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<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="">2.1.1.9246</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9247</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">
@ -81,7 +81,7 @@
<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">19 April 2025</h4>
<h4 data-toc-skip class="date">20 April 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>
@ -418,14 +418,14 @@ all SNOMED codes as comma separated values.</p>
<h2 id="antimicrobials-antibiotic-and-antifungal-drugs">
<code>antimicrobials</code>: Antibiotic and Antifungal Drugs<a class="anchor" aria-label="anchor" href="#antimicrobials-antibiotic-and-antifungal-drugs"></a>
</h2>
<p>A data set with 496 rows and 14 columns, containing the following
<p>A data set with 497 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>antimicrobials</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 19 March 2025 15:05:24 UTC. Find more info
<p>It was last updated on 20 April 2025 10:55:31 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
here</a>.</p>
<p><strong>Direct download links:</strong></p>
@ -596,38 +596,38 @@ 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 34 376 rows and 14 columns, containing the following
<p>A data set with 40 217 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 13 March 2025 14:38:39 UTC. Find more info
<p>It was last updated on 20 April 2025 10:55:31 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> (76 kB)<br>
R Data Structure (RDS) file</a> (88 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> (3.1 MB)<br>
text file</a> (3.7 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 MB)<br>
Excel workbook</a> (2.4 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> (1.5 MB)<br>
Feather file</a> (1.8 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> (5.6 MB)<br>
SPSS Statistics data file</a> (6.6 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> (9.6 MB)</li>
DTA file</a> (11.1 MB)</li>
</ul>
<p><strong>Example content</strong></p>
<table class="table">
@ -643,7 +643,7 @@ DTA file</a> (9.6 MB)</li>
<col width="2%">
<col width="14%">
<col width="8%">
<col width="9%">
<col width="7%">
<col width="6%">
<col width="6%">
<col width="3%">
@ -669,7 +669,7 @@ DTA file</a> (9.6 MB)</li>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">EUCAST 2024</td>
<td align="center">EUCAST 2025</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
@ -687,7 +687,7 @@ DTA file</a> (9.6 MB)</li>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2024</td>
<td align="center">EUCAST 2025</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
@ -705,7 +705,7 @@ DTA file</a> (9.6 MB)</li>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2024</td>
<td align="center">EUCAST 2025</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
@ -716,14 +716,14 @@ DTA file</a> (9.6 MB)</li>
<td align="center">SXT</td>
<td align="center">Trimethoprim/sulfamethoxazole</td>
<td align="center">A. xylosoxidans</td>
<td align="center">1.25 mcg/23.75 mcg</td>
<td align="center">1.25/23.75 mcg</td>
<td align="center">26.000</td>
<td align="center">26.000</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2024</td>
<td align="center">EUCAST 2025</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
@ -741,7 +741,7 @@ DTA file</a> (9.6 MB)</li>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2024</td>
<td align="center">EUCAST 2025</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
@ -752,14 +752,14 @@ DTA file</a> (9.6 MB)</li>
<td align="center">TZP</td>
<td align="center">Piperacillin/tazobactam</td>
<td align="center">A. xylosoxidans</td>
<td align="center">30 mcg/6 mcg</td>
<td align="center">30/6 mcg</td>
<td align="center">26.000</td>
<td align="center">26.000</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2024</td>
<td align="center">EUCAST 2025</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
@ -1151,37 +1151,37 @@ DTA file</a> (22.6 MB)</li>
<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
<p>A data set with 759 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
<p>It was last updated on 20 April 2025 10:55:31 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/dosage.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/dosage.rds" class="external-link">original
R Data Structure (RDS) file</a> (3 kB)<br>
R Data Structure (RDS) file</a> (4 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/dosage.txt" class="external-link">tab-separated
text file</a> (43 kB)<br>
text file</a> (66 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/dosage.xlsx" class="external-link">Microsoft
Excel workbook</a> (25 kB)<br>
Excel workbook</a> (37 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/dosage.feather" class="external-link">Apache
Feather file</a> (21 kB)<br>
Feather file</a> (28 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/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/datasets/dosage.sav" class="external-link">IBM
SPSS Statistics data file</a> (64 kB)<br>
SPSS Statistics data file</a> (97 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/dosage.dta" class="external-link">Stata
DTA file</a> (0.1 MB)</li>
DTA file</a> (0.2 MB)</li>
</ul>
<p><strong>Example content</strong></p>
<table class="table">
@ -1217,7 +1217,7 @@ DTA file</a> (0.1 MB)</li>
<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>
<td align="center">15</td>
</tr>
<tr class="even">
<td align="center">AMX</td>
@ -1228,7 +1228,7 @@ DTA file</a> (0.1 MB)</li>
<td align="center">iv</td>
<td align="center"></td>
<td align="center">2 g x 6 iv</td>
<td align="center">13</td>
<td align="center">15</td>
</tr>
<tr class="odd">
<td align="center">AMX</td>
@ -1239,7 +1239,7 @@ DTA file</a> (0.1 MB)</li>
<td align="center">iv</td>
<td align="center"></td>
<td align="center">1 g x 3-4 iv</td>
<td align="center">13</td>
<td align="center">15</td>
</tr>
<tr class="even">
<td align="center">AMX</td>
@ -1250,7 +1250,7 @@ DTA file</a> (0.1 MB)</li>
<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>
<td align="center">15</td>
</tr>
<tr class="odd">
<td align="center">AMX</td>
@ -1261,7 +1261,7 @@ DTA file</a> (0.1 MB)</li>
<td align="center">oral</td>
<td align="center"></td>
<td align="center">0.5 g x 3 oral</td>
<td align="center">13</td>
<td align="center">15</td>
</tr>
<tr class="even">
<td align="center">AMX</td>
@ -1272,7 +1272,7 @@ DTA file</a> (0.1 MB)</li>
<td align="center">oral</td>
<td align="center"></td>
<td align="center">0.5 g x 3 oral</td>
<td align="center">13</td>
<td align="center">15</td>
</tr>
</tbody>
</table>
@ -1795,29 +1795,29 @@ 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 4 971 rows and 2 columns, containing the following
<p>A data set with 5 063 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 29 September 2024 20:17:56 UTC. Find more info
<p>It was last updated on 20 April 2025 10:55:31 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> (22 kB)<br>
R Data Structure (RDS) file</a> (23 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>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.xlsx" class="external-link">Microsoft
Excel workbook</a> (82 kB)<br>
Excel workbook</a> (84 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.feather" class="external-link">Apache
Feather file</a> (85 kB)<br>
Feather file</a> (87 kB)<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> (56 kB)<br>
Parquet file</a> (59 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> (0.1 MB)<br>