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@ -44,7 +44,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
@ -198,7 +198,7 @@
<h1 data-toc-skip>How to conduct AMR data analysis</h1>
<h4 data-toc-skip class="author">Matthijs S. Berends</h4>
<h4 data-toc-skip class="date">16 August 2021</h4>
<h4 data-toc-skip class="date">17 August 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -207,7 +207,7 @@
<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 16 August 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/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 17 August 2021.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor" aria-hidden="true"></a>Introduction</h1>
@ -238,21 +238,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2021-08-16</td>
<td align="center">2021-08-17</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">2021-08-16</td>
<td align="center">2021-08-17</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">2021-08-16</td>
<td align="center">2021-08-17</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -349,42 +349,42 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-06-21</td>
<td align="center">V8</td>
<td align="center">2012-12-11</td>
<td align="center">B5</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-09-19</td>
<td align="center">E6</td>
<td align="center">Hospital C</td>
<td align="center">2012-01-03</td>
<td align="center">D5</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">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2013-10-17</td>
<td align="center">K4</td>
<td align="center">Hospital B</td>
<td align="center">2013-03-20</td>
<td align="center">E3</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-09-11</td>
<td align="center">G5</td>
<td align="center">Hospital A</td>
<td align="center">2017-02-14</td>
<td align="center">L5</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
@ -393,9 +393,9 @@
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2010-04-19</td>
<td align="center">Z2</td>
<td align="center">Hospital B</td>
<td align="center">2010-04-27</td>
<td align="center">Y6</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
@ -404,14 +404,14 @@
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-03-08</td>
<td align="center">R1</td>
<td align="center">2011-08-04</td>
<td align="center">O2</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">Staphylococcus aureus</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>
</tbody>
@ -446,18 +446,18 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,300</td>
<td align="right">51.5%</td>
<td align="right">10,300</td>
<td align="right">51.5%</td>
<td align="right">10,443</td>
<td align="right">52.22%</td>
<td align="right">10,443</td>
<td align="right">52.22%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,700</td>
<td align="right">48.5%</td>
<td align="right">9,557</td>
<td align="right">47.79%</td>
<td align="right">20,000</td>
<td align="right">100.0%</td>
<td align="right">100.00%</td>
</tr>
</tbody>
</table>
@ -510,9 +510,9 @@ 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 10,584 first weighted isolates (phenotype-based, 52.9% of total</span>
<span class="co"># =&gt; Found 10,606 first weighted isolates (phenotype-based, 53.0% of total</span>
<span class="co"># where a microbial ID was available)</span></code></pre></div>
<p>So only 52.9% 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 53.0% 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>
<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" 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></code></pre></div>
@ -520,7 +520,7 @@ 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 10,584 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,606 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" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></code></pre></div>
<table style="width:100%;" class="table">
@ -559,27 +559,27 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2016-06-21</td>
<td align="center">V8</td>
<td align="center">2012-12-11</td>
<td align="center">B5</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</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">F</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">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2017-09-19</td>
<td align="center">E6</td>
<td align="center">Hospital C</td>
<td align="center">2012-01-03</td>
<td align="center">D5</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">S</td>
<td align="center">S</td>
@ -591,9 +591,9 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2013-09-11</td>
<td align="center">G5</td>
<td align="center">Hospital A</td>
<td align="center">2017-02-14</td>
<td align="center">L5</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
@ -606,51 +606,51 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="center">2014-03-08</td>
<td align="center">R1</td>
<td align="left">7</td>
<td align="center">2012-03-07</td>
<td align="center">I8</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">F</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">7</td>
<td align="center">2015-07-22</td>
<td align="center">U6</td>
<td align="center">Hospital D</td>
<td align="left">9</td>
<td align="center">2010-12-20</td>
<td align="center">H10</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">S</td>
<td align="center">S</td>
<td align="center">F</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">8</td>
<td align="center">2015-07-26</td>
<td align="center">A1</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="left">11</td>
<td align="center">2014-01-24</td>
<td align="center">M2</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">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">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -674,8 +674,8 @@ 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" class="external-link">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: 10,584<br>
Available: 10,584 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,606<br>
Available: 10,606 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -692,33 +692,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,573</td>
<td align="right">43.21%</td>
<td align="right">4,573</td>
<td align="right">43.21%</td>
<td align="right">4,494</td>
<td align="right">42.37%</td>
<td align="right">4,494</td>
<td align="right">42.37%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,737</td>
<td align="right">25.86%</td>
<td align="right">7,310</td>
<td align="right">69.07%</td>
<td align="right">2,785</td>
<td align="right">26.26%</td>
<td align="right">7,279</td>
<td align="right">68.63%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,126</td>
<td align="right">20.09%</td>
<td align="right">9,436</td>
<td align="right">89.15%</td>
<td align="right">2,106</td>
<td align="right">19.86%</td>
<td align="right">9,385</td>
<td align="right">88.49%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,148</td>
<td align="right">10.85%</td>
<td align="right">10,584</td>
<td align="right">1,221</td>
<td align="right">11.51%</td>
<td align="right">10,606</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -765,8 +765,8 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-07-26</td>
<td align="center">A1</td>
<td align="center">2012-12-11</td>
<td align="center">B5</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
@ -780,8 +780,8 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-04-15</td>
<td align="center">E1</td>
<td align="center">2011-06-11</td>
<td align="center">L7</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
@ -795,28 +795,13 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-12-17</td>
<td align="center">D8</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">I</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2010-04-23</td>
<td align="center">M6</td>
<td align="center">Hospital A</td>
<td align="center">2012-12-19</td>
<td align="center">A10</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">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -824,34 +809,49 @@ Longest: 24</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-12-05</td>
<td align="center">M6</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="odd">
<td align="center">2013-01-18</td>
<td align="center">O5</td>
<td align="center">Hospital D</td>
<td align="center">2017-05-14</td>
<td align="center">L8</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-12-05</td>
<td align="center">S7</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">2010-12-14</td>
<td align="center">Q1</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">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -875,50 +875,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2169</td>
<td align="center">137</td>
<td align="center">2267</td>
<td align="center">4573</td>
<td align="center">2137</td>
<td align="center">139</td>
<td align="center">2218</td>
<td align="center">4494</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3389</td>
<td align="center">161</td>
<td align="center">1023</td>
<td align="center">4573</td>
<td align="center">3298</td>
<td align="center">157</td>
<td align="center">1039</td>
<td align="center">4494</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3306</td>
<td align="center">3230</td>
<td align="center">0</td>
<td align="center">1267</td>
<td align="center">4573</td>
<td align="center">1264</td>
<td align="center">4494</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4004</td>
<td align="center">3946</td>
<td align="center">0</td>
<td align="center">569</td>
<td align="center">4573</td>
<td align="center">548</td>
<td align="center">4494</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">1148</td>
<td align="center">1148</td>
<td align="center">1221</td>
<td align="center">1221</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">891</td>
<td align="center">967</td>
<td align="center">44</td>
<td align="center">213</td>
<td align="center">1148</td>
<td align="center">210</td>
<td align="center">1221</td>
</tr>
</tbody>
</table>
@ -941,34 +941,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4004</td>
<td align="center">3946</td>
<td align="center">0</td>
<td align="center">569</td>
<td align="center">4573</td>
<td align="center">548</td>
<td align="center">4494</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1048</td>
<td align="center">1088</td>
<td align="center">0</td>
<td align="center">100</td>
<td align="center">1148</td>
<td align="center">133</td>
<td align="center">1221</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2444</td>
<td align="center">2490</td>
<td align="center">0</td>
<td align="center">293</td>
<td align="center">2737</td>
<td align="center">295</td>
<td align="center">2785</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">2126</td>
<td align="center">2126</td>
<td align="center">2106</td>
<td align="center">2106</td>
</tr>
</tbody>
</table>
@ -982,7 +982,7 @@ 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] 0.5377929</span></code></pre></div>
<span class="co"># [1] 0.5427117</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 class="va">data_1st</span> <span class="op">%&gt;%</span>
@ -996,19 +996,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5389338</td>
<td align="center">0.5356582</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5440860</td>
<td align="center">0.5408108</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5516820</td>
<td align="center">0.5371153</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5145267</td>
<td align="center">0.5614714</td>
</tr>
</tbody>
</table>
@ -1027,23 +1027,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5389338</td>
<td align="center">3095</td>
<td align="center">0.5356582</td>
<td align="center">3183</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5440860</td>
<td align="center">3720</td>
<td align="center">0.5408108</td>
<td align="center">3700</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5516820</td>
<td align="center">1635</td>
<td align="center">0.5371153</td>
<td align="center">1657</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5145267</td>
<td align="center">2134</td>
<td align="center">0.5614714</td>
<td align="center">2066</td>
</tr>
</tbody>
</table>
@ -1064,27 +1064,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7762956</td>
<td align="center">0.8755740</td>
<td align="center">0.9781325</td>
<td align="center">0.7688028</td>
<td align="center">0.8780596</td>
<td align="center">0.9815309</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8144599</td>
<td align="center">0.9128920</td>
<td align="center">0.9782230</td>
<td align="center">0.8280098</td>
<td align="center">0.8910729</td>
<td align="center">0.9754300</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7939350</td>
<td align="center">0.8929485</td>
<td align="center">0.9839240</td>
<td align="center">0.7921005</td>
<td align="center">0.8940754</td>
<td align="center">0.9795332</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5352775</td>
<td align="center">0.5351377</td>
<td align="center">0.0000000</td>
<td align="center">0.5352775</td>
<td align="center">0.5351377</td>
</tr>
</tbody>
</table>
@ -1109,23 +1109,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">53.9%</td>
<td align="right">25.8%</td>
<td align="right">53.6%</td>
<td align="right">26.4%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.4%</td>
<td align="right">27.2%</td>
<td align="right">54.1%</td>
<td align="right">24.6%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">55.2%</td>
<td align="right">27.8%</td>
<td align="right">53.7%</td>
<td align="right">27.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">51.5%</td>
<td align="right">24.6%</td>
<td align="right">56.1%</td>
<td align="right">29.0%</td>
</tr>
</tbody>
</table>
@ -1209,18 +1209,16 @@ 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] 0.0625 256 32 0.002 &lt;=0.001 256 0.5 0.025 0.5 </span>
<span class="co"># [10] 2 0.002 0.005 0.005 1 32 0.01 0.002 64 </span>
<span class="co"># [19] 0.25 4 0.025 0.125 0.005 1 2 0.002 0.25 </span>
<span class="co"># [28] 0.25 32 2 0.25 0.25 0.005 0.5 0.002 0.002 </span>
<span class="co"># [37] 8 0.25 2 2 0.005 0.5 64 128 2 </span>
<span class="co"># [46] 64 0.0625 0.002 1 0.01 16 0.125 64 4 </span>
<span class="co"># [55] 16 2 32 0.025 256 16 1 0.005 32 </span>
<span class="co"># [64] 16 0.01 0.025 4 0.0625 0.125 0.025 0.5 0.5 </span>
<span class="co"># [73] 0.025 128 0.01 0.025 256 0.25 1 64 0.125 </span>
<span class="co"># [82] 2 &lt;=0.001 0.25 8 0.0625 4 16 0.025 64 </span>
<span class="co"># [91] 8 0.01 0.0625 8 128 0.5 4 0.002 0.5 </span>
<span class="co"># [100] 64</span></code></pre></div>
<span class="co"># [1] 0.25 16 0.0625 32 0.025 1 256 64 0.002 0.005 </span>
<span class="co"># [11] 0.01 0.005 8 0.01 0.025 128 0.01 8 0.005 256 </span>
<span class="co"># [21] 0.005 8 0.0625 0.125 0.005 16 8 2 0.5 4 </span>
<span class="co"># [31] 2 32 0.25 0.25 8 0.025 0.25 8 64 1 </span>
<span class="co"># [41] 0.005 0.01 0.005 256 0.025 0.5 2 0.025 0.5 0.005 </span>
<span class="co"># [51] 0.0625 128 4 1 0.0625 0.002 16 0.002 8 0.005 </span>
<span class="co"># [61] 1 1 8 32 0.002 32 0.25 8 4 0.001 </span>
<span class="co"># [71] 2 16 16 0.025 0.005 0.0625 2 128 0.001 2 </span>
<span class="co"># [81] 64 0.025 16 64 2 128 8 0.5 4 256 </span>
<span class="co"># [91] 0.5 32 0.001 0.01 2 64 4 32 4 0.0625</span></code></pre></div>
<div class="sourceCode" id="cb37"><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>
@ -1249,10 +1247,10 @@ 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] 18 22 30 28 29 31 18 21 17 31 28 25 21 22 29 26 21 30 17 20 18 21 26 19 24</span>
<span class="co"># [26] 17 30 17 26 19 29 23 23 22 26 25 20 25 29 20 28 29 31 24 23 26 29 20 17 17</span>
<span class="co"># [51] 27 18 18 29 17 20 21 24 30 17 25 27 21 30 28 26 27 20 22 19 19 24 21 28 22</span>
<span class="co"># [76] 24 21 28 24 17 29 23 31 28 25 20 18 18 30 31 17 18 17 28 24 22 24 31 25 31</span></code></pre></div>
<span class="co"># [1] 26 25 28 21 24 22 21 27 22 21 31 25 26 17 28 29 18 31 21 30 23 28 22 18 28</span>
<span class="co"># [26] 21 25 26 18 30 22 28 25 28 25 21 29 26 19 21 19 26 31 17 25 22 21 27 24 26</span>
<span class="co"># [51] 20 17 18 27 31 31 20 31 26 22 25 22 19 22 27 19 25 27 30 17 24 27 22 28 18</span>
<span class="co"># [76] 26 30 29 25 23 26 29 19 25 25 24 25 30 29 25 29 17 26 21 20 29 26 23 29 31</span></code></pre></div>
<div class="sourceCode" id="cb43"><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>