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(v1.7.1.9023) Removed filter_ functions, new set_ab_names(), ATC code update, ab selector update, fixes #46 and fixed #47

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@ -40,7 +43,7 @@
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<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9023</span>
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@ -50,6 +50,9 @@
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@ -89,7 +92,7 @@
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<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9023</span>
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docs/articles/AMR.html
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@ -21,6 +21,9 @@
<script src="../extra.js"></script><meta property="og:title" content="How to conduct AMR data analysis">
<meta property="og:description" content="AMR">
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@ -41,7 +44,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9023</span>
</span>
</div>
@ -195,7 +198,7 @@
<h1 data-toc-skip>How to conduct AMR data analysis</h1>
<h4 data-toc-skip class="author">Matthijs S. Berends</h4>
<h4 data-toc-skip class="date">23 July 2021</h4>
<h4 data-toc-skip class="date">16 August 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -204,7 +207,7 @@
<p><strong>Note:</strong> values on this page will change with every 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 23 July 2021.</p>
<p><strong>Note:</strong> values on this page will change with every 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 16 August 2021.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor" aria-hidden="true"></a>Introduction</h1>
@ -235,21 +238,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2021-07-23</td>
<td align="center">2021-08-16</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">2021-07-23</td>
<td align="center">2021-08-16</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">2021-07-23</td>
<td align="center">2021-08-16</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -346,70 +349,70 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-03-31</td>
<td align="center">U1</td>
<td align="center">2016-06-21</td>
<td align="center">V8</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-09-19</td>
<td align="center">E6</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2013-10-17</td>
<td align="center">K4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-09-11</td>
<td align="center">G5</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2010-04-19</td>
<td align="center">Z2</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2015-07-17</td>
<td align="center">M4</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2013-03-06</td>
<td align="center">B9</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-10-06</td>
<td align="center">D8</td>
<td align="center">2014-03-08</td>
<td align="center">R1</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2013-05-12</td>
<td align="center">F10</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-07-15</td>
<td align="center">H7</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
@ -443,18 +446,18 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,388</td>
<td align="right">51.94%</td>
<td align="right">10,388</td>
<td align="right">51.94%</td>
<td align="right">10,300</td>
<td align="right">51.5%</td>
<td align="right">10,300</td>
<td align="right">51.5%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,612</td>
<td align="right">48.06%</td>
<td align="right">9,700</td>
<td align="right">48.5%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
<td align="right">100.0%</td>
</tr>
</tbody>
</table>
@ -507,9 +510,9 @@ Longest: 1</p>
<span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span>
<span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span>
<span class="co"># 2</span>
<span class="co"># =&gt; Found 10,659 first weighted isolates (phenotype-based, 53.3% of total</span>
<span class="co"># =&gt; Found 10,584 first weighted isolates (phenotype-based, 52.9% of total</span>
<span class="co"># where a microbial ID was available)</span></code></pre></div>
<p>So only 53.3% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<p>So only 52.9% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
@ -517,7 +520,7 @@ Longest: 1</p>
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
<p>So we end up with 10,659 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,584 isolates for analysis. Now our data looks like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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">data_1st</span><span class="op">)</span></code></pre></div>
<table style="width:100%;" class="table">
@ -555,46 +558,30 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">2</td>
<td align="center">2015-07-17</td>
<td align="center">M4</td>
<td align="center">Hospital B</td>
<td align="left">1</td>
<td align="center">2016-06-21</td>
<td align="center">V8</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">3</td>
<td align="center">2013-03-06</td>
<td align="center">B9</td>
<td align="left">2</td>
<td align="center">2017-09-19</td>
<td align="center">E6</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="center">2013-05-12</td>
<td align="center">F10</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
@ -602,27 +589,43 @@ Longest: 1</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2016-07-27</td>
<td align="center">E3</td>
<tr class="odd">
<td align="left">4</td>
<td align="center">2013-09-11</td>
<td align="center">G5</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="center">2014-03-08</td>
<td align="center">R1</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">8</td>
<td align="center">2015-02-09</td>
<td align="center">T6</td>
<td align="center">Hospital A</td>
<td align="left">7</td>
<td align="center">2015-07-22</td>
<td align="center">U6</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
@ -635,19 +638,19 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2017-08-22</td>
<td align="center">F8</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="left">8</td>
<td align="center">2015-07-26</td>
<td align="center">A1</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -671,8 +674,8 @@ Longest: 1</p>
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,659<br>
Available: 10,659 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,584<br>
Available: 10,584 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -689,33 +692,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,644</td>
<td align="right">43.57%</td>
<td align="right">4,644</td>
<td align="right">43.57%</td>
<td align="right">4,573</td>
<td align="right">43.21%</td>
<td align="right">4,573</td>
<td align="right">43.21%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,731</td>
<td align="right">25.62%</td>
<td align="right">7,375</td>
<td align="right">69.19%</td>
<td align="right">2,737</td>
<td align="right">25.86%</td>
<td align="right">7,310</td>
<td align="right">69.07%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,125</td>
<td align="right">19.94%</td>
<td align="right">9,500</td>
<td align="right">89.13%</td>
<td align="right">2,126</td>
<td align="right">20.09%</td>
<td align="right">9,436</td>
<td align="right">89.15%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,159</td>
<td align="right">10.87%</td>
<td align="right">10,659</td>
<td align="right">1,148</td>
<td align="right">10.85%</td>
<td align="right">10,584</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -734,14 +737,14 @@ Longest: 24</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="11%">
<col width="10%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@ -762,12 +765,12 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-03-06</td>
<td align="center">B9</td>
<td align="center">Hospital C</td>
<td align="center">2015-07-26</td>
<td align="center">A1</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
@ -777,13 +780,43 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-07-27</td>
<td align="center">E3</td>
<td align="center">2016-04-15</td>
<td align="center">E1</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-12-17</td>
<td align="center">D8</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2010-04-23</td>
<td align="center">M6</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -792,63 +825,33 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-10-14</td>
<td align="center">X8</td>
<td align="center">2013-01-18</td>
<td align="center">O5</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-06-11</td>
<td align="center">V8</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2013-09-03</td>
<td align="center">S3</td>
<td align="center">2012-12-05</td>
<td align="center">S7</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-05-16</td>
<td align="center">X5</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -872,50 +875,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2213</td>
<td align="center">141</td>
<td align="center">2290</td>
<td align="center">4644</td>
<td align="center">2169</td>
<td align="center">137</td>
<td align="center">2267</td>
<td align="center">4573</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3408</td>
<td align="center">175</td>
<td align="center">1061</td>
<td align="center">4644</td>
<td align="center">3389</td>
<td align="center">161</td>
<td align="center">1023</td>
<td align="center">4573</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3393</td>
<td align="center">3306</td>
<td align="center">0</td>
<td align="center">1251</td>
<td align="center">4644</td>
<td align="center">1267</td>
<td align="center">4573</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4060</td>
<td align="center">4004</td>
<td align="center">0</td>
<td align="center">584</td>
<td align="center">4644</td>
<td align="center">569</td>
<td align="center">4573</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1159</td>
<td align="center">1159</td>
<td align="center">1148</td>
<td align="center">1148</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">905</td>
<td align="center">39</td>
<td align="center">215</td>
<td align="center">1159</td>
<td align="center">891</td>
<td align="center">44</td>
<td align="center">213</td>
<td align="center">1148</td>
</tr>
</tbody>
</table>
@ -938,34 +941,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4060</td>
<td align="center">4004</td>
<td align="center">0</td>
<td align="center">584</td>
<td align="center">4644</td>
<td align="center">569</td>
<td align="center">4573</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1052</td>
<td align="center">1048</td>
<td align="center">0</td>
<td align="center">107</td>
<td align="center">1159</td>
<td align="center">100</td>
<td align="center">1148</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2426</td>
<td align="center">2444</td>
<td align="center">0</td>
<td align="center">305</td>
<td align="center">2731</td>
<td align="center">293</td>
<td align="center">2737</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">2125</td>
<td align="center">2125</td>
<td align="center">2126</td>
<td align="center">2126</td>
</tr>
</tbody>
</table>
@ -979,7 +982,7 @@ Longest: 24</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>
<span class="co"># [1] 0.5388873</span></code></pre></div>
<span class="co"># [1] 0.5377929</span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span>
@ -993,19 +996,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5379610</td>
<td align="center">0.5389338</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5353400</td>
<td align="center">0.5440860</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5317705</td>
<td align="center">0.5516820</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5521531</td>
<td align="center">0.5145267</td>
</tr>
</tbody>
</table>
@ -1024,23 +1027,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5379610</td>
<td align="center">3227</td>
<td align="center">0.5389338</td>
<td align="center">3095</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5353400</td>
<td align="center">3721</td>
<td align="center">0.5440860</td>
<td align="center">3720</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5317705</td>
<td align="center">1621</td>
<td align="center">0.5516820</td>
<td align="center">1635</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5521531</td>
<td align="center">2090</td>
<td align="center">0.5145267</td>
<td align="center">2134</td>
</tr>
</tbody>
</table>
@ -1061,27 +1064,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7715332</td>
<td align="center">0.8742463</td>
<td align="center">0.9773902</td>
<td align="center">0.7762956</td>
<td align="center">0.8755740</td>
<td align="center">0.9781325</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8144953</td>
<td align="center">0.9076790</td>
<td align="center">0.9861950</td>
<td align="center">0.8144599</td>
<td align="center">0.9128920</td>
<td align="center">0.9782230</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8000732</td>
<td align="center">0.8883193</td>
<td align="center">0.9791285</td>
<td align="center">0.7939350</td>
<td align="center">0.8929485</td>
<td align="center">0.9839240</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5331765</td>
<td align="center">0.5352775</td>
<td align="center">0.0000000</td>
<td align="center">0.5331765</td>
<td align="center">0.5352775</td>
</tr>
</tbody>
</table>
@ -1100,29 +1103,29 @@ Longest: 24</p>
<table class="table">
<thead><tr class="header">
<th align="left">hospital</th>
<th align="right">amoxicillin</th>
<th align="right">amoxicillin_clavulanic_acid</th>
<th align="right">Amoxicillin</th>
<th align="right">Amoxicillin/clavulanic acid</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">53.8%</td>
<td align="right">26.0%</td>
<td align="right">53.9%</td>
<td align="right">25.8%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">53.5%</td>
<td align="right">26.9%</td>
<td align="right">54.4%</td>
<td align="right">27.2%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">53.2%</td>
<td align="right">26.3%</td>
<td align="right">55.2%</td>
<td align="right">27.8%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">55.2%</td>
<td align="right">26.2%</td>
<td align="right">51.5%</td>
<td align="right">24.6%</td>
</tr>
</tbody>
</table>
@ -1206,16 +1209,18 @@ Longest: 24</p>
<code class="sourceCode R"><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
<span class="va">mic_values</span>
<span class="co"># Class &lt;mic&gt;</span>
<span class="co"># [1] 0.125 128 0.25 16 0.125 32 0.125 0.0625 8 0.025 </span>
<span class="co"># [11] 0.125 128 0.01 16 1 8 0.005 0.005 64 0.005 </span>
<span class="co"># [21] 128 16 0.025 128 0.5 0.005 0.025 0.001 64 0.001 </span>
<span class="co"># [31] 32 2 256 8 128 32 256 0.5 0.125 1 </span>
<span class="co"># [41] 0.01 128 0.01 64 1 128 64 0.01 0.025 0.005 </span>
<span class="co"># [51] 128 0.0625 8 256 64 32 0.001 0.025 0.5 0.0625</span>
<span class="co"># [61] 0.5 0.002 0.002 0.01 0.0625 128 128 0.01 0.5 256 </span>
<span class="co"># [71] 0.0625 256 0.25 0.025 0.025 8 256 0.002 0.025 0.025 </span>
<span class="co"># [81] 0.002 1 0.005 32 128 256 256 0.005 16 0.025 </span>
<span class="co"># [91] 0.25 0.025 0.002 64 16 2 1 0.0625 16 256</span></code></pre></div>
<span class="co"># [1] 0.0625 256 32 0.002 &lt;=0.001 256 0.5 0.025 0.5 </span>
<span class="co"># [10] 2 0.002 0.005 0.005 1 32 0.01 0.002 64 </span>
<span class="co"># [19] 0.25 4 0.025 0.125 0.005 1 2 0.002 0.25 </span>
<span class="co"># [28] 0.25 32 2 0.25 0.25 0.005 0.5 0.002 0.002 </span>
<span class="co"># [37] 8 0.25 2 2 0.005 0.5 64 128 2 </span>
<span class="co"># [46] 64 0.0625 0.002 1 0.01 16 0.125 64 4 </span>
<span class="co"># [55] 16 2 32 0.025 256 16 1 0.005 32 </span>
<span class="co"># [64] 16 0.01 0.025 4 0.0625 0.125 0.025 0.5 0.5 </span>
<span class="co"># [73] 0.025 128 0.01 0.025 256 0.25 1 64 0.125 </span>
<span class="co"># [82] 2 &lt;=0.001 0.25 8 0.0625 4 16 0.025 64 </span>
<span class="co"># [91] 8 0.01 0.0625 8 128 0.5 4 0.002 0.5 </span>
<span class="co"># [100] 64</span></code></pre></div>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># base R:</span>
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></code></pre></div>
@ -1244,10 +1249,10 @@ Longest: 24</p>
<span class="co"># to review it.</span>
<span class="va">disk_values</span>
<span class="co"># Class &lt;disk&gt;</span>
<span class="co"># [1] 28 23 25 19 26 25 18 26 28 20 17 17 27 22 22 22 26 28 21 19 30 22 17 30 30</span>
<span class="co"># [26] 22 29 17 21 20 17 29 22 21 29 30 26 30 18 17 24 20 20 31 31 22 22 22 27 28</span>
<span class="co"># [51] 23 19 21 19 24 20 27 29 18 21 24 24 29 20 21 22 21 25 26 24 27 31 17 23 29</span>
<span class="co"># [76] 31 21 29 31 24 23 26 26 25 22 26 28 26 22 25 17 29 21 21 30 18 18 23 31 27</span></code></pre></div>
<span class="co"># [1] 18 22 30 28 29 31 18 21 17 31 28 25 21 22 29 26 21 30 17 20 18 21 26 19 24</span>
<span class="co"># [26] 17 30 17 26 19 29 23 23 22 26 25 20 25 29 20 28 29 31 24 23 26 29 20 17 17</span>
<span class="co"># [51] 27 18 18 29 17 20 21 24 30 17 25 27 21 30 28 26 27 20 22 19 19 24 21 28 22</span>
<span class="co"># [76] 24 21 28 24 17 29 23 31 28 25 20 18 18 30 31 17 18 17 28 24 22 24 31 25 31</span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># base R:</span>
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></code></pre></div>

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// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

12
docs/articles/AMR_files/header-attrs-2.4/header-attrs.js
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

12
docs/articles/AMR_files/header-attrs-2.6/header-attrs.js
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

12
docs/articles/AMR_files/header-attrs-2.8/header-attrs.js
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

5
docs/articles/EUCAST.html
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@ -21,6 +21,9 @@
<script src="../extra.js"></script><meta property="og:title" content="How to apply EUCAST rules">
<meta property="og:description" content="AMR">
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
<meta name="twitter:card" content="summary_large_image">
<meta name="twitter:creator" content="@msberends">
<meta name="twitter:site" content="@univgroningen">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@ -41,7 +44,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9023</span>
</span>
</div>

15
docs/articles/EUCAST_files/accessible-code-block-0.0.1/empty-anchor.js
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@ -1,15 +0,0 @@
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
// v0.0.1
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
document.addEventListener('DOMContentLoaded', function() {
const codeList = document.getElementsByClassName("sourceCode");
for (var i = 0; i < codeList.length; i++) {
var linkList = codeList[i].getElementsByTagName('a');
for (var j = 0; j < linkList.length; j++) {
if (linkList[j].innerHTML === "") {
linkList[j].setAttribute('aria-hidden', 'true');
}
}
}
});

4
docs/articles/EUCAST_files/anchor-sections-1.0/anchor-sections.css
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@ -1,4 +0,0 @@
/* Styles for section anchors */
a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;}
a.anchor-section::before {content: '#';}
.hasAnchor:hover a.anchor-section {visibility: visible;}

33
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@ -1,33 +0,0 @@
// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020.
document.addEventListener('DOMContentLoaded', function() {
// Do nothing if AnchorJS is used
if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) {
return;
}
const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6');
// Do nothing if sections are already anchored
if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) {
return null;
}
// Use section id when pandoc runs with --section-divs
const section_id = function(x) {
return ((x.classList.contains('section') || (x.tagName === 'SECTION'))
? x.id : '');
};
// Add anchors
h.forEach(function(x) {
const id = x.id || section_id(x.parentElement);
if (id === '') {
return null;
}
let anchor = document.createElement('a');
anchor.href = '#' + id;
anchor.classList = ['anchor-section'];
x.classList.add('hasAnchor');
x.appendChild(anchor);
});
});

12
docs/articles/EUCAST_files/header-attrs-2.3/header-attrs.js
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

12
docs/articles/EUCAST_files/header-attrs-2.4/header-attrs.js
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

12
docs/articles/EUCAST_files/header-attrs-2.6/header-attrs.js
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

12
docs/articles/EUCAST_files/header-attrs-2.8/header-attrs.js
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

61
docs/articles/MDR.html
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@ -21,6 +21,9 @@
<script src="../extra.js"></script><meta property="og:title" content="How to determine multi-drug resistance (MDR)">
<meta property="og:description" content="AMR">
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
<meta name="twitter:card" content="summary_large_image">
<meta name="twitter:creator" content="@msberends">
<meta name="twitter:site" content="@univgroningen">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@ -41,7 +44,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9023</span>
</span>
</div>
@ -262,7 +265,7 @@
<p>The outcome of the function can be used for the <code>guideline</code> argument in the <code><a href="../reference/mdro.html">mdro()</a></code> function:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">example_isolates</span>, guideline <span class="op">=</span> <span class="va">custom</span><span class="op">)</span>
<span class="co"># Determining MDROs based on custom rules, resulting in [factor] levels:</span>
<span class="co"># Determining MDROs based on custom rules, resulting in factor levels:</span>
<span class="co"># Negative &lt; Elderly Type A &lt; Elderly Type B.</span>
<span class="co"># - Custom MDRO rule 1: `CIP == "R" &amp; age &gt; 60` (198 rows matched)</span>
<span class="co"># - Custom MDRO rule 2: `ERY == "R" &amp; age &gt; 60` (732 rows matched)</span>
@ -361,17 +364,17 @@ Unique: 2</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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 class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
<span class="co"># 1 I S S R I S</span>
<span class="co"># 2 R R R R S R</span>
<span class="co"># 3 R R R I S S</span>
<span class="co"># 4 R S I R R R</span>
<span class="co"># 5 R S S S I R</span>
<span class="co"># 6 S I S S S I</span>
<span class="co"># 1 R S I S R R</span>
<span class="co"># 2 I R S S S I</span>
<span class="co"># 3 S I I S S I</span>
<span class="co"># 4 S I I R S S</span>
<span class="co"># 5 S I S S R I</span>
<span class="co"># 6 S R S I S I</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 S</span>
<span class="co"># 2 S</span>
<span class="co"># 1 I</span>
<span class="co"># 2 R</span>
<span class="co"># 3 I</span>
<span class="co"># 4 S</span>
<span class="co"># 4 I</span>
<span class="co"># 5 I</span>
<span class="co"># 6 I</span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
@ -416,40 +419,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3175</td>
<td align="right">63.50%</td>
<td align="right">3175</td>
<td align="right">63.50%</td>
<td align="right">3169</td>
<td align="right">63.38%</td>
<td align="right">3169</td>
<td align="right">63.38%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1014</td>
<td align="right">20.28%</td>
<td align="right">4189</td>
<td align="right">83.78%</td>
<td align="right">1049</td>
<td align="right">20.98%</td>
<td align="right">4218</td>
<td align="right">84.36%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">445</td>
<td align="right">8.90%</td>
<td align="right">4634</td>
<td align="right">92.68%</td>
<td align="right">458</td>
<td align="right">9.16%</td>
<td align="right">4676</td>
<td align="right">93.52%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">272</td>
<td align="right">5.44%</td>
<td align="right">4906</td>
<td align="right">98.12%</td>
<td align="right">240</td>
<td align="right">4.80%</td>
<td align="right">4916</td>
<td align="right">98.32%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">94</td>
<td align="right">1.88%</td>
<td align="right">84</td>
<td align="right">1.68%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

15
docs/articles/MDR_files/accessible-code-block-0.0.1/empty-anchor.js
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@ -1,15 +0,0 @@
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
// v0.0.1
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
document.addEventListener('DOMContentLoaded', function() {
const codeList = document.getElementsByClassName("sourceCode");
for (var i = 0; i < codeList.length; i++) {
var linkList = codeList[i].getElementsByTagName('a');
for (var j = 0; j < linkList.length; j++) {
if (linkList[j].innerHTML === "") {
linkList[j].setAttribute('aria-hidden', 'true');
}
}
}
});

4
docs/articles/MDR_files/anchor-sections-1.0/anchor-sections.css
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@ -1,4 +0,0 @@
/* Styles for section anchors */
a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;}
a.anchor-section::before {content: '#';}
.hasAnchor:hover a.anchor-section {visibility: visible;}

33
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@ -1,33 +0,0 @@
// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020.
document.addEventListener('DOMContentLoaded', function() {
// Do nothing if AnchorJS is used
if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) {
return;
}
const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6');
// Do nothing if sections are already anchored
if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) {
return null;
}
// Use section id when pandoc runs with --section-divs
const section_id = function(x) {
return ((x.classList.contains('section') || (x.tagName === 'SECTION'))
? x.id : '');
};
// Add anchors
h.forEach(function(x) {
const id = x.id || section_id(x.parentElement);
if (id === '') {
return null;
}
let anchor = document.createElement('a');
anchor.href = '#' + id;
anchor.classList = ['anchor-section'];
x.classList.add('hasAnchor');
x.appendChild(anchor);
});
});

12
docs/articles/MDR_files/header-attrs-2.3/header-attrs.js
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

12
docs/articles/MDR_files/header-attrs-2.4/header-attrs.js
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

12
docs/articles/MDR_files/header-attrs-2.6/header-attrs.js
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

12
docs/articles/MDR_files/header-attrs-2.8/header-attrs.js
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

5
docs/articles/PCA.html
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@ -21,6 +21,9 @@
<script src="../extra.js"></script><meta property="og:title" content="How to conduct principal component analysis (PCA) for AMR">
<meta property="og:description" content="AMR">
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
<meta name="twitter:card" content="summary_large_image">
<meta name="twitter:creator" content="@msberends">
<meta name="twitter:site" content="@univgroningen">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@ -41,7 +44,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9023</span>
</span>
</div>

15
docs/articles/PCA_files/accessible-code-block-0.0.1/empty-anchor.js
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@ -1,15 +0,0 @@
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
// v0.0.1
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
document.addEventListener('DOMContentLoaded', function() {
const codeList = document.getElementsByClassName("sourceCode");
for (var i = 0; i < codeList.length; i++) {
var linkList = codeList[i].getElementsByTagName('a');
for (var j = 0; j < linkList.length; j++) {
if (linkList[j].innerHTML === "") {
linkList[j].setAttribute('aria-hidden', 'true');
}
}
}
});

4
docs/articles/PCA_files/anchor-sections-1.0/anchor-sections.css
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@ -1,4 +0,0 @@
/* Styles for section anchors */
a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;}
a.anchor-section::before {content: '#';}
.hasAnchor:hover a.anchor-section {visibility: visible;}

33
docs/articles/PCA_files/anchor-sections-1.0/anchor-sections.js
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@ -1,33 +0,0 @@
// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020.
document.addEventListener('DOMContentLoaded', function() {
// Do nothing if AnchorJS is used
if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) {
return;
}
const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6');
// Do nothing if sections are already anchored
if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) {
return null;
}
// Use section id when pandoc runs with --section-divs
const section_id = function(x) {
return ((x.classList.contains('section') || (x.tagName === 'SECTION'))
? x.id : '');
};
// Add anchors
h.forEach(function(x) {
const id = x.id || section_id(x.parentElement);
if (id === '') {
return null;
}
let anchor = document.createElement('a');
anchor.href = '#' + id;
anchor.classList = ['anchor-section'];
x.classList.add('hasAnchor');
x.appendChild(anchor);
});
});

12
docs/articles/PCA_files/header-attrs-2.3/header-attrs.js
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

12
docs/articles/PCA_files/header-attrs-2.4/header-attrs.js
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

12
docs/articles/PCA_files/header-attrs-2.6/header-attrs.js
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

12
docs/articles/PCA_files/header-attrs-2.8/header-attrs.js
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

9
docs/articles/SPSS.html
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@ -21,6 +21,9 @@
<script src="../extra.js"></script><meta property="og:title" content="How to import data from SPSS / SAS / Stata">
<meta property="og:description" content="AMR">
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
<meta name="twitter:card" content="summary_large_image">
<meta name="twitter:creator" content="@msberends">
<meta name="twitter:site" content="@univgroningen">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@ -41,7 +44,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9023</span>
</span>
</div>
@ -195,7 +198,7 @@
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
<h4 data-toc-skip class="author">Matthijs S. Berends</h4>
<h4 data-toc-skip class="date">23 July 2021</h4>
<h4 data-toc-skip class="date">16 August 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="hidden name"><code>SPSS.Rmd</code></div>
@ -230,7 +233,7 @@
</li>
<li>
<p><strong>R has a huge community.</strong></p>
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">411,199 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">414,789 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
</li>
<li>
<p><strong>R understands any data type, including SPSS/SAS/Stata.</strong></p>

15
docs/articles/SPSS_files/accessible-code-block-0.0.1/empty-anchor.js
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@ -1,15 +0,0 @@
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
// v0.0.1
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
document.addEventListener('DOMContentLoaded', function() {
const codeList = document.getElementsByClassName("sourceCode");
for (var i = 0; i < codeList.length; i++) {
var linkList = codeList[i].getElementsByTagName('a');
for (var j = 0; j < linkList.length; j++) {
if (linkList[j].innerHTML === "") {
linkList[j].setAttribute('aria-hidden', 'true');
}
}
}
});

4
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@ -1,4 +0,0 @@
/* Styles for section anchors */
a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;}
a.anchor-section::before {content: '#';}
.hasAnchor:hover a.anchor-section {visibility: visible;}

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@ -1,33 +0,0 @@
// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020.
document.addEventListener('DOMContentLoaded', function() {
// Do nothing if AnchorJS is used
if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) {
return;
}
const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6');
// Do nothing if sections are already anchored
if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) {
return null;
}
// Use section id when pandoc runs with --section-divs
const section_id = function(x) {
return ((x.classList.contains('section') || (x.tagName === 'SECTION'))
? x.id : '');
};
// Add anchors
h.forEach(function(x) {
const id = x.id || section_id(x.parentElement);
if (id === '') {
return null;
}
let anchor = document.createElement('a');
anchor.href = '#' + id;
anchor.classList = ['anchor-section'];
x.classList.add('hasAnchor');
x.appendChild(anchor);
});
});

12
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

12
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

12
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

12
docs/articles/SPSS_files/header-attrs-2.8/header-attrs.js
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

5
docs/articles/WHONET.html
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@ -21,6 +21,9 @@
<script src="../extra.js"></script><meta property="og:title" content="How to work with WHONET data">
<meta property="og:description" content="AMR">
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
<meta name="twitter:card" content="summary_large_image">
<meta name="twitter:creator" content="@msberends">
<meta name="twitter:site" content="@univgroningen">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@ -41,7 +44,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9023</span>
</span>
</div>

15
docs/articles/WHONET_files/accessible-code-block-0.0.1/empty-anchor.js
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@ -1,15 +0,0 @@
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
// v0.0.1
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
document.addEventListener('DOMContentLoaded', function() {
const codeList = document.getElementsByClassName("sourceCode");
for (var i = 0; i < codeList.length; i++) {
var linkList = codeList[i].getElementsByTagName('a');
for (var j = 0; j < linkList.length; j++) {
if (linkList[j].innerHTML === "") {
linkList[j].setAttribute('aria-hidden', 'true');
}
}
}
});

4
docs/articles/WHONET_files/anchor-sections-1.0/anchor-sections.css
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@ -1,4 +0,0 @@
/* Styles for section anchors */
a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;}
a.anchor-section::before {content: '#';}
.hasAnchor:hover a.anchor-section {visibility: visible;}

33
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@ -1,33 +0,0 @@
// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020.
document.addEventListener('DOMContentLoaded', function() {
// Do nothing if AnchorJS is used
if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) {
return;
}
const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6');
// Do nothing if sections are already anchored
if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) {
return null;
}
// Use section id when pandoc runs with --section-divs
const section_id = function(x) {
return ((x.classList.contains('section') || (x.tagName === 'SECTION'))
? x.id : '');
};
// Add anchors
h.forEach(function(x) {
const id = x.id || section_id(x.parentElement);
if (id === '') {
return null;
}
let anchor = document.createElement('a');
anchor.href = '#' + id;
anchor.classList = ['anchor-section'];
x.classList.add('hasAnchor');
x.appendChild(anchor);
});
});

12
docs/articles/WHONET_files/header-attrs-2.3/header-attrs.js
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

12
docs/articles/WHONET_files/header-attrs-2.4/header-attrs.js
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

12
docs/articles/WHONET_files/header-attrs-2.6/header-attrs.js
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

12
docs/articles/WHONET_files/header-attrs-2.8/header-attrs.js
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@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

73
docs/articles/benchmarks.html
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@ -21,6 +21,9 @@
<script src="../extra.js"></script><meta property="og:title" content="Benchmarks">
<meta property="og:description" content="AMR">
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
<meta name="twitter:card" content="summary_large_image">
<meta name="twitter:creator" content="@msberends">
<meta name="twitter:site" content="@univgroningen">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@ -41,7 +44,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9023</span>
</span>
</div>
@ -229,18 +232,18 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 12.0 13.0 19.0 14 16.0 49 25</span>
<span class="co"># as.mo("stau") 55.0 58.0 80.0 91 96.0 110 25</span>
<span class="co"># as.mo("STAU") 57.0 63.0 79.0 66 96.0 110 25</span>
<span class="co"># as.mo("staaur") 13.0 13.0 19.0 14 16.0 48 25</span>
<span class="co"># as.mo("STAAUR") 13.0 13.0 22.0 15 17.0 48 25</span>
<span class="co"># as.mo("S. aureus") 27.0 30.0 42.0 33 62.0 67 25</span>
<span class="co"># as.mo("S aureus") 28.0 30.0 37.0 32 34.0 64 25</span>
<span class="co"># as.mo("Staphylococcus aureus") 3.5 3.9 5.5 4 4.4 38 25</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 260.0 270.0 280.0 270 290.0 370 25</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 170.0 200.0 210.0 210 230.0 250 25</span>
<span class="co"># as.mo("MRSA") 13.0 14.0 20.0 15 15.0 51 25</span>
<span class="co"># as.mo("VISA") 22.0 23.0 33.0 25 27.0 64 25</span></code></pre></div>
<span class="co"># as.mo("sau") 12.0 13.0 20.0 14.0 16.0 51 25</span>
<span class="co"># as.mo("stau") 56.0 60.0 77.0 85.0 94.0 100 25</span>
<span class="co"># as.mo("STAU") 54.0 59.0 78.0 85.0 95.0 100 25</span>
<span class="co"># as.mo("staaur") 12.0 13.0 20.0 14.0 15.0 57 25</span>
<span class="co"># as.mo("STAAUR") 13.0 13.0 19.0 14.0 16.0 51 25</span>
<span class="co"># as.mo("S. aureus") 27.0 29.0 39.0 34.0 50.0 64 25</span>
<span class="co"># as.mo("S aureus") 27.0 30.0 43.0 33.0 60.0 70 25</span>
<span class="co"># as.mo("Staphylococcus aureus") 3.8 4.1 5.5 4.5 4.7 31 25</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 250.0 270.0 280.0 280.0 290.0 390 25</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 190.0 200.0 200.0 200.0 200.0 220 25</span>
<span class="co"># as.mo("MRSA") 12.0 13.0 15.0 14.0 16.0 30 25</span>
<span class="co"># as.mo("VISA") 21.0 22.0 31.0 25.0 29.0 59 25</span></code></pre></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="750"></p>
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 200 times slower to determine.</p>
<p>To improve performance, we implemented two important algorithms to save unnecessary calculations: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
@ -262,8 +265,8 @@
<span class="co"># what do these values look like? They are of class &lt;mo&gt;:</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">x</span><span class="op">)</span>
<span class="co"># Class &lt;mo&gt;</span>
<span class="co"># [1] B_SERRT_MRCS B_STRPT_ORLS B_STPHY_CPTS B_STPHY_HMNS B_ESCHR_COLI</span>
<span class="co"># [6] B_ESCHR_COLI</span>
<span class="co"># [1] B_STPHY_CONS B_ESCHR_COLI B_STPHY_CONS B_ESCHR_COLI B_ESCHR_COLI</span>
<span class="co"># [6] B_STPHY_HMNS</span>
<span class="co"># as the example_isolates data set has 2,000 rows, we should have 2 million items</span>
<span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
@ -279,8 +282,8 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># mo_name(x) 190 210 273 248 347 419 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.248 seconds. That is 124 nanoseconds on average. You only lose time on your unique input values.</p>
<span class="co"># mo_name(x) 188 197 265 241 348 419 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.241 seconds. That is 121 nanoseconds on average. You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -294,9 +297,9 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 8.72 9.35 9.96 10.20 10.40 11.10 10</span>
<span class="co"># B 24.20 25.00 31.40 27.10 27.50 77.90 10</span>
<span class="co"># C 1.80 1.84 2.20 2.18 2.59 2.67 10</span></code></pre></div>
<span class="co"># A 7.98 8.26 15.80 8.35 9.35 60.00 10</span>
<span class="co"># B 22.30 22.90 23.90 23.50 24.30 27.20 10</span>
<span class="co"># C 1.74 2.02 2.16 2.16 2.24 2.65 10</span></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0022 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
@ -311,14 +314,14 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 1.73 1.79 1.89 1.84 1.95 2.31 10</span>
<span class="co"># B 1.73 1.75 1.91 1.89 1.99 2.26 10</span>
<span class="co"># C 1.76 1.81 1.90 1.83 1.98 2.17 10</span>
<span class="co"># D 1.71 1.78 1.97 1.83 2.12 2.77 10</span>
<span class="co"># E 1.70 1.74 1.80 1.80 1.85 1.89 10</span>
<span class="co"># F 1.73 1.74 1.82 1.77 1.84 2.20 10</span>
<span class="co"># G 1.69 1.75 1.91 1.79 1.85 2.70 10</span>
<span class="co"># H 1.66 1.74 1.84 1.81 1.82 2.27 10</span></code></pre></div>
<span class="co"># A 1.65 1.67 1.74 1.69 1.83 1.89 10</span>
<span class="co"># B 1.64 1.65 1.72 1.69 1.78 1.86 10</span>
<span class="co"># C 1.67 1.75 1.84 1.80 1.87 2.19 10</span>
<span class="co"># D 1.65 1.68 1.77 1.72 1.80 2.14 10</span>
<span class="co"># E 1.65 1.68 1.97 1.75 2.18 2.89 10</span>
<span class="co"># F 1.57 1.64 1.71 1.67 1.74 2.02 10</span>
<span class="co"># G 1.62 1.67 1.79 1.68 1.72 2.71 10</span>
<span class="co"># H 1.63 1.70 1.84 1.72 2.04 2.27 10</span></code></pre></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package contains all phyla of all known bacteria, it can just return the initial value immediately.</p>
</div>
<div id="results-in-other-languages" class="section level3">
@ -346,13 +349,13 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 20.17 20.83 23.58 21.44 22.59 69.64 100</span>
<span class="co"># de 31.48 32.42 42.10 34.02 36.34 204.60 100</span>
<span class="co"># nl 35.21 36.63 45.71 37.75 40.25 97.01 100</span>
<span class="co"># es 35.09 36.14 43.52 37.44 39.09 90.89 100</span>
<span class="co"># it 24.46 25.36 31.24 26.06 28.11 77.93 100</span>
<span class="co"># fr 24.11 25.02 29.21 25.70 27.61 74.69 100</span>
<span class="co"># pt 24.44 25.27 29.79 26.05 28.12 70.28 100</span></code></pre></div>
<span class="co"># en 19.21 19.99 26.19 20.57 22.10 194.10 100</span>
<span class="co"># de 30.22 31.42 42.42 32.36 35.01 94.70 100</span>
<span class="co"># nl 34.40 35.36 43.21 36.35 38.65 119.80 100</span>
<span class="co"># es 33.99 35.21 44.98 36.40 38.36 101.00 100</span>
<span class="co"># it 23.55 24.66 27.67 25.19 26.54 76.79 100</span>
<span class="co"># fr 23.47 24.32 27.80 25.02 26.51 82.05 100</span>
<span class="co"># pt 23.43 24.36 30.42 24.94 26.09 80.48 100</span></code></pre></div>
<p>Currently supported non-English languages are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>

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// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
// v0.0.1
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
document.addEventListener('DOMContentLoaded', function() {
const codeList = document.getElementsByClassName("sourceCode");
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if (linkList[j].innerHTML === "") {
linkList[j].setAttribute('aria-hidden', 'true');
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/* Styles for section anchors */
a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;}
a.anchor-section::before {content: '#';}
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// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020.
document.addEventListener('DOMContentLoaded', function() {
// Do nothing if AnchorJS is used
if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) {
return;
}
const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6');
// Do nothing if sections are already anchored
if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) {
return null;
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// Use section id when pandoc runs with --section-divs
const section_id = function(x) {
return ((x.classList.contains('section') || (x.tagName === 'SECTION'))
? x.id : '');
};
// Add anchors
h.forEach(function(x) {
const id = x.id || section_id(x.parentElement);
if (id === '') {
return null;
}
let anchor = document.createElement('a');
anchor.href = '#' + id;
anchor.classList = ['anchor-section'];
x.classList.add('hasAnchor');
x.appendChild(anchor);
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// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
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document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
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// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
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// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
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}
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// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
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// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
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}
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@ -21,6 +21,9 @@
<script src="../extra.js"></script><meta property="og:title" content="Data sets for download / own use">
<meta property="og:description" content="AMR">
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
<meta name="twitter:card" content="summary_large_image">
<meta name="twitter:creator" content="@msberends">
<meta name="twitter:site" content="@univgroningen">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@ -41,7 +44,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9023</span>
</span>
</div>
@ -194,7 +197,7 @@
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">23 July 2021</h4>
<h4 data-toc-skip class="date">16 August 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="hidden name"><code>datasets.Rmd</code></div>
@ -497,9 +500,9 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<div id="antibiotic-agents" class="section level2">
<h2 class="hasAnchor">
<a href="#antibiotic-agents" class="anchor" aria-hidden="true"></a>Antibiotic agents</h2>
<p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>atc</em>, <em>cid</em>, <em>name</em>, <em>group</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>A data set with 456 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>antibiotics</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 23 June 2021 13:07:57 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>It was last updated on 16 August 2021 13:16:15 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>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds" class="external-link">R file</a> (32 kB)<br>
@ -532,25 +535,25 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<colgroup>
<col width="1%">
<col width="2%">
<col width="3%">
<col width="8%">
<col width="7%">
<col width="7%">
<col width="13%">
<col width="18%">
<col width="17%">
<col width="6%">
<col width="14%">
<col width="3%">
<col width="3%">
<col width="13%">
<col width="2%">
<col width="3%">
<col width="2%">
<col width="2%">
<col width="9%">
</colgroup>
<thead><tr class="header">
<th align="center">ab</th>
<th align="center">atc</th>
<th align="center">cid</th>
<th align="center">name</th>
<th align="center">group</th>
<th align="center">atc</th>
<th align="center">atc_group1</th>
<th align="center">atc_group2</th>
<th align="center">abbreviations</th>
@ -564,10 +567,10 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<tbody>
<tr class="odd">
<td align="center">AMK</td>
<td align="center">J01GB06</td>
<td align="center">37768</td>
<td align="center">Amikacin</td>
<td align="center">Aminoglycosides</td>
<td align="center">D06AX12, J01GB06, S01AA21</td>
<td align="center">Aminoglycoside antibacterials</td>
<td align="center">Other aminoglycosides</td>
<td align="center">ak, ami, amik, …</td>
@ -580,10 +583,10 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr>
<tr class="even">
<td align="center">AMX</td>
<td align="center">J01CA04</td>
<td align="center">33613</td>
<td align="center">Amoxicillin</td>
<td align="center">Beta-lactams/penicillins</td>
<td align="center">J01CA04</td>
<td align="center">Beta-lactam antibacterials, penicillins</td>
<td align="center">Penicillins with extended spectrum</td>
<td align="center">ac, amox, amx</td>
@ -596,10 +599,10 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr>
<tr class="odd">
<td align="center">AMC</td>
<td align="center">J01CR02</td>
<td align="center">23665637</td>
<td align="center">Amoxicillin/clavulanic acid</td>
<td align="center">Beta-lactams/penicillins</td>
<td align="center">J01CR02</td>
<td align="center">Beta-lactam antibacterials, penicillins</td>
<td align="center">Combinations of penicillins, incl. beta-lactamase inhibitors</td>
<td align="center">a/c, amcl, aml, …</td>
@ -612,10 +615,10 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr>
<tr class="even">
<td align="center">AMP</td>
<td align="center">J01CA01</td>
<td align="center">6249</td>
<td align="center">Ampicillin</td>
<td align="center">Beta-lactams/penicillins</td>
<td align="center">J01CA01, S01AA19</td>
<td align="center">Beta-lactam antibacterials, penicillins</td>
<td align="center">Penicillins with extended spectrum</td>
<td align="center">am, amp, ampi</td>
@ -628,10 +631,10 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr>
<tr class="odd">
<td align="center">AZM</td>
<td align="center">J01FA10</td>
<td align="center">447043</td>
<td align="center">Azithromycin</td>
<td align="center">Macrolides/lincosamides</td>
<td align="center">J01FA10, S01AA26</td>
<td align="center">Macrolides, lincosamides and streptogramins</td>
<td align="center">Macrolides</td>
<td align="center">az, azi, azit, …</td>
@ -644,10 +647,10 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr>
<tr class="even">
<td align="center">PEN</td>
<td align="center">J01CE01</td>
<td align="center">5904</td>
<td align="center">Benzylpenicillin</td>
<td align="center">Beta-lactams/penicillins</td>
<td align="center">J01CE01, S01AA14</td>
<td align="center">Combinations of antibacterials</td>
<td align="center">Combinations of antibacterials</td>
<td align="center">bepe, pen, peni, …</td>

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// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
// v0.0.1
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
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a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;}
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// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020.
document.addEventListener('DOMContentLoaded', function() {
// Do nothing if AnchorJS is used
if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) {
return;
}
const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6');
// Do nothing if sections are already anchored
if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) {
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// Use section id when pandoc runs with --section-divs
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return ((x.classList.contains('section') || (x.tagName === 'SECTION'))
? x.id : '');
};
// Add anchors
h.forEach(function(x) {
const id = x.id || section_id(x.parentElement);
if (id === '') {
return null;
}
let anchor = document.createElement('a');
anchor.href = '#' + id;
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x.appendChild(anchor);
});
});

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// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
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@ -50,6 +50,9 @@
<meta property="og:title" content="Articles" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
<meta name="twitter:card" content="summary_large_image" />
<meta name="twitter:creator" content="@msberends" />
<meta name="twitter:site" content="@univgroningen" />
@ -89,7 +92,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9023</span>
</span>
</div>
@ -266,7 +269,7 @@
<dd></dt>
<dt><a href="resistance_predict.html">How to predict antimicrobial resistance</a></dt>
<dd></dt>
<dt><a href="welcome_to_AMR.html">Welcome to the AMR package</a></dt>
<dt><a href="welcome_to_AMR.html">Welcome to the `AMR` package</a></dt>
<dd></dt>
</dl>
</div>

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<script src="../extra.js"></script><meta property="og:title" content="How to predict antimicrobial resistance">
<meta property="og:description" content="AMR">
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
<meta name="twitter:card" content="summary_large_image">
<meta name="twitter:creator" content="@msberends">
<meta name="twitter:site" content="@univgroningen">
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@ -41,7 +44,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9023</span>
</span>
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/* Styles for section anchors */
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// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020.
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// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
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// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
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@ -5,7 +5,7 @@
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Welcome to the AMR package • AMR (for R)</title>
<title>Welcome to the `AMR` package • AMR (for R)</title>
<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
@ -18,9 +18,12 @@
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
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<script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script><meta property="og:title" content="Welcome to the AMR package">
<script src="../extra.js"></script><meta property="og:title" content="Welcome to the `AMR` package">
<meta property="og:description" content="AMR">
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
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@ -41,7 +44,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9023</span>
</span>
</div>
@ -192,7 +195,7 @@
</header><script src="welcome_to_AMR_files/header-attrs-2.9/header-attrs.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>Welcome to the AMR package</h1>
<h1 data-toc-skip>Welcome to the <code>AMR</code> package</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/welcome_to_AMR.Rmd" class="external-link"><code>vignettes/welcome_to_AMR.Rmd</code></a></small>
@ -202,17 +205,11 @@
<p><strong>READ ALL VIGNETTES <a href="https://msberends.github.io/AMR/articles/">ON OUR WEBSITE</a>.</strong></p>
<div id="welcome-to-the-amr-package" class="section level1">
<h1 class="hasAnchor">
<a href="#welcome-to-the-amr-package" class="anchor" aria-hidden="true"></a>Welcome to the AMR package</h1>
<p>Note: to keep the package as small as possible, we only included this vignette. You can read more vignettes on our website about how to conduct AMR data analysis, determine MDRO’s, find explanation of EUCAST rules, and much more: <a href="https://msberends.github.io/AMR/articles/" class="uri">https://msberends.github.io/AMR/articles/</a>.</p>
<hr>
<p><code>AMR</code> is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
<p>After installing this package, R knows <strong>~70,000 distinct microbial species</strong> and all <strong>~550 antibiotic, antimycotic and antiviral drugs</strong> by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This R package is actively maintained (see Changelog) and is free software (see Copyright).</p>
<p>Since its first public release in early 2018, this package has been downloaded from more than 100 countries.</p>
<div id="usage-examples" class="section level2">
<h2 class="hasAnchor">
<a href="#usage-examples" class="anchor" aria-hidden="true"></a>Usage examples</h2>
<p>After installing this package, R knows ~70,000 distinct microbial species and all ~560 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. Since its first public release in early 2018, this package has been downloaded from more than 160 countries.</p>
<p>This package can be used for:</p>
<ul>
<li>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the Catalogue of Life and List of Prokaryotic names with Standing in Nomenclature</li>
@ -232,15 +229,13 @@
<li>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI</li>
<li>Principal component analysis for AMR</li>
</ul>
</div>
</div>
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
<p>The package was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This R package is actively maintained (see <a href="https://msberends.github.io/AMR/news/index.html">Changelog</a>) and is free software (see <a href="https://msberends.github.io/AMR/#copyright">Copyright</a>).</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
</div>

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// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
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document.addEventListener('DOMContentLoaded', function() {
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/* Styles for section anchors */
a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;}
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.hasAnchor:hover a.anchor-section {visibility: visible;}

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// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020.
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// Do nothing if AnchorJS is used
if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) {
return;
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// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
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h = hs[i];
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a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

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