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@ -193,7 +193,7 @@
<h1 data-toc-skip>How to conduct AMR data analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">24 May 2021</h4>
<h4 class="date">26 May 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd"><code>vignettes/AMR.Rmd</code></a></small>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -202,7 +202,7 @@
<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/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 24 May 2021.</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/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 26 May 2021.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -233,21 +233,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2021-05-24</td>
<td align="center">2021-05-26</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">2021-05-24</td>
<td align="center">2021-05-26</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">2021-05-24</td>
<td align="center">2021-05-26</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -344,70 +344,70 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-04-11</td>
<td align="center">W8</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">2013-06-11</td>
<td align="center">I7</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2013-01-28</td>
<td align="center">G4</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-12-30</td>
<td align="center">C6</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">M</td>
</tr>
<tr class="even">
<td align="center">2010-03-16</td>
<td align="center">P5</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-03-27</td>
<td align="center">U2</td>
<td align="center">2014-08-13</td>
<td align="center">O10</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2011-10-06</td>
<td align="center">N1</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="even">
<td align="center">2016-08-07</td>
<td align="center">J6</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2010-06-21</td>
<td align="center">Q4</td>
<td align="center">Hospital D</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">2011-01-31</td>
<td align="center">E5</td>
<td align="center">Hospital B</td>
<td align="center">2016-04-25</td>
<td align="center">R4</td>
<td align="center">Hospital A</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>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
@ -424,7 +424,7 @@
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 20,000<br>
Available: 20,000 (100%, NA: 0 = 0%)<br>
Available: 20,000 (100.0%, NA: 0 = 0.0%)<br>
Unique: 2</p>
<p>Shortest: 1<br>
Longest: 1</p>
@ -441,16 +441,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,485</td>
<td align="right">52.43%</td>
<td align="right">10,485</td>
<td align="right">52.43%</td>
<td align="right">10,403</td>
<td align="right">52.02%</td>
<td align="right">10,403</td>
<td align="right">52.02%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,515</td>
<td align="right">47.58%</td>
<td align="right">9,597</td>
<td align="right">47.99%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -505,9 +505,9 @@ Longest: 1</p>
<span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span>
<span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span>
<span class="co"># 2</span>
<span class="co"># =&gt; Found 10,696 first weighted isolates (phenotype-based, 53.5% of total</span>
<span class="co"># =&gt; Found 10,682 first weighted isolates (phenotype-based, 53.4% of total</span>
<span class="co"># where a microbial ID was available)</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">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">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 class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">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></code></pre></div>
@ -515,7 +515,7 @@ Longest: 1</p>
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
<p>So we end up with 10,696 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,682 isolates for analysis. Now our data looks like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></code></pre></div>
<table class="table">
@ -553,45 +553,13 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">6</td>
<td align="center">2011-01-31</td>
<td align="center">E5</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">R</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">8</td>
<td align="center">2016-02-04</td>
<td align="center">A9</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">9</td>
<td align="center">2015-07-09</td>
<td align="center">N1</td>
<td align="center">Hospital B</td>
<td align="left">4</td>
<td align="center">2016-08-07</td>
<td align="center">J6</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">S</td>
<td align="center">R</td>
<td align="center">M</td>
@ -601,30 +569,46 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2013-11-10</td>
<td align="center">M10</td>
<td align="center">Hospital B</td>
<td align="left">6</td>
<td align="center">2016-04-25</td>
<td align="center">R4</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">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">12</td>
<td align="center">2013-12-10</td>
<td align="center">W8</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="left">10</td>
<td align="center">2016-01-17</td>
<td align="center">R3</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">11</td>
<td align="center">2013-01-18</td>
<td align="center">S1</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>
@ -632,20 +616,36 @@ Longest: 1</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">15</td>
<td align="center">2016-11-20</td>
<td align="center">U2</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<tr class="odd">
<td align="left">16</td>
<td align="center">2017-07-05</td>
<td align="center">X9</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">19</td>
<td align="center">2013-10-30</td>
<td align="center">D4</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>
</tbody>
@ -669,8 +669,8 @@ Longest: 1</p>
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,696<br>
Available: 10,696 (100%, NA: 0 = 0%)<br>
Length: 10,682<br>
Available: 10,682 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -687,33 +687,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,648</td>
<td align="right">43.46%</td>
<td align="right">4,648</td>
<td align="right">43.46%</td>
<td align="right">4,559</td>
<td align="right">42.68%</td>
<td align="right">4,559</td>
<td align="right">42.68%</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">25.51%</td>
<td align="right">7,377</td>
<td align="right">68.97%</td>
<td align="right">2,844</td>
<td align="right">26.62%</td>
<td align="right">7,403</td>
<td align="right">69.30%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,136</td>
<td align="right">19.97%</td>
<td align="right">9,513</td>
<td align="right">88.94%</td>
<td align="right">2,082</td>
<td align="right">19.49%</td>
<td align="right">9,485</td>
<td align="right">88.79%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,183</td>
<td align="right">11.06%</td>
<td align="right">10,696</td>
<td align="right">1,197</td>
<td align="right">11.21%</td>
<td align="right">10,682</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -760,89 +760,89 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-02-04</td>
<td align="center">A9</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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="center">2015-07-09</td>
<td align="center">N1</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">2017-06-21</td>
<td align="center">M8</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">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2010-09-28</td>
<td align="center">V7</td>
<td align="center">2016-08-07</td>
<td align="center">J6</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-08-30</td>
<td align="center">N9</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">F</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">2010-08-23</td>
<td align="center">I4</td>
<td align="center">2016-01-17</td>
<td align="center">R3</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-07-05</td>
<td align="center">X9</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-10-30</td>
<td align="center">D4</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">2012-02-20</td>
<td align="center">M7</td>
<td align="center">Hospital B</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">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="center">2010-02-18</td>
<td align="center">F5</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>
@ -870,50 +870,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2236</td>
<td align="center">124</td>
<td align="center">2288</td>
<td align="center">4648</td>
<td align="center">2129</td>
<td align="center">151</td>
<td align="center">2279</td>
<td align="center">4559</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3462</td>
<td align="center">154</td>
<td align="center">1032</td>
<td align="center">4648</td>
<td align="center">3355</td>
<td align="center">151</td>
<td align="center">1053</td>
<td align="center">4559</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3400</td>
<td align="center">3320</td>
<td align="center">0</td>
<td align="center">1248</td>
<td align="center">4648</td>
<td align="center">1239</td>
<td align="center">4559</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4040</td>
<td align="center">3995</td>
<td align="center">0</td>
<td align="center">608</td>
<td align="center">4648</td>
<td align="center">564</td>
<td align="center">4559</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">1183</td>
<td align="center">1183</td>
<td align="center">1197</td>
<td align="center">1197</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">937</td>
<td align="center">48</td>
<td align="center">198</td>
<td align="center">1183</td>
<td align="center">949</td>
<td align="center">46</td>
<td align="center">202</td>
<td align="center">1197</td>
</tr>
</tbody>
</table>
@ -936,34 +936,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4040</td>
<td align="center">3995</td>
<td align="center">0</td>
<td align="center">608</td>
<td align="center">4648</td>
<td align="center">564</td>
<td align="center">4559</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1066</td>
<td align="center">1077</td>
<td align="center">0</td>
<td align="center">117</td>
<td align="center">1183</td>
<td align="center">120</td>
<td align="center">1197</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2418</td>
<td align="center">2523</td>
<td align="center">0</td>
<td align="center">311</td>
<td align="center">2729</td>
<td align="center">321</td>
<td align="center">2844</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">2136</td>
<td align="center">2136</td>
<td align="center">2082</td>
<td align="center">2082</td>
</tr>
</tbody>
</table>
@ -977,7 +977,7 @@ 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 class="va">data_1st</span> <span class="op">%&gt;%</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 class="co"># [1] 0.5431002</span></code></pre></div>
<span class="co"># [1] 0.5449354</span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">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 class="va">data_1st</span> <span class="op">%&gt;%</span>
@ -991,19 +991,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5389075</td>
<td align="center">0.5437286</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5612520</td>
<td align="center">0.5478284</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5325596</td>
<td align="center">0.5407268</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5259019</td>
<td align="center">0.5448113</td>
</tr>
</tbody>
</table>
@ -1022,23 +1022,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5389075</td>
<td align="center">3277</td>
<td align="center">0.5437286</td>
<td align="center">3213</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5612520</td>
<td align="center">3706</td>
<td align="center">0.5478284</td>
<td align="center">3753</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5325596</td>
<td align="center">1551</td>
<td align="center">0.5407268</td>
<td align="center">1596</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5259019</td>
<td align="center">2162</td>
<td align="center">0.5448113</td>
<td align="center">2120</td>
</tr>
</tbody>
</table>
@ -1059,27 +1059,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7779690</td>
<td align="center">0.8691910</td>
<td align="center">0.9733219</td>
<td align="center">0.7690283</td>
<td align="center">0.8762887</td>
<td align="center">0.9782847</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8326289</td>
<td align="center">0.9010989</td>
<td align="center">0.9805579</td>
<td align="center">0.8312448</td>
<td align="center">0.8997494</td>
<td align="center">0.9874687</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7933309</td>
<td align="center">0.8860388</td>
<td align="center">0.9805790</td>
<td align="center">0.7960619</td>
<td align="center">0.8871308</td>
<td align="center">0.9820675</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5397940</td>
<td align="center">0.5249760</td>
<td align="center">0.0000000</td>
<td align="center">0.5397940</td>
<td align="center">0.5249760</td>
</tr>
</tbody>
</table>
@ -1163,19 +1163,19 @@ Longest: 24</p>
<code class="sourceCode R"><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 class="va">mic_values</span>
<span class="co"># Class &lt;mic&gt;</span>
<span class="co"># [1] &gt;=128 &lt;=0.0625 64 4 0.25 16 8 2 </span>
<span class="co"># [9] 0.25 &gt;=128 0.25 &gt;=128 0.25 0.5 64 0.125 </span>
<span class="co"># [17] 2 &lt;=0.0625 0.5 2 1 0.5 32 &gt;=128 </span>
<span class="co"># [25] 0.5 32 &gt;=128 0.25 &lt;=0.0625 &lt;=0.0625 0.5 2 </span>
<span class="co"># [33] &gt;=128 &gt;=128 4 8 &lt;=0.0625 &lt;=0.0625 4 16 </span>
<span class="co"># [41] &gt;=128 32 &lt;=0.0625 &gt;=128 1 &lt;=0.0625 0.5 8 </span>
<span class="co"># [49] 0.125 4 &lt;=0.0625 16 4 32 0.125 8 </span>
<span class="co"># [57] 4 4 16 4 &gt;=128 &lt;=0.0625 4 32 </span>
<span class="co"># [65] 0.125 64 0.5 0.125 0.5 4 16 32 </span>
<span class="co"># [73] 0.125 0.25 4 0.25 4 &gt;=128 &gt;=128 16 </span>
<span class="co"># [81] 1 &lt;=0.0625 0.125 1 4 4 &lt;=0.0625 0.125 </span>
<span class="co"># [89] 0.125 &gt;=128 16 2 0.25 64 8 16 </span>
<span class="co"># [97] 4 &gt;=128 8 &gt;=128</span></code></pre></div>
<span class="co"># [1] 4 &lt;=0.0625 64 0.5 0.5 0.125 128 128 </span>
<span class="co"># [9] 0.5 &lt;=0.0625 4 32 256 0.25 64 8 </span>
<span class="co"># [17] 32 64 4 2 1 4 16 128 </span>
<span class="co"># [25] 128 32 &lt;=0.0625 32 2 4 16 0.125 </span>
<span class="co"># [33] 0.25 0.5 32 128 64 128 0.125 256 </span>
<span class="co"># [41] 1 &lt;=0.0625 64 1 0.25 0.5 &lt;=0.0625 64 </span>
<span class="co"># [49] 8 1 4 2 32 &lt;=0.0625 &lt;=0.0625 4 </span>
<span class="co"># [57] 128 4 32 128 128 32 0.25 64 </span>
<span class="co"># [65] 16 0.5 4 0.5 0.25 4 &lt;=0.0625 2 </span>
<span class="co"># [73] 0.125 0.5 256 &lt;=0.0625 0.5 1 256 0.25 </span>
<span class="co"># [81] 64 64 8 256 16 256 64 16 </span>
<span class="co"># [89] 128 0.125 8 &lt;=0.0625 4 16 128 128 </span>
<span class="co"># [97] 16 128 0.5 1</span></code></pre></div>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># base R:</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></code></pre></div>
@ -1204,10 +1204,10 @@ Longest: 24</p>
<span class="co"># to review it.</span>
<span class="va">disk_values</span>
<span class="co"># Class &lt;disk&gt;</span>
<span class="co"># [1] 21 24 22 27 19 23 24 30 27 27 30 22 26 21 29 18 31 31 17 20 24 28 21 20 25</span>
<span class="co"># [26] 21 17 19 26 28 21 17 30 27 25 30 30 22 21 25 21 19 17 19 28 25 24 27 23 27</span>
<span class="co"># [51] 26 21 17 18 26 19 31 27 27 25 28 24 20 17 24 21 26 26 26 22 27 27 22 19 23</span>
<span class="co"># [76] 17 27 22 17 26 30 31 28 27 19 23 24 31 22 28 31 27 31 23 29 19 18 30 27 28</span></code></pre></div>
<span class="co"># [1] 22 19 28 26 29 31 30 27 29 17 20 21 19 28 28 24 30 31 17 26 19 30 31 29 24</span>
<span class="co"># [26] 18 22 25 26 25 26 21 25 25 21 29 29 22 30 25 30 28 29 29 21 20 22 18 20 25</span>
<span class="co"># [51] 25 21 27 31 26 17 23 28 21 22 24 25 30 18 26 24 22 22 18 31 20 21 25 22 26</span>
<span class="co"># [76] 31 30 23 18 31 20 24 21 28 31 18 24 27 28 30 28 29 29 22 28 30 30 25 24 31</span></code></pre></div>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># base R:</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></code></pre></div>