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<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">23 June 2024</h4>
<h4 data-toc-skip class="date">16 July 2024</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
</div>
@ -215,43 +105,44 @@ of the data sets look like.</p>
<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
<p>A data set with 70 547 rows and 26 columns, containing the following
column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>,
<em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>,
<em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>,
<em>ref</em>, <em>oxygen_tolerance</em>, <em>source</em>, <em>lpsn</em>,
<em>lpsn_parent</em>, <em>lpsn_renamed_to</em>, <em>gbif</em>,
<em>lpsn_parent</em>, <em>lpsn_renamed_to</em>, <em>mycobank</em>,
<em>mycobank_parent</em>, <em>mycobank_renamed_to</em>, <em>gbif</em>,
<em>gbif_parent</em>, <em>gbif_renamed_to</em>, <em>prevalence</em>, and
<em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 14 July 2023 08:49:06 UTC. Find more info
<p>It was last updated on 16 July 2024 12:51:57 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>
R Data Structure (RDS) file</a> (1.6 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>
text file</a> (15.9 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>
Excel workbook</a> (7.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.feather" class="external-link">Apache
Feather file</a> (5.5 MB)<br>
Feather file</a> (19 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>
Parquet file</a> (0 kB)<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>
transport (XPT) file</a> (69.5 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>
SPSS Statistics data file</a> (24.5 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>
DTA file</a> (69.5 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
@ -263,16 +154,16 @@ 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>
</h3>
<p>This data set contains the full microbial taxonomy of five kingdoms
<p>This data set contains the full microbial taxonomy of six 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>
5607-5612; . Accessed from <a href="https://lpsn.dsmz.de" class="external-link uri">https://lpsn.dsmz.de</a> on June 24th, 2024.</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>
Accessed from <a href="https://www.gbif.org" class="external-link uri">https://www.gbif.org</a> on June 24th, 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>
@ -295,52 +186,55 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
</tr>
<tr class="even">
<td align="center">Animalia</td>
<td align="center">1 379</td>
<td align="center">1 713</td>
</tr>
<tr class="odd">
<td align="center">Archaea</td>
<td align="center">1 314</td>
<td align="center">1 418</td>
</tr>
<tr class="even">
<td align="center">Bacteria</td>
<td align="center">36 501</td>
<td align="center">39 238</td>
</tr>
<tr class="odd">
<td align="center">Fungi</td>
<td align="center">7 905</td>
<td align="center">Chromista</td>
<td align="center">164</td>
</tr>
<tr class="even">
<td align="center">Protozoa</td>
<td align="center">5 071</td>
<td align="center">Fungi</td>
<td align="center">19 878</td>
</tr>
</tbody>
</table>
<p>Example rows when filtering on genus <em>Escherichia</em>:</p>
<table class="table">
<table style="width:100%;" class="table">
<colgroup>
<col width="3%">
<col width="7%">
<col width="2%">
<col width="2%">
<col width="4%">
<col width="5%">
<col width="4%">
<col width="5%">
<col width="3%">
<col width="4%">
<col width="3%">
<col width="2%">
<col width="6%">
<col width="7%">
<col width="2%">
<col width="2%">
<col width="3%">
<col width="4%">
<col width="4%">
<col width="4%">
<col width="2%">
<col width="3%">
<col width="2%">
<col width="2%">
<col width="5%">
<col width="6%">
<col width="1%">
<col width="1%">
<col width="2%">
<col width="3%">
<col width="2%">
<col width="3%">
<col width="4%">
<col width="2%">
<col width="2%">
<col width="3%">
<col width="11%">
<col width="2%">
<col width="10%">
</colgroup>
<thead><tr class="header">
<th align="center">mo</th>
@ -361,6 +255,9 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<th align="center">lpsn</th>
<th align="center">lpsn_parent</th>
<th align="center">lpsn_renamed_to</th>
<th align="center">mycobank</th>
<th align="center">mycobank_parent</th>
<th align="center">mycobank_renamed_to</th>
<th align="center">gbif</th>
<th align="center">gbif_parent</th>
<th align="center">gbif_renamed_to</th>
@ -387,7 +284,10 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<td align="center">515602</td>
<td align="center">482</td>
<td align="center"></td>
<td align="center">3221780</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">11158430</td>
<td align="center"></td>
<td align="center">1.0</td>
@ -407,7 +307,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<td align="center"></td>
<td align="center">species</td>
<td align="center">Leclerc, 1962</td>
<td align="center">aerobe</td>
<td align="center">likely facultative anaerobe</td>
<td align="center">LPSN</td>
<td align="center">776052</td>
<td align="center">515602</td>
@ -415,6 +315,9 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<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">1.0</td>
<td align="center"></td>
</tr>
@ -432,13 +335,16 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<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">facultative anaerobe</td>
<td align="center">LPSN</td>
<td align="center">776053</td>
<td align="center">515602</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">5427575</td>
<td align="center">3221780</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">1.0</td>
<td align="center">419388003</td>
@ -465,6 +371,9 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<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">1.5</td>
<td align="center"></td>
</tr>
@ -487,15 +396,18 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<td align="center">776057</td>
<td align="center">515602</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">11286021</td>
<td align="center">3221780</td>
<td align="center"></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">B_ESCHR_COLI_COLI</td>
<td align="center">Escherichia coli coli</td>
<td align="center">accepted</td>
<td align="center">Bacteria</td>
<td align="center">Pseudomonadota</td>
@ -503,19 +415,22 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<td align="center">Enterobacterales</td>
<td align="center">Enterobacteriaceae</td>
<td align="center">Escherichia</td>
<td align="center">dysenteriae</td>
<td align="center">coli</td>
<td align="center">coli</td>
<td align="center">subspecies</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>
<td align="center"></td>
<td align="center">12233256</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">1.0</td>
<td align="center"></td>
</tr>
</tbody>
@ -912,7 +827,7 @@ column names:<br><em>guideline</em>, <em>type</em>, <em>host</em>, <em>method</e
<em>breakpoint_R</em>, <em>uti</em>, and <em>is_SDD</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 19 June 2024 13:08:23 UTC. Find more info
<p>It was last updated on 16 July 2024 12:51:57 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>
@ -923,7 +838,7 @@ R Data Structure (RDS) file</a> (70 kB)<br>
text file</a> (3.1 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> (1.7 MB)<br>
Excel workbook</a> (2 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> (4.9 MB)<br>
@ -1125,37 +1040,37 @@ use.</p>
<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
<p>A data set with 340 804 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
<p>It was last updated on 16 July 2024 12:51:57 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>
R Data Structure (RDS) file</a> (0.1 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">tab-separated
text file</a> (5.1 MB)<br>
text file</a> (12.4 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>
Excel workbook</a> (3.4 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>
Feather file</a> (13.1 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>
Parquet file</a> (0 kB)<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>
transport (XPT) file</a> (28.3 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>
SPSS Statistics data file</a> (18.4 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>
DTA file</a> (28.3 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
@ -2188,7 +2103,7 @@ which are used in the <code>clinical_breakpoints</code> data set.</p>
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 16 June 2024 09:28:56 UTC. Find more info
<p>It was last updated on 16 July 2024 12:51:57 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>
@ -2199,7 +2114,7 @@ R Data Structure (RDS) file</a> (22 kB)<br>
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>
Excel workbook</a> (82 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> (0.1 MB)<br>
@ -2259,7 +2174,7 @@ laboratory systems and <a href="https://whonet.org" class="external-link">WHONET
</table>
</div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
</nav></aside>
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@ -2276,9 +2191,9 @@ laboratory systems and <a href="https://whonet.org" class="external-link">WHONET
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