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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="">1.8.1.9045</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</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">28 August 2022</h4>
<h4 data-toc-skip class="date">29 August 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 28 August 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 29 August 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">2022-08-28</td>
<td align="center">2022-08-29</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">2022-08-28</td>
<td align="center">2022-08-29</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">2022-08-28</td>
<td align="center">2022-08-29</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -325,10 +325,10 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-01-18</td>
<td align="center">C5</td>
<td align="center">2016-07-19</td>
<td align="center">D10</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
@ -336,20 +336,9 @@
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-12-30</td>
<td align="center">G6</td>
<td align="center">2016-10-24</td>
<td align="center">H3</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2013-12-06</td>
<td align="center">B1</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
@ -357,38 +346,49 @@
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-04-15</td>
<td align="center">V2</td>
<tr class="odd">
<td align="center">2013-03-15</td>
<td align="center">D4</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</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>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-08-08</td>
<td align="center">N3</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2014-11-22</td>
<td align="center">Q1</td>
<td align="center">Hospital A</td>
<td align="center">2015-05-24</td>
<td align="center">O2</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</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="even">
<td align="center">2012-03-08</td>
<td align="center">E5</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">2013-06-30</td>
<td align="center">Y9</td>
<td align="center">Hospital C</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>
<td align="center">F</td>
</tr>
</tbody>
</table>
@ -422,16 +422,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,364</td>
<td align="right">51.82%</td>
<td align="right">10,364</td>
<td align="right">51.82%</td>
<td align="right">10,459</td>
<td align="right">52.30%</td>
<td align="right">10,459</td>
<td align="right">52.30%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,636</td>
<td align="right">48.18%</td>
<td align="right">9,541</td>
<td align="right">47.71%</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 10,729 'phenotype-based' first isolates (53.6% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,686 'phenotype-based' first isolates (53.4% 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 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 53.4% 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 10,729 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,686 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">
@ -537,13 +537,45 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">2</td>
<td align="center">2014-12-30</td>
<td align="center">G6</td>
<td align="left">1</td>
<td align="center">2016-07-19</td>
<td align="center">D10</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">2</td>
<td align="center">2016-10-24</td>
<td align="center">H3</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">3</td>
<td align="center">2013-03-15</td>
<td align="center">D4</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">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
@ -554,61 +586,29 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">2016-04-15</td>
<td align="center">V2</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">2015-08-08</td>
<td align="center">N3</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">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">6</td>
<td align="center">2012-03-08</td>
<td align="center">E5</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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">7</td>
<td align="center">2012-03-22</td>
<td align="center">K6</td>
<td align="center">2013-06-30</td>
<td align="center">Y9</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">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">8</td>
<td align="center">2013-02-09</td>
<td align="center">P4</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
@ -617,19 +617,19 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2014-06-11</td>
<td align="center">G9</td>
<td align="left">8</td>
<td align="center">2017-03-07</td>
<td align="center">Q1</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</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-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</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>
</tbody>
@ -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: 10,729<br>
Available: 10,729 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,686<br>
Available: 10,686 (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">4,652</td>
<td align="right">43.36%</td>
<td align="right">4,652</td>
<td align="right">43.36%</td>
<td align="right">4,720</td>
<td align="right">44.17%</td>
<td align="right">4,720</td>
<td align="right">44.17%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,729</td>
<td align="right">25.44%</td>
<td align="right">7,381</td>
<td align="right">68.79%</td>
<td align="right">2,738</td>
<td align="right">25.62%</td>
<td align="right">7,458</td>
<td align="right">69.79%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,153</td>
<td align="right">20.07%</td>
<td align="right">9,534</td>
<td align="right">88.86%</td>
<td align="right">2,049</td>
<td align="right">19.17%</td>
<td align="right">9,507</td>
<td align="right">88.97%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,195</td>
<td align="right">11.14%</td>
<td align="right">10,729</td>
<td align="right">1,179</td>
<td align="right">11.03%</td>
<td align="right">10,686</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -744,12 +744,12 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-12-30</td>
<td align="center">G6</td>
<td align="center">Hospital B</td>
<td align="center">2013-03-15</td>
<td align="center">D4</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">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
@ -759,23 +759,23 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-03-22</td>
<td align="center">K6</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">2010-01-01</td>
<td align="center">M2</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-positive</td>
<td align="center">Streptococcus</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">2013-08-11</td>
<td align="center">A1</td>
<td align="center">2015-02-16</td>
<td align="center">B7</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
@ -789,43 +789,13 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-05-02</td>
<td align="center">H8</td>
<td align="center">2015-06-01</td>
<td align="center">D1</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">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">2010-06-19</td>
<td align="center">Y9</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">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">2016-07-18</td>
<td align="center">M1</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</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-negative</td>
@ -833,6 +803,36 @@ Longest: 24</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-05-09</td>
<td align="center">D6</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">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">2011-02-23</td>
<td align="center">I2</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>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> function:</p>
@ -854,50 +854,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2176</td>
<td align="center">119</td>
<td align="center">2357</td>
<td align="center">4652</td>
<td align="center">2211</td>
<td align="center">120</td>
<td align="center">2389</td>
<td align="center">4720</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3369</td>
<td align="center">148</td>
<td align="center">1135</td>
<td align="center">4652</td>
<td align="center">3448</td>
<td align="center">174</td>
<td align="center">1098</td>
<td align="center">4720</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3443</td>
<td align="center">3483</td>
<td align="center">0</td>
<td align="center">1209</td>
<td align="center">4652</td>
<td align="center">1237</td>
<td align="center">4720</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4080</td>
<td align="center">4124</td>
<td align="center">0</td>
<td align="center">572</td>
<td align="center">4652</td>
<td align="center">596</td>
<td align="center">4720</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">1195</td>
<td align="center">1195</td>
<td align="center">1179</td>
<td align="center">1179</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">948</td>
<td align="center">45</td>
<td align="center">946</td>
<td align="center">31</td>
<td align="center">202</td>
<td align="center">1195</td>
<td align="center">1179</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">4080</td>
<td align="center">4124</td>
<td align="center">0</td>
<td align="center">572</td>
<td align="center">4652</td>
<td align="center">596</td>
<td align="center">4720</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1083</td>
<td align="center">1076</td>
<td align="center">0</td>
<td align="center">112</td>
<td align="center">1195</td>
<td align="center">103</td>
<td align="center">1179</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2404</td>
<td align="center">2428</td>
<td align="center">0</td>
<td align="center">325</td>
<td align="center">2729</td>
<td align="center">310</td>
<td align="center">2738</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">2153</td>
<td align="center">2153</td>
<td align="center">2049</td>
<td align="center">2049</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] 0.5527076</span></span></code></pre></div>
<span><span class="co"># [1] 0.5416433</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">0.5551059</td>
<td align="center">0.5344992</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5576464</td>
<td align="center">0.5487072</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5445860</td>
<td align="center">0.5348558</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5464581</td>
<td align="center">0.5449219</td>
</tr>
</tbody>
</table>
@ -1008,23 +1008,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5551059</td>
<td align="center">3212</td>
<td align="center">0.5344992</td>
<td align="center">3145</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5576464</td>
<td align="center">3773</td>
<td align="center">0.5487072</td>
<td align="center">3829</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5445860</td>
<td align="center">1570</td>
<td align="center">0.5348558</td>
<td align="center">1664</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5464581</td>
<td align="center">2174</td>
<td align="center">0.5449219</td>
<td align="center">2048</td>
</tr>
</tbody>
</table>
@ -1047,27 +1047,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7560189</td>
<td align="center">0.8770421</td>
<td align="center">0.9804385</td>
<td align="center">0.7673729</td>
<td align="center">0.8737288</td>
<td align="center">0.9779661</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8309623</td>
<td align="center">0.9062762</td>
<td align="center">0.9866109</td>
<td align="center">0.8286684</td>
<td align="center">0.9126378</td>
<td align="center">0.9838846</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7805057</td>
<td align="center">0.8809088</td>
<td align="center">0.9783804</td>
<td align="center">0.8027757</td>
<td align="center">0.8867787</td>
<td align="center">0.9788167</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5332095</td>
<td align="center">0.5451440</td>
<td align="center">0.0000000</td>
<td align="center">0.5332095</td>
<td align="center">0.5451440</td>
</tr>
</tbody>
</table>
@ -1092,23 +1092,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">55.5%</td>
<td align="right">28.0%</td>
<td align="right">53.4%</td>
<td align="right">25.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">55.8%</td>
<td align="right">27.5%</td>
<td align="right">54.9%</td>
<td align="right">26.0%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">54.5%</td>
<td align="right">27.8%</td>
<td align="right">53.5%</td>
<td align="right">25.7%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">54.6%</td>
<td align="right">26.2%</td>
<td align="right">54.5%</td>
<td align="right">27.0%</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] 2 64 0.25 &gt;=256 4 0.025 128 0.125 2 </span></span>
<span><span class="co"># [10] 0.25 32 32 2 0.25 32 0.125 16 32 </span></span>
<span><span class="co"># [19] 0.025 1 16 0.01 64 8 32 128 2 </span></span>
<span><span class="co"># [28] 1 2 0.002 0.01 2 0.25 0.002 0.01 1 </span></span>
<span><span class="co"># [37] 4 8 0.005 0.002 0.005 0.025 8 0.5 8 </span></span>
<span><span class="co"># [46] 128 0.25 0.025 0.01 0.01 128 32 1 &lt;=0.001</span></span>
<span><span class="co"># [55] 16 0.002 8 0.0625 0.125 64 0.125 0.0625 0.5 </span></span>
<span><span class="co"># [64] 0.025 &lt;=0.001 128 0.01 0.01 1 0.002 &gt;=256 128 </span></span>
<span><span class="co"># [73] 0.005 32 0.25 0.002 0.25 0.5 0.5 16 16 </span></span>
<span><span class="co"># [82] 2 64 0.005 2 0.025 2 32 0.005 0.0625 </span></span>
<span><span class="co"># [91] &lt;=0.001 0.0625 64 0.002 0.025 0.005 64 0.002 1 </span></span>
<span><span class="co"># [100] 32</span></span></code></pre></div>
<span><span class="co"># [1] &lt;=0.001 64 2 0.25 64 8 32 0.125 2 </span></span>
<span><span class="co"># [10] 1 8 0.01 0.0625 8 &gt;=256 64 4 4 </span></span>
<span><span class="co"># [19] 32 128 16 0.0625 0.0625 2 16 64 128 </span></span>
<span><span class="co"># [28] 0.0625 &lt;=0.001 0.002 128 0.0625 128 64 16 0.002 </span></span>
<span><span class="co"># [37] 0.002 64 0.01 0.002 1 0.125 1 0.01 32 </span></span>
<span><span class="co"># [46] 0.002 0.0625 128 &gt;=256 2 16 0.5 0.005 0.125 </span></span>
<span><span class="co"># [55] 0.005 64 16 16 4 0.01 8 1 0.005 </span></span>
<span><span class="co"># [64] 4 0.002 32 64 0.125 &lt;=0.001 1 32 1 </span></span>
<span><span class="co"># [73] 8 0.005 &gt;=256 32 0.5 64 0.01 8 &gt;=256 </span></span>
<span><span class="co"># [82] &gt;=256 0.0625 32 64 0.01 &lt;=0.001 128 0.025 0.5 </span></span>
<span><span class="co"># [91] 1 128 16 32 128 &lt;=0.001 4 0.002 &lt;=0.001</span></span>
<span><span class="co"># [100] 2</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>
@ -1246,10 +1246,10 @@ Longest: 24</p>
<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] 21 31 26 23 25 28 30 26 17 25 18 25 17 26 22 27 19 20 31 23 20 20 19 24 18</span></span>
<span><span class="co"># [26] 25 28 29 18 17 27 29 31 17 20 18 18 18 30 26 26 31 25 27 26 31 19 21 22 25</span></span>
<span><span class="co"># [51] 31 26 30 20 25 31 18 18 17 31 20 24 26 20 26 23 17 27 17 24 21 22 23 24 31</span></span>
<span><span class="co"># [76] 17 21 22 22 19 25 23 28 18 28 25 18 17 17 18 23 29 28 20 31 19 30 27 28 17</span></span></code></pre></div>
<span><span class="co"># [1] 19 21 22 30 19 24 27 19 25 31 29 25 30 17 22 31 20 27 20 24 28 23 30 31 31</span></span>
<span><span class="co"># [26] 30 23 19 29 20 17 20 25 21 25 29 17 17 18 24 21 24 18 17 24 21 18 20 23 29</span></span>
<span><span class="co"># [51] 26 25 30 27 23 24 18 22 27 31 24 25 22 27 23 18 18 22 17 19 31 30 25 24 19</span></span>
<span><span class="co"># [76] 21 28 24 18 31 20 19 29 26 29 31 17 17 18 28 18 21 26 27 23 17 21 25 30 26</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 +1321,7 @@ Longest: 24</p>
<div class="pkgdown-footer-right">
<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: 200px;"></a></p>
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