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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9224</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9227</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -82,7 +82,7 @@
<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">20 March 2025</h4>
<h4 data-toc-skip class="date">27 March 2025</h4>
<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>
@ -103,7 +103,7 @@ 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 78 678 rows and 26 columns, containing the following
<p>A data set with 78 679 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>,
@ -114,7 +114,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
<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 13 March 2025 13:30:14 UTC. Find more info
<p>It was last updated on 26 March 2025 16:19:17 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>
@ -134,10 +134,10 @@ Feather file</a> (8.3 MB)<br>
Parquet file</a> (3.8 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> (29 MB)<br>
SPSS Statistics data file</a> (28.4 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> (92.5 MB)</li>
DTA file</a> (89.5 MB)</li>
</ul>
<p><strong>NOTE: The exported files for SPSS and Stata contain only the
first 50 SNOMED codes per record, as their file size would otherwise
@ -196,7 +196,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
</tr>
<tr class="even">
<td align="center">Bacteria</td>
<td align="center">39 248</td>
<td align="center">39 249</td>
</tr>
<tr class="odd">
<td align="center">Chromista</td>
@ -1033,34 +1033,34 @@ 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 301 583 rows and 2 columns, containing the following
<p>A data set with 196 665 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 29 September 2024 20:17:56 UTC. Find more info
<p>It was last updated on 27 March 2025 14:20:22 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> (0.1 MB)<br>
R Data Structure (RDS) file</a> (33 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> (10.9 MB)<br>
text file</a> (7.3 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> (3 MB)<br>
Excel workbook</a> (2.1 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> (2.5 MB)<br>
Feather file</a> (1.6 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> (0.3 MB)<br>
Parquet file</a> (66 kB)<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> (16.2 MB)<br>
SPSS Statistics data file</a> (10.7 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> (25 MB)</li>
DTA file</a> (15.6 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
@ -1118,115 +1118,115 @@ v3.3</a> (2021).</p>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cadazolid</td>
<td align="center">Bleomycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cadazolid</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cefadroxil</td>
</tr>
<tr class="even">
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cefalexin</td>
</tr>
<tr class="odd">
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cefalotin</td>
</tr>
<tr class="even">
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cefazolin</td>
</tr>
<tr class="odd">
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cefoxitin</td>
</tr>
<tr class="even">
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Clarithromycin</td>
</tr>
<tr class="odd">
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Clindamycin</td>
</tr>
<tr class="even">
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cycloserine</td>
</tr>
<tr class="odd">
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Dalbavancin</td>
</tr>
<tr class="even">
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Dirithromycin</td>
</tr>
<tr class="odd">
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Erythromycin</td>
</tr>
<tr class="even">
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Flurithromycin</td>
</tr>
<tr class="odd">
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Fusidic acid</td>
</tr>
<tr class="even">
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Gamithromycin</td>
</tr>
<tr class="odd">
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Josamycin</td>
</tr>
<tr class="even">
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Kitasamycin</td>
</tr>
<tr class="odd">
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Lincomycin</td>
</tr>
<tr class="even">
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Linezolid</td>
</tr>
<tr class="odd">
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Meleumycin</td>
</tr>
<tr class="even">
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Midecamycin</td>
</tr>
<tr class="odd">
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Miocamycin</td>
</tr>
<tr class="even">
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Nafithromycin</td>
</tr>
<tr class="odd">
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Norvancomycin</td>
</tr>
<tr class="even">
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Oleandomycin</td>
</tr>
<tr class="odd">
<tr class="even">
<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>
<td align="center">Pirlimycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
@ -1985,24 +1985,24 @@ reality and can be used to practise AMR data analysis.</p>
<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
<p>A data set with 534 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 29 September 2024 20:17:56 UTC. Find more info
<p>It was last updated on 26 March 2025 16:19:17 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> (5 kB)<br>
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>
text file</a> (50 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> (19 kB)<br>
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>
@ -2011,10 +2011,10 @@ Feather file</a> (19 kB)<br>
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.sav" class="external-link">IBM
SPSS Statistics data file</a> (63 kB)<br>
SPSS Statistics data file</a> (65 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>
DTA file</a> (83 kB)</li>
</ul>
<div class="section level3">
<h3 id="source-8">Source<a class="anchor" aria-label="anchor" href="#source-8"></a>