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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9064</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9065</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -168,7 +168,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">17 December 2022</h4>
<h4 data-toc-skip class="date">19 December 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="d-none name"><code>AMR.Rmd</code></div>
@ -180,7 +180,7 @@ Berends</h4>
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 17 December 2022.</p>
generated on 19 December 2022.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -236,21 +236,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-12-17</td>
<td align="center">2022-12-19</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">2022-12-17</td>
<td align="center">2022-12-19</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">2022-12-17</td>
<td align="center">2022-12-19</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -400,10 +400,10 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-12-20</td>
<td align="center">L9</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">2015-05-10</td>
<td align="center">F2</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -411,9 +411,31 @@ data set:</p>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-07-06</td>
<td align="center">N2</td>
<td align="center">2012-08-03</td>
<td align="center">K4</td>
<td align="center">Hospital B</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">R</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-06-06</td>
<td align="center">J2</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</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">2014-12-29</td>
<td align="center">E7</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
@ -422,44 +444,22 @@ data set:</p>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2014-06-14</td>
<td align="center">Z5</td>
<td align="center">2012-04-15</td>
<td align="center">F2</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-12-21</td>
<td align="center">O3</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2013-04-17</td>
<td align="center">C4</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-04-22</td>
<td align="center">N3</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">2014-12-04</td>
<td align="center">K2</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>
@ -499,16 +499,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,365</td>
<td align="right">51.83%</td>
<td align="right">10,365</td>
<td align="right">51.83%</td>
<td align="right">10,311</td>
<td align="right">51.56%</td>
<td align="right">10,311</td>
<td align="right">51.56%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,635</td>
<td align="right">48.18%</td>
<td align="right">9,689</td>
<td align="right">48.45%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -621,9 +621,9 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,653 'phenotype-based' first isolates (53.3% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,715 'phenotype-based' first isolates (53.6% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.3% is suitable for resistance analysis! We can now filter
<p>So only 53.6% 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">
@ -634,7 +634,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,653 isolates for analysis. Now our data looks
<p>So we end up with 10,715 isolates for analysis. Now our data looks
like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
@ -673,14 +673,46 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2015-05-10</td>
<td align="center">F2</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">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="even">
<td align="left">2</td>
<td align="center">2010-07-06</td>
<td align="center">N2</td>
<td align="center">2012-08-03</td>
<td align="center">K4</td>
<td align="center">Hospital B</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">R</td>
<td align="center">M</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="odd">
<td align="left">3</td>
<td align="center">2016-06-06</td>
<td align="center">J2</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</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">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -689,29 +721,29 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">3</td>
<td align="center">2014-06-14</td>
<td align="center">Z5</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="left">6</td>
<td align="center">2014-12-04</td>
<td align="center">K2</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</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">S</td>
<td align="center">S</td>
<td align="center">S</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">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2014-12-21</td>
<td align="center">O3</td>
<td align="left">9</td>
<td align="center">2012-06-24</td>
<td align="center">R1</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">F</td>
@ -721,26 +753,10 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="center">2010-04-22</td>
<td align="center">N3</td>
<td align="center">Hospital D</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-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2010-09-06</td>
<td align="center">W7</td>
<td align="center">Hospital B</td>
<td align="left">10</td>
<td align="center">2013-11-23</td>
<td align="center">P7</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
@ -752,22 +768,6 @@ like:</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2014-10-08</td>
<td align="center">I6</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</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">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -801,8 +801,8 @@ readable:</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/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></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,653<br>
Available: 10,653 (100%, NA: 0 = 0%)<br>
Length: 10,715<br>
Available: 10,715 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -827,33 +827,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,579</td>
<td align="right">42.98%</td>
<td align="right">4,579</td>
<td align="right">42.98%</td>
<td align="right">4,647</td>
<td align="right">43.37%</td>
<td align="right">4,647</td>
<td align="right">43.37%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,787</td>
<td align="right">26.16%</td>
<td align="right">7,366</td>
<td align="right">69.14%</td>
<td align="right">2,745</td>
<td align="right">25.62%</td>
<td align="right">7,392</td>
<td align="right">68.99%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,119</td>
<td align="right">19.89%</td>
<td align="right">9,485</td>
<td align="right">89.04%</td>
<td align="right">2,110</td>
<td align="right">19.69%</td>
<td align="right">9,502</td>
<td align="right">88.68%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,168</td>
<td align="right">10.96%</td>
<td align="right">10,653</td>
<td align="right">1,213</td>
<td align="right">11.32%</td>
<td align="right">10,715</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -902,90 +902,90 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-06-14</td>
<td align="center">Z5</td>
<td align="center">Hospital B</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">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">2017-04-17</td>
<td align="center">K4</td>
<td align="center">Hospital A</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">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">2015-12-19</td>
<td align="center">Y3</td>
<td align="center">Hospital C</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-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-05-11</td>
<td align="center">Y3</td>
<td align="center">Hospital B</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">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">2014-07-26</td>
<td align="center">Z10</td>
<td align="center">2015-05-10</td>
<td align="center">F2</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">S</td>
<td align="center">R</td>
<td align="center">F</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="even">
<td align="center">2012-12-01</td>
<td align="center">D6</td>
<td align="center">2012-08-03</td>
<td align="center">K4</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</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">R</td>
<td align="center">M</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="odd">
<td align="center">2012-09-23</td>
<td align="center">W8</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_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">F</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="center">2017-07-17</td>
<td align="center">G9</td>
<td align="center">Hospital B</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">2016-09-24</td>
<td align="center">F9</td>
<td align="center">Hospital B</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">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="even">
<td align="center">2017-08-15</td>
<td align="center">N6</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">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>
@ -1013,50 +1013,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2116</td>
<td align="center">135</td>
<td align="center">2328</td>
<td align="center">4579</td>
<td align="center">2225</td>
<td align="center">126</td>
<td align="center">2296</td>
<td align="center">4647</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3340</td>
<td align="center">172</td>
<td align="center">1067</td>
<td align="center">4579</td>
<td align="center">3426</td>
<td align="center">150</td>
<td align="center">1071</td>
<td align="center">4647</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3387</td>
<td align="center">3424</td>
<td align="center">0</td>
<td align="center">1192</td>
<td align="center">4579</td>
<td align="center">1223</td>
<td align="center">4647</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">3983</td>
<td align="center">4059</td>
<td align="center">0</td>
<td align="center">596</td>
<td align="center">4579</td>
<td align="center">588</td>
<td align="center">4647</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">1168</td>
<td align="center">1168</td>
<td align="center">1213</td>
<td align="center">1213</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">917</td>
<td align="center">35</td>
<td align="center">216</td>
<td align="center">1168</td>
<td align="center">953</td>
<td align="center">49</td>
<td align="center">211</td>
<td align="center">1213</td>
</tr>
</tbody>
</table>
@ -1078,34 +1078,34 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">3983</td>
<td align="center">4059</td>
<td align="center">0</td>
<td align="center">596</td>
<td align="center">4579</td>
<td align="center">588</td>
<td align="center">4647</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1066</td>
<td align="center">1098</td>
<td align="center">0</td>
<td align="center">102</td>
<td align="center">1168</td>
<td align="center">115</td>
<td align="center">1213</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2468</td>
<td align="center">2427</td>
<td align="center">0</td>
<td align="center">319</td>
<td align="center">2787</td>
<td align="center">318</td>
<td align="center">2745</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">2119</td>
<td align="center">2119</td>
<td align="center">2110</td>
<td align="center">2110</td>
</tr>
</tbody>
</table>
@ -1137,7 +1137,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></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>
<span><span class="co"># [1] 0.5518633</span></span></code></pre></div>
<span><span class="co"># [1] 0.545217</span></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="cb26"><pre class="downlit sourceCode r">
@ -1152,19 +1152,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5650169</td>
<td align="center">0.5543512</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5469568</td>
<td align="center">0.5427041</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5635802</td>
<td align="center">0.5265432</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5314100</td>
<td align="center">0.5499765</td>
</tr>
</tbody>
</table>
@ -1189,23 +1189,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5650169</td>
<td align="center">3253</td>
<td align="center">0.5543512</td>
<td align="center">3229</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5469568</td>
<td align="center">3631</td>
<td align="center">0.5427041</td>
<td align="center">3735</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5635802</td>
<td align="center">0.5265432</td>
<td align="center">1620</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5314100</td>
<td align="center">2149</td>
<td align="center">0.5499765</td>
<td align="center">2131</td>
</tr>
</tbody>
</table>
@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7669797</td>
<td align="center">0.8698406</td>
<td align="center">0.9744486</td>
<td align="center">0.7695287</td>
<td align="center">0.8734668</td>
<td align="center">0.9771896</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8150685</td>
<td align="center">0.9126712</td>
<td align="center">0.9845890</td>
<td align="center">0.8260511</td>
<td align="center">0.9051937</td>
<td align="center">0.9785655</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7865088</td>
<td align="center">0.8855400</td>
<td align="center">0.9788303</td>
<td align="center">0.7865209</td>
<td align="center">0.8841530</td>
<td align="center">0.9759563</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5304389</td>
<td align="center">0.5341232</td>
<td align="center">0.0000000</td>
<td align="center">0.5304389</td>
<td align="center">0.5341232</td>
</tr>
</tbody>
</table>
@ -1278,23 +1278,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">56.5%</td>
<td align="right">27.3%</td>
<td align="right">55.4%</td>
<td align="right">26.4%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.7%</td>
<td align="right">54.3%</td>
<td align="right">27.0%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">56.4%</td>
<td align="right">28.1%</td>
<td align="right">52.7%</td>
<td align="right">27.0%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">53.1%</td>
<td align="right">25.5%</td>
<td align="right">55.0%</td>
<td align="right">26.1%</td>
</tr>
</tbody>
</table>
@ -1410,16 +1410,18 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<code class="sourceCode R"><span><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>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 128 32 0.002 0.005 0.01 32 0.25 128 32 &gt;=256 </span></span>
<span><span class="co"># [11] 0.005 0.125 16 2 0.01 4 &gt;=256 4 0.01 0.001 </span></span>
<span><span class="co"># [21] 16 &gt;=256 32 0.25 16 0.001 128 0.001 8 0.0625</span></span>
<span><span class="co"># [31] 16 16 1 16 0.125 16 8 2 &gt;=256 2 </span></span>
<span><span class="co"># [41] 0.002 0.01 0.5 16 1 0.0625 0.01 0.025 0.002 0.0625</span></span>
<span><span class="co"># [51] 0.25 64 0.01 0.125 0.0625 0.005 0.0625 &gt;=256 0.0625 32 </span></span>
<span><span class="co"># [61] 1 0.002 0.125 32 0.002 128 0.01 8 0.25 8 </span></span>
<span><span class="co"># [71] 0.005 &gt;=256 2 0.01 32 4 &gt;=256 2 0.002 0.01 </span></span>
<span><span class="co"># [81] 1 16 0.025 16 4 0.5 32 32 64 0.25 </span></span>
<span><span class="co"># [91] 0.01 &gt;=256 0.01 16 0.025 16 1 0.005 0.25 0.025</span></span></code></pre></div>
<span><span class="co"># [1] 32 0.005 0.25 &lt;=0.001 128 0.005 16 1 128 </span></span>
<span><span class="co"># [10] 256 0.025 0.25 128 0.5 &lt;=0.001 &lt;=0.001 0.01 0.005 </span></span>
<span><span class="co"># [19] 0.005 0.025 0.0625 8 0.005 16 1 16 0.0625 </span></span>
<span><span class="co"># [28] 256 4 256 64 1 0.5 0.125 0.005 4 </span></span>
<span><span class="co"># [37] 2 32 0.002 0.0625 0.002 4 128 8 0.0625 </span></span>
<span><span class="co"># [46] 1 8 1 0.5 8 &lt;=0.001 0.0625 0.01 0.125 </span></span>
<span><span class="co"># [55] 0.01 4 &lt;=0.001 16 0.025 0.125 2 16 32 </span></span>
<span><span class="co"># [64] 0.025 2 0.01 0.125 0.025 8 2 0.01 2 </span></span>
<span><span class="co"># [73] 0.25 0.5 8 0.002 8 1 0.5 1 0.002 </span></span>
<span><span class="co"># [82] 2 0.005 &lt;=0.001 2 0.0625 1 4 0.25 32 </span></span>
<span><span class="co"># [91] 0.25 1 0.125 0.25 4 0.5 32 0.5 0.5 </span></span>
<span><span class="co"># [100] 0.025</span></span></code></pre></div>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<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></span></code></pre></div>
@ -1453,10 +1455,10 @@ plotting:</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</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></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 18 29 28 22 20 28 25 20 28 23 23 31 24 26 31 31 30 20 29 20 31 29 28 29 25</span></span>
<span><span class="co"># [26] 28 26 23 27 22 21 23 17 25 30 30 29 28 25 28 19 17 28 18 31 20 29 29 23 23</span></span>
<span><span class="co"># [51] 19 25 29 20 27 29 19 24 22 24 31 22 25 29 18 31 17 23 26 19 24 31 29 31 28</span></span>
<span><span class="co"># [76] 31 22 27 30 27 30 22 22 27 23 24 28 25 26 24 29 20 26 20 29 29 22 19 25 26</span></span></code></pre></div>
<span><span class="co"># [1] 19 31 23 24 26 26 27 23 21 24 17 27 19 30 24 17 17 17 25 31 22 31 26 24 29</span></span>
<span><span class="co"># [26] 31 22 25 28 28 23 19 19 22 29 29 21 21 17 22 27 21 18 25 30 18 21 18 21 18</span></span>
<span><span class="co"># [51] 31 28 25 18 19 22 20 20 19 25 28 29 18 26 28 28 31 24 24 26 24 20 28 18 24</span></span>
<span><span class="co"># [76] 19 29 29 30 25 19 20 21 17 22 30 25 24 27 27 27 30 29 29 30 21 20 23 27 26</span></span></code></pre></div>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<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></span></code></pre></div>

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2
articles/EUCAST.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9064</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9065</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

58
articles/MDR.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9064</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9065</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -375,18 +375,18 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 R R I I S I</span></span>
<span><span class="co"># 2 S I S I R R</span></span>
<span><span class="co"># 3 R I S I R S</span></span>
<span><span class="co"># 4 I R S I I R</span></span>
<span><span class="co"># 5 R R R R S I</span></span>
<span><span class="co"># 6 R I S S I I</span></span>
<span><span class="co"># 1 I R R I R R</span></span>
<span><span class="co"># 2 I I I R S R</span></span>
<span><span class="co"># 3 I R S I I R</span></span>
<span><span class="co"># 4 I R R R S R</span></span>
<span><span class="co"># 5 S R S R I S</span></span>
<span><span class="co"># 6 R R S S R S</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 I</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 5 R</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
@ -428,40 +428,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3211</td>
<td align="right">64.22%</td>
<td align="right">3211</td>
<td align="right">64.22%</td>
<td align="right">3234</td>
<td align="right">64.68%</td>
<td align="right">3234</td>
<td align="right">64.68%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">993</td>
<td align="right">19.86%</td>
<td align="right">4204</td>
<td align="right">84.08%</td>
<td align="right">973</td>
<td align="right">19.46%</td>
<td align="right">4207</td>
<td align="right">84.14%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">431</td>
<td align="right">8.62%</td>
<td align="right">4635</td>
<td align="right">92.70%</td>
<td align="right">414</td>
<td align="right">8.28%</td>
<td align="right">4621</td>
<td align="right">92.42%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">243</td>
<td align="right">4.86%</td>
<td align="right">4878</td>
<td align="right">97.56%</td>
<td align="right">284</td>
<td align="right">5.68%</td>
<td align="right">4905</td>
<td align="right">98.10%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">122</td>
<td align="right">2.44%</td>
<td align="right">95</td>
<td align="right">1.90%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
articles/PCA.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9064</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9065</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

6
articles/SPSS.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9064</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9065</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -168,7 +168,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">17 December 2022</h4>
<h4 data-toc-skip class="date">19 December 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="d-none name"><code>SPSS.Rmd</code></div>
@ -247,7 +247,7 @@ data using a custom made website. The webdesign knowledge needed
<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">474,212
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">475,076
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

2
articles/WHONET.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9064</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9065</small>
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articles/datasets.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9064</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9065</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -166,7 +166,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">17 December 2022</h4>
<h4 data-toc-skip class="date">19 December 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
@ -196,7 +196,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
<em>gbif_renamed_to</em>, <em>prevalence</em> and <em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 17 December 2022 13:31:33 UTC. Find more info
<p>It was last updated on 19 December 2022 14:32:41 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -219,7 +219,7 @@ Parquet file</a> (2.6 MB)<br>
data file</a> (50.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">IBM
SPSS Statistics data file</a> (16.8 MB)<br>
SPSS Statistics data file</a> (16.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata
DTA file</a> (47.1 MB)</li>
@ -357,7 +357,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
<td align="center">3221780</td>
<td align="center">11158430</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">2.5</td>
<td align="center">407310004, 407251000, 407281008, …</td>
</tr>
<tr class="even">
@ -381,7 +381,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">1.0</td>
<td align="center"></td>
</tr>
<tr class="odd">
@ -405,7 +405,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
<td align="center">5427575</td>
<td align="center">3221780</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">1.0</td>
<td align="center">419388003</td>
</tr>
<tr class="even">
@ -429,7 +429,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">2.5</td>
<td align="center"></td>
</tr>
<tr class="odd">
@ -453,7 +453,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
<td align="center">11286021</td>
<td align="center">3221780</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">1.0</td>
<td align="center">1095001000112106, 715307006, 737528008, …</td>
</tr>
<tr class="even">
@ -477,7 +477,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
<td align="center">10862979</td>
<td align="center">3221780</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">2.5</td>
<td align="center"></td>
</tr>
</tbody>

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