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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="">1.8.2.9018</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</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">
@ -162,7 +162,7 @@
<img src="../logo.svg" class="logo" alt=""><h1>How to conduct AMR data analysis</h1>
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
<h4 data-toc-skip class="date">15 October 2022</h4>
<h4 data-toc-skip class="date">18 October 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>
@ -170,7 +170,7 @@
<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 15 October 2022.</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 18 October 2022.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -201,21 +201,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-10-15</td>
<td align="center">2022-10-18</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">2022-10-15</td>
<td align="center">2022-10-18</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">2022-10-15</td>
<td align="center">2022-10-18</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -325,54 +325,54 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-11-03</td>
<td align="center">S4</td>
<td align="center">2015-11-08</td>
<td align="center">S1</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>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-09-07</td>
<td align="center">B1</td>
<td align="center">Hospital C</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">F</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2014-08-17</td>
<td align="center">K1</td>
<td align="center">Hospital C</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="even">
<td align="center">2010-09-09</td>
<td align="center">P3</td>
<td align="center">2015-03-30</td>
<td align="center">O4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">Staphylococcus aureus</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">F</td>
</tr>
<tr class="odd">
<td align="center">2011-01-31</td>
<td align="center">E10</td>
<td align="center">Hospital D</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">2012-02-03</td>
<td align="center">D6</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2015-06-15</td>
<td align="center">V10</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">2015-11-12</td>
<td align="center">T8</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>
@ -380,15 +380,15 @@
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-03-18</td>
<td align="center">U8</td>
<td align="center">2011-12-03</td>
<td align="center">I9</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">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
@ -422,16 +422,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,447</td>
<td align="right">52.24%</td>
<td align="right">10,447</td>
<td align="right">52.24%</td>
<td align="right">10,419</td>
<td align="right">52.10%</td>
<td align="right">10,419</td>
<td align="right">52.10%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,553</td>
<td align="right">47.77%</td>
<td align="right">9,581</td>
<td align="right">47.91%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -488,9 +488,9 @@ Longest: 1</p>
<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 10,641 'phenotype-based' first isolates (53.2% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,701 'phenotype-based' first isolates (53.5% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.2% 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 53.5% 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><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="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></span></code></pre></div>
@ -499,7 +499,7 @@ Longest: 1</p>
<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 10,641 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,701 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>
<table style="width:100%;" class="table">
@ -537,78 +537,94 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2013-11-03</td>
<td align="center">S4</td>
<td align="center">Hospital D</td>
<td align="left">2</td>
<td align="center">2013-09-07</td>
<td align="center">B1</td>
<td align="center">Hospital C</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">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="left">9</td>
<td align="center">2016-10-09</td>
<td align="center">U9</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">S</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="odd">
<td align="left">10</td>
<td align="center">2016-12-03</td>
<td align="center">D2</td>
<td align="center">Hospital A</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">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">12</td>
<td align="center">2017-12-08</td>
<td align="center">C5</td>
<td align="left">7</td>
<td align="center">2014-10-09</td>
<td align="center">X9</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</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>
<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">13</td>
<td align="center">2015-07-26</td>
<td align="center">W6</td>
<td align="left">8</td>
<td align="center">2016-01-09</td>
<td align="center">V8</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="even">
<td align="left">10</td>
<td align="center">2013-10-07</td>
<td align="center">X9</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</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="left">11</td>
<td align="center">2017-09-13</td>
<td align="center">G8</td>
<td align="center">Hospital B</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">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="even">
<td align="left">13</td>
<td align="center">2014-10-23</td>
<td align="center">Y3</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">F</td>
<td align="center">Gram-negative</td>
@ -616,22 +632,6 @@ Longest: 1</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">14</td>
<td align="center">2014-06-06</td>
<td align="center">I9</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</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">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -653,8 +653,8 @@ Longest: 1</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://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></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,641<br>
Available: 10,641 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,701<br>
Available: 10,701 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -671,33 +671,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,650</td>
<td align="right">43.70%</td>
<td align="right">4,650</td>
<td align="right">43.70%</td>
<td align="right">4,606</td>
<td align="right">43.04%</td>
<td align="right">4,606</td>
<td align="right">43.04%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,752</td>
<td align="right">25.86%</td>
<td align="right">7,402</td>
<td align="right">69.56%</td>
<td align="right">2,751</td>
<td align="right">25.71%</td>
<td align="right">7,357</td>
<td align="right">68.75%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,109</td>
<td align="right">19.82%</td>
<td align="right">9,511</td>
<td align="right">89.38%</td>
<td align="right">2,166</td>
<td align="right">20.24%</td>
<td align="right">9,523</td>
<td align="right">88.99%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,130</td>
<td align="right">10.62%</td>
<td align="right">10,641</td>
<td align="right">1,178</td>
<td align="right">11.01%</td>
<td align="right">10,701</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -716,14 +716,14 @@ Longest: 24</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="10%">
<col width="11%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@ -744,14 +744,44 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-06-06</td>
<td align="center">I9</td>
<td align="center">Hospital D</td>
<td align="center">2016-01-09</td>
<td align="center">V8</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</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">2013-10-07</td>
<td align="center">X9</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">2012-07-31</td>
<td align="center">E10</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-positive</td>
<td align="center">Streptococcus</td>
@ -759,75 +789,45 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-11-06</td>
<td align="center">S6</td>
<td align="center">Hospital C</td>
<td align="center">2017-01-14</td>
<td align="center">L10</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">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">2013-06-12</td>
<td align="center">X6</td>
<td align="center">2013-01-17</td>
<td align="center">B3</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">2012-09-05</td>
<td align="center">A8</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">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">2012-05-27</td>
<td align="center">U4</td>
<td align="center">Hospital B</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">R</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="center">2011-05-24</td>
<td align="center">T10</td>
<td align="center">Hospital B</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">2016-12-19</td>
<td align="center">T6</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</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>
@ -854,50 +854,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2161</td>
<td align="center">117</td>
<td align="center">2372</td>
<td align="center">4650</td>
<td align="center">2177</td>
<td align="center">144</td>
<td align="center">2285</td>
<td align="center">4606</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3443</td>
<td align="center">155</td>
<td align="center">1052</td>
<td align="center">4650</td>
<td align="center">3399</td>
<td align="center">161</td>
<td align="center">1046</td>
<td align="center">4606</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3401</td>
<td align="center">3382</td>
<td align="center">0</td>
<td align="center">1249</td>
<td align="center">4650</td>
<td align="center">1224</td>
<td align="center">4606</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4070</td>
<td align="center">4032</td>
<td align="center">0</td>
<td align="center">580</td>
<td align="center">4650</td>
<td align="center">574</td>
<td align="center">4606</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">1130</td>
<td align="center">1130</td>
<td align="center">1178</td>
<td align="center">1178</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">902</td>
<td align="center">47</td>
<td align="center">181</td>
<td align="center">1130</td>
<td align="center">927</td>
<td align="center">40</td>
<td align="center">211</td>
<td align="center">1178</td>
</tr>
</tbody>
</table>
@ -920,34 +920,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4070</td>
<td align="center">4032</td>
<td align="center">0</td>
<td align="center">580</td>
<td align="center">4650</td>
<td align="center">574</td>
<td align="center">4606</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1013</td>
<td align="center">1059</td>
<td align="center">0</td>
<td align="center">117</td>
<td align="center">1130</td>
<td align="center">119</td>
<td align="center">1178</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2450</td>
<td align="center">2442</td>
<td align="center">0</td>
<td align="center">302</td>
<td align="center">2752</td>
<td align="center">309</td>
<td align="center">2751</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">2109</td>
<td align="center">2109</td>
<td align="center">2166</td>
<td align="center">2166</td>
</tr>
</tbody>
</table>
@ -961,7 +961,7 @@ 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><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] 0.5466591</span></span></code></pre></div>
<span><span class="co"># [1] 0.5415382</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="cb27"><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>
@ -975,19 +975,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5511962</td>
<td align="center">0.5472908</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5518367</td>
<td align="center">0.5424089</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5463475</td>
<td align="center">0.5286935</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5317893</td>
<td align="center">0.5414567</td>
</tr>
</tbody>
</table>
@ -1008,23 +1008,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5511962</td>
<td align="center">3135</td>
<td align="center">0.5472908</td>
<td align="center">3119</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5518367</td>
<td align="center">3675</td>
<td align="center">0.5424089</td>
<td align="center">3761</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5463475</td>
<td align="center">1629</td>
<td align="center">0.5286935</td>
<td align="center">1638</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5317893</td>
<td align="center">2202</td>
<td align="center">0.5414567</td>
<td align="center">2183</td>
</tr>
</tbody>
</table>
@ -1047,27 +1047,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7737634</td>
<td align="center">0.8752688</td>
<td align="center">0.9750538</td>
<td align="center">0.7729049</td>
<td align="center">0.8753799</td>
<td align="center">0.9780721</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8398230</td>
<td align="center">0.8964602</td>
<td align="center">0.9787611</td>
<td align="center">0.8208829</td>
<td align="center">0.8989813</td>
<td align="center">0.9813243</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7914244</td>
<td align="center">0.8902616</td>
<td align="center">0.9792878</td>
<td align="center">0.7931661</td>
<td align="center">0.8876772</td>
<td align="center">0.9756452</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5400664</td>
<td align="center">0.5420129</td>
<td align="center">0.0000000</td>
<td align="center">0.5400664</td>
<td align="center">0.5420129</td>
</tr>
</tbody>
</table>
@ -1092,23 +1092,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">55.1%</td>
<td align="right">26.5%</td>
<td align="right">54.7%</td>
<td align="right">26.4%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">55.2%</td>
<td align="right">26.7%</td>
<td align="right">54.2%</td>
<td align="right">26.5%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">54.6%</td>
<td align="right">25.0%</td>
<td align="right">52.9%</td>
<td align="right">25.6%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">53.2%</td>
<td align="right">25.3%</td>
<td align="right">54.1%</td>
<td align="right">26.4%</td>
</tr>
</tbody>
</table>
@ -1206,16 +1206,18 @@ Longest: 24</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 &lt;mic&gt;</span></span>
<span><span class="co"># [1] 128 64 128 0.001 4 0.25 64 0.5 32 0.25 </span></span>
<span><span class="co"># [11] 0.025 0.002 1 16 0.005 0.025 0.25 0.005 0.001 64 </span></span>
<span><span class="co"># [21] 0.025 1 16 &gt;=256 16 1 16 0.001 0.125 64 </span></span>
<span><span class="co"># [31] 8 0.002 0.5 0.005 0.005 4 8 0.002 0.025 32 </span></span>
<span><span class="co"># [41] 0.0625 0.001 0.125 2 8 16 0.25 1 128 4 </span></span>
<span><span class="co"># [51] 0.001 0.125 0.005 0.25 0.5 0.0625 0.0625 0.005 0.5 1 </span></span>
<span><span class="co"># [61] 0.005 16 4 0.025 32 16 128 0.5 16 4 </span></span>
<span><span class="co"># [71] 0.002 1 0.5 0.5 0.025 8 32 16 64 32 </span></span>
<span><span class="co"># [81] 4 32 2 &gt;=256 0.125 0.025 &gt;=256 16 2 0.01 </span></span>
<span><span class="co"># [91] 0.5 128 0.01 0.0625 128 32 0.125 1 0.125 0.025</span></span></code></pre></div>
<span><span class="co"># [1] 0.025 &lt;=0.001 &lt;=0.001 128 4 0.0625 0.0625 2 64 </span></span>
<span><span class="co"># [10] 4 8 0.25 16 0.002 0.5 0.125 64 0.0625 </span></span>
<span><span class="co"># [19] 16 2 0.25 0.01 0.25 32 &lt;=0.001 32 64 </span></span>
<span><span class="co"># [28] 0.0625 &lt;=0.001 0.005 2 0.5 0.01 0.25 1 &lt;=0.001</span></span>
<span><span class="co"># [37] 0.125 0.25 4 128 64 0.25 2 16 256 </span></span>
<span><span class="co"># [46] 4 0.005 8 0.25 16 0.005 0.125 0.005 1 </span></span>
<span><span class="co"># [55] &lt;=0.001 32 1 0.25 256 1 16 128 0.002 </span></span>
<span><span class="co"># [64] 64 8 16 0.005 0.5 1 0.025 &lt;=0.001 &lt;=0.001</span></span>
<span><span class="co"># [73] 0.005 0.002 0.0625 64 64 2 0.125 0.002 0.125 </span></span>
<span><span class="co"># [82] 1 0.025 1 2 8 0.0625 1 256 256 </span></span>
<span><span class="co"># [91] &lt;=0.001 32 0.002 2 0.002 &lt;=0.001 1 0.01 2 </span></span>
<span><span class="co"># [100] 0.01</span></span></code></pre></div>
<div class="sourceCode" id="cb37"><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>
@ -1242,10 +1244,10 @@ Longest: 24</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 &lt;disk&gt;</span></span>
<span><span class="co"># [1] 28 21 23 24 17 19 17 17 29 20 28 20 31 17 24 25 21 29 19 18 30 21 22 29 19</span></span>
<span><span class="co"># [26] 24 27 18 19 28 20 19 21 30 17 29 28 26 23 19 20 30 25 19 19 28 19 25 23 19</span></span>
<span><span class="co"># [51] 20 18 23 27 28 28 17 30 22 24 30 27 18 24 25 22 30 21 29 30 29 31 23 28 31</span></span>
<span><span class="co"># [76] 19 17 22 25 25 21 17 31 31 24 30 30 26 20 19 20 25 25 23 17 24 21 20 18 18</span></span></code></pre></div>
<span><span class="co"># [1] 19 20 26 23 18 29 19 26 26 18 19 29 31 31 18 25 23 19 25 26 19 24 17 25 26</span></span>
<span><span class="co"># [26] 30 23 19 17 31 19 25 26 22 24 26 24 31 21 20 29 23 19 21 18 31 24 18 29 22</span></span>
<span><span class="co"># [51] 22 19 29 17 30 27 26 24 23 21 19 27 22 22 27 17 22 18 28 27 23 19 20 25 18</span></span>
<span><span class="co"># [76] 31 31 27 30 29 29 24 27 30 28 24 23 26 18 29 21 27 27 25 25 18 21 28 19 19</span></span></code></pre></div>
<div class="sourceCode" id="cb43"><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>