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@@ -30,7 +30,7 @@
<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="">3.0.1.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
@@ -80,7 +80,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
<h4 data-toc-skip class="date">24 March 2026</h4>
<h4 data-toc-skip class="date">30 March 2026</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>
@@ -595,38 +595,38 @@ inhibitors</td>
<code>clinical_breakpoints</code>: Interpretation from MIC values
&amp; 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 40 217 rows and 14 columns, containing the following
<p>A data set with 45 797 rows and 14 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>, <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 20 April 2025 10:55:31 UTC. Find more info
<p>It was last updated on 30 March 2026 08:01:49 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/clinical_breakpoints.html">data
set 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/datasets/clinical_breakpoints.rds" class="external-link">original
R Data Structure (RDS) file</a> (88 kB)<br>
R Data Structure (RDS) file</a> (92 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.txt" class="external-link">tab-separated
text file</a> (3.7 MB)<br>
text file</a> (4.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.xlsx" class="external-link">Microsoft
Excel workbook</a> (2.4 MB)<br>
Excel workbook</a> (2.7 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.feather" class="external-link">Apache
Feather file</a> (1.8 MB)<br>
Feather file</a> (2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.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/datasets/clinical_breakpoints.sav" class="external-link">IBM
SPSS Statistics data file</a> (6.6 MB)<br>
SPSS Statistics data file</a> (7.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.dta" class="external-link">Stata
DTA file</a> (11.1 MB)</li>
DTA file</a> (12.6 MB)</li>
</ul>
<p><strong>Example content</strong></p>
<table class="table">
@@ -668,7 +668,7 @@ DTA file</a> (11.1 MB)</li>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">EUCAST 2025</td>
<td align="center">EUCAST 2026</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
@@ -686,7 +686,7 @@ DTA file</a> (11.1 MB)</li>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2025</td>
<td align="center">EUCAST 2026</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
@@ -704,7 +704,7 @@ DTA file</a> (11.1 MB)</li>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2025</td>
<td align="center">EUCAST 2026</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
@@ -722,7 +722,7 @@ DTA file</a> (11.1 MB)</li>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2025</td>
<td align="center">EUCAST 2026</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
@@ -740,7 +740,7 @@ DTA file</a> (11.1 MB)</li>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2025</td>
<td align="center">EUCAST 2026</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
@@ -758,7 +758,7 @@ DTA file</a> (11.1 MB)</li>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2025</td>
<td align="center">EUCAST 2026</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
@@ -1794,17 +1794,17 @@ set here</a>.</p>
<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 6 036 rows and 2 columns, containing the following
<p>A data set with 6 050 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 4 May 2025 16:50:25 UTC. Find more info about
the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/microorganisms.codes.html">data
<p>It was last updated on 30 March 2026 08:01:49 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/microorganisms.codes.html">data
set 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/datasets/microorganisms.codes.rds" class="external-link">original
R Data Structure (RDS) file</a> (27 kB)<br>
R Data Structure (RDS) file</a> (28 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.txt" class="external-link">tab-separated
text file</a> (0.1 MB)<br>
@@ -1816,7 +1816,7 @@ Excel workbook</a> (98 kB)<br>
Feather file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.parquet" class="external-link">Apache
Parquet file</a> (68 kB)<br>
Parquet file</a> (69 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.sav" class="external-link">IBM
SPSS Statistics data file</a> (0.2 MB)<br>