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@ -38,7 +38,7 @@
<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="">2.1.1.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</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">
@ -193,7 +193,7 @@
<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">13 February 2024</h4>
<h4 data-toc-skip class="date">24 February 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>
<div class="d-none name"><code>datasets.Rmd</code></div>
@ -532,7 +532,7 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
<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 20 October 2023 12:51:48 UTC. Find more info
<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>
@ -543,7 +543,7 @@ R Data Structure (RDS) file</a> (44 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/antibiotics.xlsx" class="external-link">Microsoft
Excel workbook</a> (72 kB)<br>
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>
@ -904,40 +904,40 @@ 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 29 747 rows and 12 columns, containing the following
column names:<br><em>guideline</em>, <em>type</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>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 20 October 2023 13:07:11 UTC. Find more info
<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> (59 kB)<br>
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> (2.3 MB)<br>
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> (1.3 MB)<br>
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> (1.2 MB)<br>
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> (96 kB)<br>
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> (7.9 MB)<br>
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> (4.6 MB)<br>
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> (7.8 MB)</li>
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>
@ -973,13 +973,14 @@ use.</p>
<colgroup>
<col width="6%">
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<col width="7%">
<col width="14%">
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@ -989,6 +990,7 @@ use.</p>
<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>
@ -1006,6 +1008,7 @@ use.</p>
<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>
@ -1022,6 +1025,7 @@ use.</p>
<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>
@ -1038,6 +1042,7 @@ use.</p>
<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>
@ -1054,6 +1059,7 @@ use.</p>
<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>
@ -1070,6 +1076,7 @@ use.</p>
<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>
@ -1086,6 +1093,7 @@ use.</p>
<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>