7%">
|
||
<col width="7%">
|
||
<col width="7%">
|
||
<col width="7%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="center">patient_id</th>
|
||
<th align="center">hospital</th>
|
||
<th align="center">date</th>
|
||
<th align="center">bacteria</th>
|
||
<th align="center">AMX</th>
|
||
<th align="center">AMC</th>
|
||
<th align="center">CIP</th>
|
||
<th align="center">GEN</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="center">J3</td>
|
||
<td align="center">A</td>
|
||
<td align="center">2012-11-21</td>
|
||
<td align="center">E. coli</td>
|
||
<td align="center">R</td>
|
||
<td align="center">I</td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">R7</td>
|
||
<td align="center">A</td>
|
||
<td align="center">2018-04-03</td>
|
||
<td align="center">K. pneumoniae</td>
|
||
<td align="center">R</td>
|
||
<td align="center">I</td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">P3</td>
|
||
<td align="center">A</td>
|
||
<td align="center">2014-09-19</td>
|
||
<td align="center">E. coli</td>
|
||
<td align="center">R</td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">P10</td>
|
||
<td align="center">A</td>
|
||
<td align="center">2015-12-10</td>
|
||
<td align="center">E. coli</td>
|
||
<td align="center">S</td>
|
||
<td align="center">I</td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">B7</td>
|
||
<td align="center">A</td>
|
||
<td align="center">2015-03-02</td>
|
||
<td align="center">E. coli</td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
<td align="center">S</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">W3</td>
|
||
<td align="center">A</td>
|
||
<td align="center">2018-03-31</td>
|
||
<td align="center">S. aureus</td>
|
||
<td align="center">R</td>
|
||
<td align="center">S</td>
|
||
<td align="center">R</td>
|
||
<td align="center">S</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="microorganisms-groups-species-groups-and-microbiological-complexes">
|
||
<code>microorganisms.groups</code>: Species Groups and
|
||
Microbiological Complexes<a class="anchor" aria-label="anchor" href="#microorganisms-groups-species-groups-and-microbiological-complexes"></a>
|
||
</h2>
|
||
<p>A data set with 521 rows and 4 columns, containing the following
|
||
column names:<br><em>mo_group</em>, <em>mo</em>, <em>mo_group_name</em>, and
|
||
<em>mo_name</em>.</p>
|
||
<p>This data set is in R available as
|
||
<code>microorganisms.groups</code>, after you load the <code>AMR</code>
|
||
package.</p>
|
||
<p>It was last updated on 14 July 2023 08:49:06 UTC. Find more info
|
||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.groups.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.groups.rds" class="external-link">original
|
||
R Data Structure (RDS) file</a> (6 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.txt" class="external-link">tab-separated
|
||
text file</a> (49 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.xlsx" class="external-link">Microsoft
|
||
Excel workbook</a> (20 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.feather" class="external-link">Apache
|
||
Feather file</a> (19 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.parquet" class="external-link">Apache
|
||
Parquet file</a> (13 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.xpt" class="external-link">SAS
|
||
transport (XPT) file</a> (0 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.sav" class="external-link">IBM
|
||
SPSS Statistics data file</a> (64 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.dta" class="external-link">Stata
|
||
DTA file</a> (81 kB)</li>
|
||
</ul>
|
||
<div class="section level3">
|
||
<h3 id="source-8">Source<a class="anchor" aria-label="anchor" href="#source-8"></a>
|
||
</h3>
|
||
<p>This data set contains species groups and microbiological complexes,
|
||
which are used in the <code>clinical_breakpoints</code> data set.</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>
|
||
<table class="table">
|
||
<colgroup>
|
||
<col width="17%">
|
||
<col width="15%">
|
||
<col width="35%">
|
||
<col width="31%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="center">mo_group</th>
|
||
<th align="center">mo</th>
|
||
<th align="center">mo_group_name</th>
|
||
<th align="center">mo_name</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="center">B_ACNTB_BMNN-C</td>
|
||
<td align="center">B_ACNTB_BMNN</td>
|
||
<td align="center">Acinetobacter baumannii complex</td>
|
||
<td align="center">Acinetobacter baumannii</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">B_ACNTB_BMNN-C</td>
|
||
<td align="center">B_ACNTB_CLCC</td>
|
||
<td align="center">Acinetobacter baumannii complex</td>
|
||
<td align="center">Acinetobacter calcoaceticus</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">B_ACNTB_BMNN-C</td>
|
||
<td align="center">B_ACNTB_DJKS</td>
|
||
<td align="center">Acinetobacter baumannii complex</td>
|
||
<td align="center">Acinetobacter dijkshoorniae</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">B_ACNTB_BMNN-C</td>
|
||
<td align="center">B_ACNTB_NSCM</td>
|
||
<td align="center">Acinetobacter baumannii complex</td>
|
||
<td align="center">Acinetobacter nosocomialis</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">B_ACNTB_BMNN-C</td>
|
||
<td align="center">B_ACNTB_PITT</td>
|
||
<td align="center">Acinetobacter baumannii complex</td>
|
||
<td align="center">Acinetobacter pittii</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">B_ACNTB_BMNN-C</td>
|
||
<td align="center">B_ACNTB_SFRT</td>
|
||
<td align="center">Acinetobacter baumannii complex</td>
|
||
<td align="center">Acinetobacter seifertii</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="microorganisms-codes-common-laboratory-codes">
|
||
<code>microorganisms.codes</code>: Common Laboratory Codes<a class="anchor" aria-label="anchor" href="#microorganisms-codes-common-laboratory-codes"></a>
|
||
</h2>
|
||
<p>A data set with 4 957 rows and 2 columns, containing the following
|
||
column names:<br><em>code</em> and <em>mo</em>.</p>
|
||
<p>This data set is in R available as <code>microorganisms.codes</code>,
|
||
after you load the <code>AMR</code> package.</p>
|
||
<p>It was last updated on 8 July 2023 15:30:05 UTC. Find more info about
|
||
the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.codes.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.codes.rds" class="external-link">original
|
||
R Data Structure (RDS) file</a> (22 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.txt" class="external-link">tab-separated
|
||
text file</a> (0.1 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.xlsx" class="external-link">Microsoft
|
||
Excel workbook</a> (91 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.feather" class="external-link">Apache
|
||
Feather file</a> (85 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.parquet" class="external-link">Apache
|
||
Parquet file</a> (57 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.xpt" class="external-link">SAS
|
||
transport (XPT) file</a> (0 kB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.sav" class="external-link">IBM
|
||
SPSS Statistics data file</a> (0.1 MB)<br>
|
||
</li>
|
||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.dta" class="external-link">Stata
|
||
DTA file</a> (0.1 MB)</li>
|
||
</ul>
|
||
<div class="section level3">
|
||
<h3 id="source-9">Source<a class="anchor" aria-label="anchor" href="#source-9"></a>
|
||
</h3>
|
||
<p>This data set contains commonly used codes for microorganisms, from
|
||
laboratory systems and <a href="https://whonet.org" class="external-link">WHONET</a>.</p>
|
||
</div>
|
||
<div class="section level3">
|
||
<h3 id="example-content-9">Example content<a class="anchor" aria-label="anchor" href="#example-content-9"></a>
|
||
</h3>
|
||
<table class="table">
|
||
<thead><tr class="header">
|
||
<th align="center">code</th>
|
||
<th align="center">mo</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="center">1011</td>
|
||
<td align="center">B_GRAMP</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">1012</td>
|
||
<td align="center">B_GRAMP</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">1013</td>
|
||
<td align="center">B_GRAMN</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">1014</td>
|
||
<td align="center">B_GRAMN</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">1015</td>
|
||
<td align="center">F_YEAST</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">103</td>
|
||
<td align="center">B_ESCHR_COLI</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||
</nav></aside>
|
||
</div>
|
||
|
||
|
||
|
||
<footer><div class="pkgdown-footer-left">
|
||
<p></p>
|
||
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
|
||
</div>
|
||
|
||
<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: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style="max-width: 150px;"></a></p>
|
||
</div>
|
||
|
||
</footer>
|
||
</div>
|
||
|
||
|
||
|
||
|
||
|
||
</body>
|
||
</html>
|