P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-27 17:47:54 +02:00
Code Releases Activity

Built site for AMR: 1.8.2.9021@f203928

Browse Source
This commit is contained in:
github-actions
2022-10-19 05:06:14 +00:00
parent 4cc1967eab
commit 553d074b96
94 changed files with 543 additions and 547 deletions
Download Patch File Download Diff File Expand all files Collapse all files

572
articles/AMR.html
View File

@ -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="">1.8.2.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9021</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">18 October 2022</h4>
<h4 data-toc-skip class="date">19 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 18 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 19 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">2022-10-18</td>
<td align="center">2022-10-19</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2022-10-18</td>
<td align="center">2022-10-19</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2022-10-18</td>
<td align="center">2022-10-19</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -325,65 +325,65 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-11-08</td>
<td align="center">S1</td>
<td align="center">2011-04-01</td>
<td align="center">Z8</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-03-26</td>
<td align="center">O7</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</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>
</tr>
<tr class="odd">
<td align="center">2015-02-03</td>
<td align="center">E10</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-05-24</td>
<td align="center">Q1</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">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2010-09-09</td>
<td align="center">J8</td>
<td align="center">Hospital A</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">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">2015-03-30</td>
<td align="center">O4</td>
<td align="center">2015-01-05</td>
<td align="center">C1</td>
<td align="center">Hospital B</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">F</td>
</tr>
<tr class="odd">
<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>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-12-03</td>
<td align="center">I9</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -422,16 +422,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</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>
<td align="right">10,351</td>
<td align="right">51.76%</td>
<td align="right">10,351</td>
<td align="right">51.76%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,581</td>
<td align="right">47.91%</td>
<td align="right">9,649</td>
<td align="right">48.25%</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 10,701 'phenotype-based' first isolates (53.5% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,548 '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 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>
<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">
<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 10,701 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,548 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">
@ -537,95 +537,95 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<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="left">1</td>
<td align="center">2011-04-01</td>
<td align="center">Z8</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">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<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="left">3</td>
<td align="center">2015-02-03</td>
<td align="center">E10</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</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">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="left">4</td>
<td align="center">2010-05-24</td>
<td align="center">Q1</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">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">Staphylococcus</td>
<td align="center">aureus</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="left">5</td>
<td align="center">2010-09-09</td>
<td align="center">J8</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">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">11</td>
<td align="center">2017-09-13</td>
<td align="center">G8</td>
<td align="left">6</td>
<td align="center">2015-01-05</td>
<td align="center">C1</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">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">12</td>
<td align="center">2014-08-04</td>
<td align="center">T9</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
@ -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: 10,701<br>
Available: 10,701 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,548<br>
Available: 10,548 (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">4,606</td>
<td align="right">43.04%</td>
<td align="right">4,606</td>
<td align="right">43.04%</td>
<td align="right">4,585</td>
<td align="right">43.47%</td>
<td align="right">4,585</td>
<td align="right">43.47%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</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>
<td align="right">2,650</td>
<td align="right">25.12%</td>
<td align="right">7,235</td>
<td align="right">68.59%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</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>
<td align="right">2,086</td>
<td align="right">19.78%</td>
<td align="right">9,321</td>
<td align="right">88.37%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,178</td>
<td align="right">11.01%</td>
<td align="right">10,701</td>
<td align="right">1,227</td>
<td align="right">11.63%</td>
<td align="right">10,548</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="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>
@ -744,89 +744,89 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<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="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>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<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">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">2013-01-17</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">2010-05-24</td>
<td align="center">Q1</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">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="even">
<td align="center">2010-09-09</td>
<td align="center">J8</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="odd">
<td align="center">2014-08-04</td>
<td align="center">T9</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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">2013-09-08</td>
<td align="center">Q4</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">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">2010-09-14</td>
<td align="center">Y8</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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-05-26</td>
<td align="center">D5</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>
@ -854,50 +854,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2177</td>
<td align="center">144</td>
<td align="center">2285</td>
<td align="center">4606</td>
<td align="center">2153</td>
<td align="center">149</td>
<td align="center">2283</td>
<td align="center">4585</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3399</td>
<td align="center">161</td>
<td align="center">1046</td>
<td align="center">4606</td>
<td align="center">3379</td>
<td align="center">149</td>
<td align="center">1057</td>
<td align="center">4585</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3382</td>
<td align="center">3329</td>
<td align="center">0</td>
<td align="center">1224</td>
<td align="center">4606</td>
<td align="center">1256</td>
<td align="center">4585</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4032</td>
<td align="center">4023</td>
<td align="center">0</td>
<td align="center">574</td>
<td align="center">4606</td>
<td align="center">562</td>
<td align="center">4585</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">1178</td>
<td align="center">1178</td>
<td align="center">1227</td>
<td align="center">1227</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">927</td>
<td align="center">40</td>
<td align="center">211</td>
<td align="center">1178</td>
<td align="center">978</td>
<td align="center">36</td>
<td align="center">213</td>
<td align="center">1227</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">4032</td>
<td align="center">4023</td>
<td align="center">0</td>
<td align="center">574</td>
<td align="center">4606</td>
<td align="center">562</td>
<td align="center">4585</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1059</td>
<td align="center">1099</td>
<td align="center">0</td>
<td align="center">119</td>
<td align="center">1178</td>
<td align="center">128</td>
<td align="center">1227</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2442</td>
<td align="center">2317</td>
<td align="center">0</td>
<td align="center">309</td>
<td align="center">2751</td>
<td align="center">333</td>
<td align="center">2650</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">2166</td>
<td align="center">2166</td>
<td align="center">2086</td>
<td align="center">2086</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] 0.5415382</span></span></code></pre></div>
<span><span class="co"># [1] 0.544653</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">0.5472908</td>
<td align="center">0.5401018</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5424089</td>
<td align="center">0.5452092</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5286935</td>
<td align="center">0.5366162</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5414567</td>
<td align="center">0.5564478</td>
</tr>
</tbody>
</table>
@ -1008,23 +1008,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5472908</td>
<td align="center">3119</td>
<td align="center">0.5401018</td>
<td align="center">3142</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5424089</td>
<td align="center">3761</td>
<td align="center">0.5452092</td>
<td align="center">3705</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5286935</td>
<td align="center">1638</td>
<td align="center">0.5366162</td>
<td align="center">1584</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5414567</td>
<td align="center">2183</td>
<td align="center">0.5564478</td>
<td align="center">2117</td>
</tr>
</tbody>
</table>
@ -1047,27 +1047,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7729049</td>
<td align="center">0.8753799</td>
<td align="center">0.9780721</td>
<td align="center">0.7694656</td>
<td align="center">0.8774264</td>
<td align="center">0.9790622</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8208829</td>
<td align="center">0.8989813</td>
<td align="center">0.9813243</td>
<td align="center">0.8264059</td>
<td align="center">0.8956805</td>
<td align="center">0.9812551</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7931661</td>
<td align="center">0.8876772</td>
<td align="center">0.9756452</td>
<td align="center">0.8060377</td>
<td align="center">0.8743396</td>
<td align="center">0.9784906</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5420129</td>
<td align="center">0.5359540</td>
<td align="center">0.0000000</td>
<td align="center">0.5420129</td>
<td align="center">0.5359540</td>
</tr>
</tbody>
</table>
@ -1092,23 +1092,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.7%</td>
<td align="right">26.4%</td>
<td align="right">54.0%</td>
<td align="right">27.0%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.2%</td>
<td align="right">26.5%</td>
<td align="right">54.5%</td>
<td align="right">25.4%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">52.9%</td>
<td align="right">25.6%</td>
<td align="right">53.7%</td>
<td align="right">24.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">54.1%</td>
<td align="right">26.4%</td>
<td align="right">55.6%</td>
<td align="right">26.8%</td>
</tr>
</tbody>
</table>
@ -1206,18 +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] 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>
<span><span class="co"># [1] 0.125 2 32 0.025 4 0.01 0.025 4 8 </span></span>
<span><span class="co"># [10] 2 1 2 0.25 2 16 8 0.0625 1 </span></span>
<span><span class="co"># [19] 0.5 0.01 0.125 0.25 0.0625 0.01 0.025 8 8 </span></span>
<span><span class="co"># [28] 0.002 128 0.0625 128 1 4 0.025 0.5 4 </span></span>
<span><span class="co"># [37] 0.125 0.0625 0.5 2 0.002 8 0.125 &gt;=256 0.01 </span></span>
<span><span class="co"># [46] &gt;=256 0.01 2 32 64 4 16 &lt;=0.001 0.25 </span></span>
<span><span class="co"># [55] 16 128 128 8 0.25 &lt;=0.001 0.5 &gt;=256 32 </span></span>
<span><span class="co"># [64] 0.025 0.25 16 32 0.002 128 8 8 128 </span></span>
<span><span class="co"># [73] 0.25 128 0.005 128 &lt;=0.001 0.002 0.002 0.5 0.0625 </span></span>
<span><span class="co"># [82] 4 0.125 0.002 0.25 0.025 &lt;=0.001 2 0.005 0.0625 </span></span>
<span><span class="co"># [91] 32 8 0.005 0.0625 &gt;=256 0.5 0.125 0.25 4 </span></span>
<span><span class="co"># [100] 0.5</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>
@ -1244,10 +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] 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>
<span><span class="co"># [1] 17 29 17 23 23 22 26 31 29 30 23 23 24 22 23 24 23 22 18 25 25 26 30 23 23</span></span>
<span><span class="co"># [26] 18 24 22 26 19 22 22 25 17 29 30 28 27 17 31 30 17 28 29 31 27 19 18 21 23</span></span>
<span><span class="co"># [51] 18 22 24 28 20 27 21 23 18 18 28 31 27 21 21 24 29 18 18 18 26 21 18 23 22</span></span>
<span><span class="co"># [76] 29 19 19 27 22 21 25 18 21 19 22 28 25 18 27 25 19 17 19 29 19 23 25 26 21</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>