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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="">1.8.2.9069</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9071</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">21 December 2022</h4>
<h4 data-toc-skip class="date">27 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 21 December 2022.</p>
generated on 27 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">2022-12-21</td>
<td align="center">2022-12-27</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">2022-12-21</td>
<td align="center">2022-12-27</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">2022-12-21</td>
<td align="center">2022-12-27</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -380,12 +380,12 @@ data set:</p>
<col width="13%">
<col width="13%">
<col width="13%">
<col width="26%">
<col width="28%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="9%">
<col width="8%">
</colgroup>
<thead><tr class="header">
<th align="center">date</th>
@ -400,71 +400,71 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-06-23</td>
<td align="center">Y9</td>
<td align="center">Hospital B</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">F</td>
</tr>
<tr class="even">
<td align="center">2012-11-25</td>
<td align="center">K4</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</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">2014-11-07</td>
<td align="center">W7</td>
<td align="center">2012-11-11</td>
<td align="center">N2</td>
<td align="center">Hospital C</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">2014-03-27</td>
<td align="center">L4</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2014-07-15</td>
<td align="center">F6</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella 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">2014-09-21</td>
<td align="center">F5</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">2015-06-02</td>
<td align="center">R6</td>
<td align="center">Hospital B</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">F</td>
</tr>
<tr class="even">
<td align="center">2013-08-15</td>
<td align="center">R1</td>
<td align="center">Hospital B</td>
<td align="center">2015-04-10</td>
<td align="center">O7</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-03-28</td>
<td align="center">I6</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="even">
<td align="center">2010-01-20</td>
<td align="center">A9</td>
<td align="center">Hospital B</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>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -499,16 +499,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,369</td>
<td align="right">51.85%</td>
<td align="right">10,369</td>
<td align="right">51.85%</td>
<td align="right">10,313</td>
<td align="right">51.57%</td>
<td align="right">10,313</td>
<td align="right">51.57%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,631</td>
<td align="right">48.16%</td>
<td align="right">9,687</td>
<td align="right">48.44%</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 10,556 'phenotype-based' first isolates (52.8% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,540 'phenotype-based' first isolates (52.7% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 52.8% is suitable for resistance analysis! We can now filter
<p>So only 52.7% 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 10,556 isolates for analysis. Now our data looks
<p>So we end up with 10,540 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>
@ -673,9 +673,41 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2016-06-23</td>
<td align="center">Y9</td>
<td align="left">2</td>
<td align="center">2014-03-27</td>
<td align="center">L4</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">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="left">4</td>
<td align="center">2014-09-21</td>
<td align="center">F5</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>
<tr class="odd">
<td align="left">5</td>
<td align="center">2015-06-02</td>
<td align="center">R6</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
@ -689,25 +721,9 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">2013-08-15</td>
<td align="center">R1</td>
<td align="center">Hospital B</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">S</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="odd">
<td align="left">9</td>
<td align="center">2010-06-10</td>
<td align="center">R1</td>
<td align="left">6</td>
<td align="center">2015-04-10</td>
<td align="center">O7</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
@ -720,49 +736,33 @@ like:</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">12</td>
<td align="center">2013-04-05</td>
<td align="center">R3</td>
<td align="center">Hospital C</td>
<td align="center">B_KLBSL_PNMN</td>
<tr class="odd">
<td align="left">7</td>
<td align="center">2012-11-02</td>
<td align="center">X3</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">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">Klebsiella</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">14</td>
<td align="center">2016-09-25</td>
<td align="center">C9</td>
<td align="center">Hospital D</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">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="even">
<td align="left">15</td>
<td align="center">2016-12-29</td>
<td align="center">X9</td>
<td align="center">Hospital C</td>
<td align="left">8</td>
<td align="center">2011-02-19</td>
<td align="center">A8</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_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">S</td>
<td align="center">F</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>
@ -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: 10,556<br>
Available: 10,556 (100%, NA: 0 = 0%)<br>
Length: 10,540<br>
Available: 10,540 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -827,34 +827,34 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,539</td>
<td align="right">43.00%</td>
<td align="right">4,539</td>
<td align="right">43.0%</td>
<td align="right">4,563</td>
<td align="right">43.29%</td>
<td align="right">4,563</td>
<td align="right">43.29%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,724</td>
<td align="right">25.81%</td>
<td align="right">7,263</td>
<td align="right">68.8%</td>
<td align="right">2,684</td>
<td align="right">25.46%</td>
<td align="right">7,247</td>
<td align="right">68.76%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,121</td>
<td align="right">20.09%</td>
<td align="right">9,384</td>
<td align="right">88.9%</td>
<td align="right">2,122</td>
<td align="right">20.13%</td>
<td align="right">9,369</td>
<td align="right">88.89%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,172</td>
<td align="right">11.10%</td>
<td align="right">10,556</td>
<td align="right">100.0%</td>
<td align="right">1,171</td>
<td align="right">11.11%</td>
<td align="right">10,540</td>
<td align="right">100.00%</td>
</tr>
</tbody>
</table>
@ -902,13 +902,13 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-05-30</td>
<td align="center">G4</td>
<td align="center">2014-03-27</td>
<td align="center">L4</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">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -917,78 +917,78 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-09-30</td>
<td align="center">R6</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">2012-11-02</td>
<td align="center">X3</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">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">2011-02-19</td>
<td align="center">A8</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</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">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2010-02-01</td>
<td align="center">J9</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">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="center">2012-08-14</td>
<td align="center">G4</td>
<td align="center">2012-12-07</td>
<td align="center">R5</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">R</td>
<td align="center">M</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">2013-10-07</td>
<td align="center">B5</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">2013-03-24</td>
<td align="center">D4</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">R</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">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-06-29</td>
<td align="center">K10</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">2016-11-16</td>
<td align="center">B9</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">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>
@ -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">2172</td>
<td align="center">112</td>
<td align="center">2255</td>
<td align="center">4539</td>
<td align="center">2177</td>
<td align="center">146</td>
<td align="center">2240</td>
<td align="center">4563</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3374</td>
<td align="center">137</td>
<td align="center">1028</td>
<td align="center">4539</td>
<td align="center">3425</td>
<td align="center">150</td>
<td align="center">988</td>
<td align="center">4563</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3321</td>
<td align="center">3341</td>
<td align="center">0</td>
<td align="center">1218</td>
<td align="center">4539</td>
<td align="center">1222</td>
<td align="center">4563</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">3979</td>
<td align="center">3966</td>
<td align="center">0</td>
<td align="center">560</td>
<td align="center">4539</td>
<td align="center">597</td>
<td align="center">4563</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">1172</td>
<td align="center">1172</td>
<td align="center">1171</td>
<td align="center">1171</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">913</td>
<td align="center">54</td>
<td align="center">205</td>
<td align="center">1172</td>
<td align="center">902</td>
<td align="center">49</td>
<td align="center">220</td>
<td align="center">1171</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">3979</td>
<td align="center">3966</td>
<td align="center">0</td>
<td align="center">560</td>
<td align="center">4539</td>
<td align="center">597</td>
<td align="center">4563</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1061</td>
<td align="center">1052</td>
<td align="center">0</td>
<td align="center">111</td>
<td align="center">1172</td>
<td align="center">119</td>
<td align="center">1171</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2420</td>
<td align="center">2397</td>
<td align="center">0</td>
<td align="center">304</td>
<td align="center">2724</td>
<td align="center">287</td>
<td align="center">2684</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">2121</td>
<td align="center">2121</td>
<td align="center">2122</td>
<td align="center">2122</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] 0.5442402</span></span></code></pre></div>
<span><span class="co"># [1] 0.542315</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">0.5429724</td>
<td align="center">0.5399227</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5454295</td>
<td align="center">0.5454792</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5458488</td>
<td align="center">0.5585914</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5428845</td>
<td align="center">0.5274725</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">0.5429724</td>
<td align="center">3223</td>
<td align="center">0.5399227</td>
<td align="center">3106</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5454295</td>
<td align="center">3632</td>
<td align="center">0.5454792</td>
<td align="center">3694</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5458488</td>
<td align="center">1614</td>
<td align="center">0.5585914</td>
<td align="center">1647</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5428845</td>
<td align="center">2087</td>
<td align="center">0.5274725</td>
<td align="center">2093</td>
</tr>
</tbody>
</table>
@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7735184</td>
<td align="center">0.8766248</td>
<td align="center">0.9806125</td>
<td align="center">0.7834758</td>
<td align="center">0.8691650</td>
<td align="center">0.9783037</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8250853</td>
<td align="center">0.9052901</td>
<td align="center">0.9880546</td>
<td align="center">0.8121264</td>
<td align="center">0.8983775</td>
<td align="center">0.9803587</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7991924</td>
<td align="center">0.8883994</td>
<td align="center">0.9801762</td>
<td align="center">0.7984352</td>
<td align="center">0.8930700</td>
<td align="center">0.9813711</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5299387</td>
<td align="center">0.5278040</td>
<td align="center">0.0000000</td>
<td align="center">0.5299387</td>
<td align="center">0.5278040</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">54.3%</td>
<td align="right">25.1%</td>
<td align="right">54.0%</td>
<td align="right">26.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.5%</td>
<td align="right">26.6%</td>
<td align="right">25.9%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">54.6%</td>
<td align="right">26.7%</td>
<td align="right">55.9%</td>
<td align="right">27.6%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">54.3%</td>
<td align="right">27.4%</td>
<td align="right">52.7%</td>
<td align="right">25.0%</td>
</tr>
</tbody>
</table>
@ -1410,18 +1410,16 @@ 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] 0.25 &gt;=256 128 0.125 16 1 0.025 32 0.0625 </span></span>
<span><span class="co"># [10] 0.125 1 0.5 32 4 128 0.125 8 8 </span></span>
<span><span class="co"># [19] 128 0.01 0.125 0.01 0.01 0.25 0.005 32 32 </span></span>
<span><span class="co"># [28] 0.025 0.25 &lt;=0.001 0.5 0.25 2 4 64 0.002 </span></span>
<span><span class="co"># [37] 2 0.5 0.002 8 &gt;=256 16 128 0.0625 4 </span></span>
<span><span class="co"># [46] 0.01 0.5 &gt;=256 1 32 1 32 32 0.25 </span></span>
<span><span class="co"># [55] 0.01 &lt;=0.001 0.25 128 2 0.25 0.5 128 0.005 </span></span>
<span><span class="co"># [64] &gt;=256 32 128 &gt;=256 16 &lt;=0.001 0.002 32 32 </span></span>
<span><span class="co"># [73] 0.005 32 0.025 0.005 0.01 0.25 0.5 32 128 </span></span>
<span><span class="co"># [82] &lt;=0.001 0.125 0.025 1 &lt;=0.001 32 0.5 4 1 </span></span>
<span><span class="co"># [91] 2 32 16 0.0625 0.01 0.125 16 &gt;=256 2 </span></span>
<span><span class="co"># [100] 0.01</span></span></code></pre></div>
<span><span class="co"># [1] 4 0.125 1 2 1 0.25 4 &gt;=256 2 0.001 </span></span>
<span><span class="co"># [11] 0.01 0.25 0.002 32 0.125 0.005 0.01 0.001 2 0.025 </span></span>
<span><span class="co"># [21] 8 0.0625 0.002 2 16 128 0.005 0.125 0.01 2 </span></span>
<span><span class="co"># [31] 0.01 0.125 4 0.002 0.005 4 1 0.125 2 0.002 </span></span>
<span><span class="co"># [41] 0.025 0.125 16 2 0.125 0.01 0.0625 0.125 0.005 4 </span></span>
<span><span class="co"># [51] 16 0.001 0.005 1 4 1 &gt;=256 0.002 0.001 0.5 </span></span>
<span><span class="co"># [61] 32 0.5 0.005 0.125 0.002 2 0.005 0.025 0.002 0.002 </span></span>
<span><span class="co"># [71] 0.25 128 64 64 2 0.001 0.25 32 32 0.025 </span></span>
<span><span class="co"># [81] 64 0.125 16 8 0.5 8 4 0.01 0.001 0.001 </span></span>
<span><span class="co"># [91] 32 0.002 0.0625 128 0.0625 128 0.001 32 2 0.002</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>
@ -1455,10 +1453,10 @@ 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] 19 18 19 27 29 19 23 21 19 20 17 24 29 25 24 29 19 21 25 21 23 27 28 28 25</span></span>
<span><span class="co"># [26] 31 31 26 27 26 29 29 20 25 31 22 25 25 18 29 17 22 21 26 23 24 18 17 28 21</span></span>
<span><span class="co"># [51] 26 19 28 22 20 26 24 19 24 23 31 27 23 24 25 20 30 25 25 22 30 28 22 29 26</span></span>
<span><span class="co"># [76] 28 26 25 28 27 30 21 19 22 25 30 29 28 31 30 21 26 20 31 28 26 17 19 26 22</span></span></code></pre></div>
<span><span class="co"># [1] 27 28 28 21 22 25 29 24 25 25 28 30 27 23 25 23 30 29 31 23 17 18 18 28 28</span></span>
<span><span class="co"># [26] 17 20 23 22 23 31 22 23 25 25 20 28 31 28 20 18 24 20 26 26 21 21 20 28 27</span></span>
<span><span class="co"># [51] 30 19 20 31 27 20 21 27 27 30 18 24 18 19 22 20 31 26 25 26 26 29 22 24 22</span></span>
<span><span class="co"># [76] 23 25 27 21 29 17 24 22 21 17 20 28 20 27 20 19 21 29 29 31 27 25 27 21 30</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="">1.8.2.9069</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9071</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">

60
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="">1.8.2.9069</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9071</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 I I S S S</span></span>
<span><span class="co"># 2 R R I R S R</span></span>
<span><span class="co"># 3 R R I R R I</span></span>
<span><span class="co"># 4 R R R R S S</span></span>
<span><span class="co"># 5 S I R I I I</span></span>
<span><span class="co"># 6 S R R S I S</span></span>
<span><span class="co"># 1 R I I I I R</span></span>
<span><span class="co"># 2 I S R I R S</span></span>
<span><span class="co"># 3 R S S R R S</span></span>
<span><span class="co"># 4 R S S S S S</span></span>
<span><span class="co"># 5 S I S S I R</span></span>
<span><span class="co"># 6 R S I 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 I</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 S</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 R</span></span>
<span><span class="co"># 5 I</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">3215</td>
<td align="right">64.30%</td>
<td align="right">3215</td>
<td align="right">64.30%</td>
<td align="right">3280</td>
<td align="right">65.60%</td>
<td align="right">3280</td>
<td align="right">65.60%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">997</td>
<td align="right">19.94%</td>
<td align="right">4212</td>
<td align="right">84.24%</td>
<td align="right">952</td>
<td align="right">19.04%</td>
<td align="right">4232</td>
<td align="right">84.64%</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">4657</td>
<td align="right">93.14%</td>
<td align="right">402</td>
<td align="right">8.04%</td>
<td align="right">4634</td>
<td align="right">92.68%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">242</td>
<td align="right">4.84%</td>
<td align="right">4899</td>
<td align="right">97.98%</td>
<td align="right">241</td>
<td align="right">4.82%</td>
<td align="right">4875</td>
<td align="right">97.50%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">101</td>
<td align="right">2.02%</td>
<td align="right">125</td>
<td align="right">2.50%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

4
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="">1.8.2.9069</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9071</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">
@ -280,7 +280,7 @@ function:</p>
<span><span class="co"># [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></span>
<span><span class="co"># Importance of components:</span></span>
<span><span class="co"># PC1 PC2 PC3 PC4 PC5 PC6 PC7</span></span>
<span><span class="co"># Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17</span></span>
<span><span class="co"># Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16</span></span>
<span><span class="co"># Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span></span>
<span><span class="co"># Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></span></code></pre></div>
<pre><code><span><span class="co"># Groups (n=4, named as 'order'):</span></span>

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<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">21 December 2022</h4>
<h4 data-toc-skip class="date">27 December 2022</h4>
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@ -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">475,076
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">475,704
R-related questions</a> have already been asked on this platform (that
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<h4 data-toc-skip class="date">27 December 2022</h4>
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