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10
articles/AMR.html
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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">
@ -204,7 +204,7 @@
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 13 February 2024.</p>
generated on 24 February 2024.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -260,21 +260,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2024-02-13</td>
<td align="center">2024-02-24</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2024-02-13</td>
<td align="center">2024-02-24</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2024-02-13</td>
<td align="center">2024-02-24</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>

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articles/EUCAST.html
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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>
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54
articles/MDR.html
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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>
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@ -401,19 +401,19 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co">#&gt; rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co">#&gt; 1 S R S S S S</span></span>
<span><span class="co">#&gt; 2 R S S S I I</span></span>
<span><span class="co">#&gt; 3 I S I R R S</span></span>
<span><span class="co">#&gt; 4 R R S S S S</span></span>
<span><span class="co">#&gt; 5 R R S I R I</span></span>
<span><span class="co">#&gt; 6 I R I I I R</span></span>
<span><span class="co">#&gt; 1 S I R I S I</span></span>
<span><span class="co">#&gt; 2 S R I S S R</span></span>
<span><span class="co">#&gt; 3 S I S R I S</span></span>
<span><span class="co">#&gt; 4 I S R R S S</span></span>
<span><span class="co">#&gt; 5 S R R S S I</span></span>
<span><span class="co">#&gt; 6 R S S I R S</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 S</span></span>
<span><span class="co">#&gt; 2 S</span></span>
<span><span class="co">#&gt; 3 R</span></span>
<span><span class="co">#&gt; 3 S</span></span>
<span><span class="co">#&gt; 4 R</span></span>
<span><span class="co">#&gt; 5 R</span></span>
<span><span class="co">#&gt; 6 I</span></span></code></pre></div>
<span><span class="co">#&gt; 6 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -454,40 +454,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3206</td>
<td align="right">64.12%</td>
<td align="right">3206</td>
<td align="right">64.12%</td>
<td align="right">3243</td>
<td align="right">64.86%</td>
<td align="right">3243</td>
<td align="right">64.86%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">991</td>
<td align="right">19.82%</td>
<td align="right">4197</td>
<td align="right">83.94%</td>
<td align="right">946</td>
<td align="right">18.92%</td>
<td align="right">4189</td>
<td align="right">83.78%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">434</td>
<td align="right">8.68%</td>
<td align="right">4631</td>
<td align="right">92.62%</td>
<td align="right">439</td>
<td align="right">8.78%</td>
<td align="right">4628</td>
<td align="right">92.56%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">260</td>
<td align="right">5.20%</td>
<td align="right">4891</td>
<td align="right">97.82%</td>
<td align="right">272</td>
<td align="right">5.44%</td>
<td align="right">4900</td>
<td align="right">98.00%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">109</td>
<td align="right">2.18%</td>
<td align="right">100</td>
<td align="right">2.00%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
articles/PCA.html
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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>
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articles/WHONET.html
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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>
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articles/datasets.html
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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>
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@ -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%">
<col width="3%">
<col width="3%">
<col width="4%">
<col width="3%">
<col width="7%">
<col width="14%">
<col width="6%">
<col width="2%">
<col width="16%">
<col width="15%">
<col width="8%">
<col width="8%">
<col width="7%">
@ -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>

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articles/index.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -38,7 +38,7 @@
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@ -38,7 +38,7 @@
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articles/welcome_to_AMR.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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