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@@ -14,8 +14,8 @@
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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<script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.4/font.css" rel="stylesheet">
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<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
@@ -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="">1.8.2.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9066</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">19 December 2022</h4>
<h4 data-toc-skip class="date">20 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 19 December 2022.</p>
generated on 20 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">2022-12-19</td>
<td align="center">2022-12-20</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">2022-12-19</td>
<td align="center">2022-12-20</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">2022-12-19</td>
<td align="center">2022-12-20</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="28%">
<col width="26%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="8%">
<col width="9%">
</colgroup>
<thead><tr class="header">
<th align="center">date</th>
@@ -400,53 +400,9 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<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>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<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>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-04-15</td>
<td align="center">F2</td>
<td align="center">Hospital B</td>
<td align="center">2016-12-25</td>
<td align="center">G9</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
@@ -455,16 +411,60 @@ data set:</p>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-12-04</td>
<td align="center">K2</td>
<td align="center">Hospital A</td>
<td align="center">2016-09-15</td>
<td align="center">Q1</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</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">2010-12-29</td>
<td align="center">J7</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</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="even">
<td align="center">2013-01-07</td>
<td align="center">D5</td>
<td align="center">Hospital C</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">R</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2015-05-08</td>
<td align="center">H8</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-01-28</td>
<td align="center">S8</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</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>
</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">10,311</td>
<td align="right">51.56%</td>
<td align="right">10,311</td>
<td align="right">51.56%</td>
<td align="right">10,511</td>
<td align="right">52.56%</td>
<td align="right">10,511</td>
<td align="right">52.56%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,689</td>
<td align="right">48.45%</td>
<td align="right">9,489</td>
<td align="right">47.45%</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 10,715 'phenotype-based' first isolates (53.6% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,638 'phenotype-based' first isolates (53.2% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.6% is suitable for resistance analysis! We can now filter
<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>
<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 10,715 isolates for analysis. Now our data looks
<p>So we end up with 10,638 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>
@@ -673,80 +673,16 @@ 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">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">2010-12-29</td>
<td align="center">J7</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">R</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="even">
<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">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">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">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
@@ -754,12 +690,44 @@ like:</p>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2013-11-23</td>
<td align="center">P7</td>
<td align="center">2010-01-25</td>
<td align="center">M8</td>
<td align="center">Hospital A</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="odd">
<td align="left">12</td>
<td align="center">2012-01-18</td>
<td align="center">J5</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="even">
<td align="left">13</td>
<td align="center">2011-08-17</td>
<td align="center">S4</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</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>
@@ -768,6 +736,38 @@ like:</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">14</td>
<td align="center">2016-12-27</td>
<td align="center">H6</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_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>
<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">16</td>
<td align="center">2017-10-23</td>
<td align="center">D6</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">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>
</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: 10,715<br>
Available: 10,715 (100%, NA: 0 = 0%)<br>
Length: 10,638<br>
Available: 10,638 (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">4,647</td>
<td align="right">43.37%</td>
<td align="right">4,647</td>
<td align="right">43.37%</td>
<td align="right">4,659</td>
<td align="right">43.80%</td>
<td align="right">4,659</td>
<td align="right">43.80%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</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>
<td align="right">2,645</td>
<td align="right">24.86%</td>
<td align="right">7,304</td>
<td align="right">68.66%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</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>
<td align="right">2,119</td>
<td align="right">19.92%</td>
<td align="right">9,423</td>
<td align="right">88.58%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,213</td>
<td align="right">11.32%</td>
<td align="right">10,715</td>
<td align="right">1,215</td>
<td align="right">11.42%</td>
<td align="right">10,638</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@@ -874,14 +874,14 @@ antibiotic class they are in:</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="11%">
<col width="10%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@@ -902,39 +902,9 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<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="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="center">2012-09-23</td>
<td align="center">W8</td>
<td align="center">Hospital D</td>
<td align="center">2012-02-06</td>
<td align="center">W3</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
@@ -947,14 +917,44 @@ antibiotic class they are in:</p>
<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">2015-10-05</td>
<td align="center">W7</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">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">2011-08-06</td>
<td align="center">V1</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</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">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-05-13</td>
<td align="center">I2</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>
@@ -962,33 +962,33 @@ antibiotic class they are in:</p>
<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">2015-09-18</td>
<td align="center">I5</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">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">Staphylococcus</td>
<td align="center">aureus</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">2017-10-13</td>
<td align="center">N3</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">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>
</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">2225</td>
<td align="center">126</td>
<td align="center">2296</td>
<td align="center">4647</td>
<td align="center">2200</td>
<td align="center">119</td>
<td align="center">2340</td>
<td align="center">4659</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3426</td>
<td align="center">150</td>
<td align="center">1071</td>
<td align="center">4647</td>
<td align="center">3418</td>
<td align="center">146</td>
<td align="center">1095</td>
<td align="center">4659</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3424</td>
<td align="center">3409</td>
<td align="center">0</td>
<td align="center">1223</td>
<td align="center">4647</td>
<td align="center">1250</td>
<td align="center">4659</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4059</td>
<td align="center">4110</td>
<td align="center">0</td>
<td align="center">588</td>
<td align="center">4647</td>
<td align="center">549</td>
<td align="center">4659</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">1213</td>
<td align="center">1213</td>
<td align="center">1215</td>
<td align="center">1215</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">953</td>
<td align="center">49</td>
<td align="center">211</td>
<td align="center">1213</td>
<td align="center">963</td>
<td align="center">50</td>
<td align="center">202</td>
<td align="center">1215</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">4059</td>
<td align="center">4110</td>
<td align="center">0</td>
<td align="center">588</td>
<td align="center">4647</td>
<td align="center">549</td>
<td align="center">4659</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1098</td>
<td align="center">1070</td>
<td align="center">0</td>
<td align="center">115</td>
<td align="center">1213</td>
<td align="center">145</td>
<td align="center">1215</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2427</td>
<td align="center">2366</td>
<td align="center">0</td>
<td align="center">318</td>
<td align="center">2745</td>
<td align="center">279</td>
<td align="center">2645</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">2110</td>
<td align="center">2110</td>
<td align="center">2119</td>
<td align="center">2119</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] 0.545217</span></span></code></pre></div>
<span><span class="co"># [1] 0.5423952</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">0.5543512</td>
<td align="center">0.5512821</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5427041</td>
<td align="center">0.5344323</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5265432</td>
<td align="center">0.5549206</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5499765</td>
<td align="center">0.5337452</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">0.5543512</td>
<td align="center">3229</td>
<td align="center">0.5512821</td>
<td align="center">3198</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5427041</td>
<td align="center">3735</td>
<td align="center">0.5344323</td>
<td align="center">3761</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5265432</td>
<td align="center">1620</td>
<td align="center">0.5549206</td>
<td align="center">1575</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5499765</td>
<td align="center">2131</td>
<td align="center">0.5337452</td>
<td align="center">2104</td>
</tr>
</tbody>
</table>
@@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7695287</td>
<td align="center">0.8734668</td>
<td align="center">0.9771896</td>
<td align="center">0.7649710</td>
<td align="center">0.8821636</td>
<td align="center">0.9778923</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8260511</td>
<td align="center">0.9051937</td>
<td align="center">0.9785655</td>
<td align="center">0.8337449</td>
<td align="center">0.8806584</td>
<td align="center">0.9777778</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7865209</td>
<td align="center">0.8841530</td>
<td align="center">0.9759563</td>
<td align="center">0.8003781</td>
<td align="center">0.8945180</td>
<td align="center">0.9826087</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5341232</td>
<td align="center">0.5450684</td>
<td align="center">0.0000000</td>
<td align="center">0.5341232</td>
<td align="center">0.5450684</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">55.4%</td>
<td align="right">26.4%</td>
<td align="right">55.1%</td>
<td align="right">26.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.3%</td>
<td align="right">27.0%</td>
<td align="right">53.4%</td>
<td align="right">26.3%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">52.7%</td>
<td align="right">27.0%</td>
<td align="right">55.5%</td>
<td align="right">25.6%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">55.0%</td>
<td align="right">26.1%</td>
<td align="right">53.4%</td>
<td align="right">26.0%</td>
</tr>
</tbody>
</table>
@@ -1410,18 +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] 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>
<span><span class="co"># [1] 128 32 0.01 &lt;=0.001 0.125 0.125 64 0.025 8 </span></span>
<span><span class="co"># [10] 8 32 8 0.002 1 0.125 0.125 0.002 0.01 </span></span>
<span><span class="co"># [19] 128 1 &lt;=0.001 8 0.005 0.01 0.002 64 1 </span></span>
<span><span class="co"># [28] 0.125 0.5 256 256 2 1 0.025 4 8 </span></span>
<span><span class="co"># [37] 0.025 1 0.5 &lt;=0.001 0.0625 0.002 64 0.002 0.005 </span></span>
<span><span class="co"># [46] 256 0.01 0.0625 &lt;=0.001 0.025 2 1 256 1 </span></span>
<span><span class="co"># [55] 2 32 0.25 32 64 0.5 &lt;=0.001 0.005 0.5 </span></span>
<span><span class="co"># [64] 0.5 32 0.25 4 16 0.025 0.5 &lt;=0.001 16 </span></span>
<span><span class="co"># [73] 2 0.0625 128 4 2 2 0.005 256 0.125 </span></span>
<span><span class="co"># [82] 0.002 256 8 &lt;=0.001 0.0625 64 &lt;=0.001 0.002 1 </span></span>
<span><span class="co"># [91] 64 16 0.025 16 0.025 0.002 1 0.25 32 </span></span>
<span><span class="co"># [100] 64</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 +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] 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>
<span><span class="co"># [1] 27 25 21 24 18 18 19 26 23 28 19 21 28 28 31 28 22 26 17 29 19 27 21 24 23</span></span>
<span><span class="co"># [26] 20 26 18 18 18 17 28 31 23 23 22 29 29 23 20 21 20 30 22 26 26 31 19 18 25</span></span>
<span><span class="co"># [51] 19 22 23 26 21 30 21 27 18 27 21 26 21 30 31 21 31 18 18 18 21 30 27 29 19</span></span>
<span><span class="co"># [76] 26 29 25 19 25 20 31 20 24 18 26 28 21 28 18 25 31 17 23 28 21 25 30 26 23</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>