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@ -24,7 +24,7 @@
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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="">1.8.1.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</small>
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@ -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">01 September 2022</h4>
<h4 data-toc-skip class="date">05 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 01 September 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 05 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">2022-09-01</td>
<td align="center">2022-10-05</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">2022-09-01</td>
<td align="center">2022-10-05</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">2022-09-01</td>
<td align="center">2022-10-05</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -325,69 +325,69 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-11-10</td>
<td align="center">P6</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">2014-01-04</td>
<td align="center">G6</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-10-29</td>
<td align="center">T4</td>
<td align="center">2017-04-24</td>
<td align="center">D3</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2011-07-22</td>
<td align="center">G4</td>
<td align="center">2016-11-13</td>
<td align="center">J4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">2011-04-20</td>
<td align="center">O10</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2012-08-21</td>
<td align="center">I2</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">2017-03-26</td>
<td align="center">T2</td>
<td align="center">2017-08-20</td>
<td align="center">V6</td>
<td align="center">Hospital B</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2012-05-20</td>
<td align="center">U5</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-12-01</td>
<td align="center">X4</td>
<td align="center">Hospital B</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>
</tbody>
@ -422,16 +422,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,422</td>
<td align="right">52.11%</td>
<td align="right">10,422</td>
<td align="right">52.11%</td>
<td align="right">10,348</td>
<td align="right">51.74%</td>
<td align="right">10,348</td>
<td align="right">51.74%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,578</td>
<td align="right">47.89%</td>
<td align="right">9,652</td>
<td align="right">48.26%</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 10,604 'phenotype-based' first isolates (53.0% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,738 'phenotype-based' first isolates (53.7% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.0% 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 53.7% 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>
@ -499,10 +499,10 @@ 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 10,604 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,738 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 class="table">
<table style="width:100%;" class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -516,7 +516,7 @@ Longest: 1</p>
<col width="6%">
<col width="11%">
<col width="12%">
<col width="7%">
<col width="9%">
<col width="5%">
</colgroup>
<thead><tr class="header">
@ -537,43 +537,59 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2016-11-10</td>
<td align="center">P6</td>
<td align="center">Hospital C</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">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="left">2</td>
<td align="center">2011-10-29</td>
<td align="center">T4</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">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="odd">
<td align="left">7</td>
<td align="center">2015-01-09</td>
<td align="center">J10</td>
<td align="left">3</td>
<td align="center">2016-11-13</td>
<td align="center">J4</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">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">4</td>
<td align="center">2017-08-20</td>
<td align="center">V6</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">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">6</td>
<td align="center">2017-12-01</td>
<td align="center">X4</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">S</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="left">7</td>
<td align="center">2014-03-15</td>
<td align="center">H7</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>
@ -584,30 +600,14 @@ Longest: 1</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2016-05-25</td>
<td align="center">F8</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">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">10</td>
<td align="center">2010-01-21</td>
<td align="center">Z8</td>
<td align="center">Hospital A</td>
<td align="left">8</td>
<td align="center">2011-03-12</td>
<td align="center">Y2</td>
<td align="center">Hospital C</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">S</td>
<td align="center">F</td>
@ -618,15 +618,15 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="left">11</td>
<td align="center">2012-10-12</td>
<td align="center">B5</td>
<td align="center">Hospital D</td>
<td align="center">2013-12-31</td>
<td align="center">R4</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</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: 10,604<br>
Available: 10,604 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,738<br>
Available: 10,738 (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">4,672</td>
<td align="right">44.06%</td>
<td align="right">4,672</td>
<td align="right">44.06%</td>
<td align="right">4,690</td>
<td align="right">43.68%</td>
<td align="right">4,690</td>
<td align="right">43.68%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,714</td>
<td align="right">25.59%</td>
<td align="right">7,386</td>
<td align="right">69.65%</td>
<td align="right">2,765</td>
<td align="right">25.75%</td>
<td align="right">7,455</td>
<td align="right">69.43%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,051</td>
<td align="right">19.34%</td>
<td align="right">9,437</td>
<td align="right">88.99%</td>
<td align="right">2,119</td>
<td align="right">19.73%</td>
<td align="right">9,574</td>
<td align="right">89.16%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,167</td>
<td align="right">11.01%</td>
<td align="right">10,604</td>
<td align="right">1,164</td>
<td align="right">10.84%</td>
<td align="right">10,738</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>
@ -744,38 +744,8 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-10-12</td>
<td align="center">B5</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">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="center">2017-11-10</td>
<td align="center">A8</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="odd">
<td align="center">2010-08-21</td>
<td align="center">Y3</td>
<td align="center">2017-08-20</td>
<td align="center">V6</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
@ -789,8 +759,38 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-12-30</td>
<td align="center">B1</td>
<td align="center">2011-09-19</td>
<td align="center">V5</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">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">2015-07-01</td>
<td align="center">C5</td>
<td align="center">Hospital D</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="even">
<td align="center">2010-02-13</td>
<td align="center">D1</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
@ -804,23 +804,23 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-10-15</td>
<td align="center">N2</td>
<td align="center">2010-03-01</td>
<td align="center">T3</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">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">2016-04-25</td>
<td align="center">H4</td>
<td align="center">2010-02-18</td>
<td align="center">H2</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</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">2216</td>
<td align="center">117</td>
<td align="center">2339</td>
<td align="center">4672</td>
<td align="center">2203</td>
<td align="center">147</td>
<td align="center">2340</td>
<td align="center">4690</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3414</td>
<td align="center">156</td>
<td align="center">1102</td>
<td align="center">4672</td>
<td align="center">3438</td>
<td align="center">180</td>
<td align="center">1072</td>
<td align="center">4690</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3392</td>
<td align="center">3410</td>
<td align="center">0</td>
<td align="center">1280</td>
<td align="center">4672</td>
<td align="center">4690</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4084</td>
<td align="center">4094</td>
<td align="center">0</td>
<td align="center">588</td>
<td align="center">4672</td>
<td align="center">596</td>
<td align="center">4690</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">1167</td>
<td align="center">1167</td>
<td align="center">1164</td>
<td align="center">1164</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">912</td>
<td align="center">53</td>
<td align="center">202</td>
<td align="center">1167</td>
<td align="center">902</td>
<td align="center">39</td>
<td align="center">223</td>
<td align="center">1164</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">4084</td>
<td align="center">4094</td>
<td align="center">0</td>
<td align="center">588</td>
<td align="center">4672</td>
<td align="center">596</td>
<td align="center">4690</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1054</td>
<td align="center">1060</td>
<td align="center">0</td>
<td align="center">113</td>
<td align="center">1167</td>
<td align="center">104</td>
<td align="center">1164</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2439</td>
<td align="center">2435</td>
<td align="center">0</td>
<td align="center">275</td>
<td align="center">2714</td>
<td align="center">330</td>
<td align="center">2765</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">2051</td>
<td align="center">2051</td>
<td align="center">2119</td>
<td align="center">2119</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] 0.5453602</span></span></code></pre></div>
<span><span class="co"># [1] 0.5406035</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">0.5524672</td>
<td align="center">0.5406669</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5320304</td>
<td align="center">0.5451918</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5509434</td>
<td align="center">0.5203562</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5535714</td>
<td align="center">0.5471874</td>
</tr>
</tbody>
</table>
@ -1008,23 +1008,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5524672</td>
<td align="center">3202</td>
<td align="center">0.5406669</td>
<td align="center">3209</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5320304</td>
<td align="center">3684</td>
<td align="center">0.5451918</td>
<td align="center">3806</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5509434</td>
<td align="center">1590</td>
<td align="center">0.5203562</td>
<td align="center">1572</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5535714</td>
<td align="center">2128</td>
<td align="center">0.5471874</td>
<td align="center">2151</td>
</tr>
</tbody>
</table>
@ -1047,27 +1047,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7641267</td>
<td align="center">0.8741438</td>
<td align="center">0.9762414</td>
<td align="center">0.7714286</td>
<td align="center">0.8729211</td>
<td align="center">0.9754797</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8269066</td>
<td align="center">0.9031705</td>
<td align="center">0.9837189</td>
<td align="center">0.8084192</td>
<td align="center">0.9106529</td>
<td align="center">0.9862543</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7940310</td>
<td align="center">0.8986735</td>
<td align="center">0.9812085</td>
<td align="center">0.7895118</td>
<td align="center">0.8806510</td>
<td align="center">0.9793852</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5324232</td>
<td align="center">0.5394054</td>
<td align="center">0.0000000</td>
<td align="center">0.5324232</td>
<td align="center">0.5394054</td>
</tr>
</tbody>
</table>
@ -1092,23 +1092,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">55.2%</td>
<td align="right">26.6%</td>
<td align="right">54.1%</td>
<td align="right">25.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">53.2%</td>
<td align="right">26.1%</td>
<td align="right">54.5%</td>
<td align="right">27.3%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">55.1%</td>
<td align="right">27.3%</td>
<td align="right">52.0%</td>
<td align="right">27.1%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">55.4%</td>
<td align="right">27.0%</td>
<td align="right">54.7%</td>
<td align="right">26.5%</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] 0.0625 128 32 32 0.125 2 0.0625 8 0.002 </span></span>
<span><span class="co"># [10] 2 0.0625 64 2 128 0.025 0.125 0.002 64 </span></span>
<span><span class="co"># [19] 0.025 4 0.002 &lt;=0.001 0.0625 0.125 8 16 0.0625 </span></span>
<span><span class="co"># [28] 128 128 256 8 8 16 0.0625 &lt;=0.001 &lt;=0.001</span></span>
<span><span class="co"># [37] 8 256 0.025 &lt;=0.001 32 0.125 128 0.125 1 </span></span>
<span><span class="co"># [46] 0.01 64 0.125 4 2 0.005 128 0.25 32 </span></span>
<span><span class="co"># [55] 1 0.01 0.25 0.0625 0.01 0.25 0.25 8 0.125 </span></span>
<span><span class="co"># [64] 0.25 0.025 &lt;=0.001 8 1 4 1 32 64 </span></span>
<span><span class="co"># [73] 0.5 32 2 2 0.125 0.01 32 64 &lt;=0.001</span></span>
<span><span class="co"># [82] 4 0.5 0.5 4 0.25 4 &lt;=0.001 256 1 </span></span>
<span><span class="co"># [91] 4 4 0.002 0.125 0.125 2 0.002 8 16 </span></span>
<span><span class="co"># [100] 1</span></span></code></pre></div>
<span><span class="co"># [1] 128 128 1 &lt;=0.001 &gt;=256 0.002 0.5 0.25 0.125 </span></span>
<span><span class="co"># [10] &lt;=0.001 128 &lt;=0.001 1 &lt;=0.001 2 0.25 &gt;=256 &gt;=256 </span></span>
<span><span class="co"># [19] 0.0625 0.002 128 0.01 0.025 0.01 0.01 8 0.0625 </span></span>
<span><span class="co"># [28] &lt;=0.001 &lt;=0.001 4 0.125 4 0.01 0.125 &lt;=0.001 4 </span></span>
<span><span class="co"># [37] 0.005 0.0625 0.0625 &gt;=256 4 0.025 8 16 0.005 </span></span>
<span><span class="co"># [46] 0.0625 0.005 0.002 1 0.025 32 64 8 2 </span></span>
<span><span class="co"># [55] 1 0.25 0.0625 &lt;=0.001 4 16 0.002 0.0625 2 </span></span>
<span><span class="co"># [64] 0.5 4 64 0.005 &gt;=256 0.025 0.25 0.25 8 </span></span>
<span><span class="co"># [73] 0.25 0.0625 0.125 &lt;=0.001 1 1 64 0.25 0.0625 </span></span>
<span><span class="co"># [82] 0.0625 0.025 32 64 0.025 0.025 16 64 0.25 </span></span>
<span><span class="co"># [91] &gt;=256 0.025 16 128 0.01 0.5 0.002 0.5 0.0625 </span></span>
<span><span class="co"># [100] 0.125</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>
@ -1242,14 +1242,12 @@ Longest: 24</p>
<p>For disk diffusion values, there is not much of a difference in plotting:</p>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<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="co"># ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span></span>
<span><span class="co"># coli). Run `mo_uncertainties()` to review this.</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 26 29 24 22 28 18 17 22 24 17 18 20 25 23 22 30 21 24 30 26 18 23 28 19</span></span>
<span><span class="co"># [26] 25 24 25 17 25 21 25 20 30 20 29 20 22 25 19 17 29 21 28 28 18 24 26 25 28</span></span>
<span><span class="co"># [51] 20 26 24 19 24 27 19 22 18 28 29 30 31 30 30 30 17 18 20 26 27 27 28 24 23</span></span>
<span><span class="co"># [76] 25 30 29 20 20 20 20 30 24 28 20 30 31 17 17 23 25 27 26 18 23 21 18 22 21</span></span></code></pre></div>
<span><span class="co"># [1] 28 24 28 24 21 20 19 24 27 24 27 26 23 27 19 31 28 20 25 29 23 18 22 18 23</span></span>
<span><span class="co"># [26] 20 19 30 31 22 22 19 18 25 30 30 28 27 20 23 31 20 22 29 31 25 29 19 27 31</span></span>
<span><span class="co"># [51] 18 21 27 31 20 19 30 30 30 22 22 23 18 26 30 17 25 29 19 19 24 26 22 18 20</span></span>
<span><span class="co"># [76] 28 29 20 28 21 18 19 28 26 28 22 30 27 24 21 28 26 25 23 28 26 21 20 26 18</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>
@ -1321,7 +1319,7 @@ Longest: 24</p>
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<p></p>
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<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a></p>
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