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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="">1.8.2.9011</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9012</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">
@ -325,69 +325,69 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-05-04</td>
<td align="center">P4</td>
<td align="center">Hospital D</td>
<td align="center">2017-04-25</td>
<td align="center">U7</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">F</td>
</tr>
<tr class="even">
<td align="center">2014-07-05</td>
<td align="center">K8</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2010-05-31</td>
<td align="center">N4</td>
<td align="center">Hospital C</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">2015-09-13</td>
<td align="center">M2</td>
<td align="center">Hospital A</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">2014-03-03</td>
<td align="center">N3</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</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>
</tr>
<tr class="odd">
<td align="center">2016-09-06</td>
<td align="center">M1</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-01-03</td>
<td align="center">T9</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2013-12-05</td>
<td align="center">T7</td>
<td align="center">2010-11-26</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-01-24</td>
<td align="center">A5</td>
<td align="center">2010-11-30</td>
<td align="center">E9</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">R</td>
<td align="center">R</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">M</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">10,425</td>
<td align="right">52.13%</td>
<td align="right">10,425</td>
<td align="right">52.13%</td>
<td align="right">10,401</td>
<td align="right">52.01%</td>
<td align="right">10,401</td>
<td align="right">52.01%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,575</td>
<td align="right">47.88%</td>
<td align="right">9,599</td>
<td align="right">48.00%</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 10,700 'phenotype-based' first isolates (53.5% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,666 'phenotype-based' first isolates (53.3% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.5% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<p>So only 53.3% 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 10,700 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,666 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">
@ -537,78 +537,14 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">5</td>
<td align="center">2013-12-05</td>
<td align="center">T7</td>
<td align="left">2</td>
<td align="center">2014-07-05</td>
<td align="center">K8</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-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="center">2017-01-24</td>
<td align="center">A5</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">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">7</td>
<td align="center">2011-12-23</td>
<td align="center">B5</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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="left">8</td>
<td align="center">2012-06-13</td>
<td align="center">C3</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">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">9</td>
<td align="center">2017-04-10</td>
<td align="center">C3</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">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -617,16 +553,80 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2013-09-19</td>
<td align="center">R2</td>
<td align="center">Hospital A</td>
<td align="left">7</td>
<td align="center">2016-07-20</td>
<td align="center">I10</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">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">8</td>
<td align="center">2016-01-03</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">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="even">
<td align="left">10</td>
<td align="center">2014-06-25</td>
<td align="center">X6</td>
<td align="center">Hospital B</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="odd">
<td align="left">14</td>
<td align="center">2015-04-05</td>
<td align="center">P10</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">R</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">16</td>
<td align="center">2015-07-19</td>
<td align="center">L8</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">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</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: 10,700<br>
Available: 10,700 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,666<br>
Available: 10,666 (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">4,656</td>
<td align="right">43.51%</td>
<td align="right">4,656</td>
<td align="right">43.51%</td>
<td align="right">4,672</td>
<td align="right">43.80%</td>
<td align="right">4,672</td>
<td align="right">43.80%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,775</td>
<td align="right">25.93%</td>
<td align="right">7,431</td>
<td align="right">69.45%</td>
<td align="right">2,720</td>
<td align="right">25.50%</td>
<td align="right">7,392</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">2,097</td>
<td align="right">19.60%</td>
<td align="right">9,528</td>
<td align="right">89.05%</td>
<td align="right">2,083</td>
<td align="right">19.53%</td>
<td align="right">9,475</td>
<td align="right">88.83%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,172</td>
<td align="right">10.95%</td>
<td align="right">10,700</td>
<td align="right">1,191</td>
<td align="right">11.17%</td>
<td align="right">10,666</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -744,53 +744,53 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-01-24</td>
<td align="center">A5</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">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">2011-12-23</td>
<td align="center">B5</td>
<td align="center">Hospital A</td>
<td align="center">2016-01-03</td>
<td align="center">V5</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">S</td>
<td align="center">R</td>
<td align="center">M</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">2016-03-01</td>
<td align="center">W9</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<tr class="even">
<td align="center">2016-11-05</td>
<td align="center">U5</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-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="odd">
<td align="center">2015-04-17</td>
<td align="center">I4</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="even">
<td align="center">2011-10-21</td>
<td align="center">M6</td>
<td align="center">2015-01-11</td>
<td align="center">K6</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
@ -804,30 +804,30 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-09-13</td>
<td align="center">D7</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">2014-08-09</td>
<td align="center">U1</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">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">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">2011-06-26</td>
<td align="center">L7</td>
<td align="center">Hospital C</td>
<td align="center">2011-12-13</td>
<td align="center">W1</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</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">2196</td>
<td align="center">122</td>
<td align="center">2338</td>
<td align="center">4656</td>
<td align="center">2238</td>
<td align="center">117</td>
<td align="center">2317</td>
<td align="center">4672</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3393</td>
<td align="center">163</td>
<td align="center">1100</td>
<td align="center">4656</td>
<td align="center">3470</td>
<td align="center">155</td>
<td align="center">1047</td>
<td align="center">4672</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3421</td>
<td align="center">3430</td>
<td align="center">0</td>
<td align="center">1235</td>
<td align="center">4656</td>
<td align="center">1242</td>
<td align="center">4672</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4068</td>
<td align="center">4080</td>
<td align="center">0</td>
<td align="center">588</td>
<td align="center">4656</td>
<td align="center">592</td>
<td align="center">4672</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">1172</td>
<td align="center">1172</td>
<td align="center">1191</td>
<td align="center">1191</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">905</td>
<td align="center">39</td>
<td align="center">228</td>
<td align="center">1172</td>
<td align="center">910</td>
<td align="center">35</td>
<td align="center">246</td>
<td align="center">1191</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">4068</td>
<td align="center">4080</td>
<td align="center">0</td>
<td align="center">588</td>
<td align="center">4656</td>
<td align="center">592</td>
<td align="center">4672</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1068</td>
<td align="center">1082</td>
<td align="center">0</td>
<td align="center">104</td>
<td align="center">1172</td>
<td align="center">109</td>
<td align="center">1191</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2464</td>
<td align="center">2414</td>
<td align="center">0</td>
<td align="center">311</td>
<td align="center">2775</td>
<td align="center">306</td>
<td align="center">2720</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">2097</td>
<td align="center">2097</td>
<td align="center">2083</td>
<td align="center">2083</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] 0.5437383</span></span></code></pre></div>
<span><span class="co"># [1] 0.5417214</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">0.5490758</td>
<td align="center">0.5304916</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5407427</td>
<td align="center">0.5437333</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5584975</td>
<td align="center">0.5332512</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5302961</td>
<td align="center">0.5620789</td>
</tr>
</tbody>
</table>
@ -1008,23 +1008,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5490758</td>
<td align="center">3138</td>
<td align="center">0.5304916</td>
<td align="center">3214</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5407427</td>
<td align="center">3743</td>
<td align="center">0.5437333</td>
<td align="center">3750</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5584975</td>
<td align="center">0.5332512</td>
<td align="center">1624</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5302961</td>
<td align="center">2195</td>
<td align="center">0.5620789</td>
<td align="center">2078</td>
</tr>
</tbody>
</table>
@ -1047,27 +1047,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7637457</td>
<td align="center">0.8737113</td>
<td align="center">0.9755155</td>
<td align="center">0.7758990</td>
<td align="center">0.8732877</td>
<td align="center">0.9796661</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8054608</td>
<td align="center">0.9112628</td>
<td align="center">0.9778157</td>
<td align="center">0.7934509</td>
<td align="center">0.9084803</td>
<td align="center">0.9798489</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7895495</td>
<td align="center">0.8879279</td>
<td align="center">0.9819820</td>
<td align="center">0.7886029</td>
<td align="center">0.8875000</td>
<td align="center">0.9786765</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5398188</td>
<td align="center">0.5424868</td>
<td align="center">0.0000000</td>
<td align="center">0.5398188</td>
<td align="center">0.5424868</td>
</tr>
</tbody>
</table>
@ -1092,23 +1092,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.9%</td>
<td align="right">26.7%</td>
<td align="right">53.0%</td>
<td align="right">25.4%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.1%</td>
<td align="right">27.4%</td>
<td align="right">54.4%</td>
<td align="right">26.4%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">55.8%</td>
<td align="right">27.2%</td>
<td align="right">53.3%</td>
<td align="right">25.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">53.0%</td>
<td align="right">26.1%</td>
<td align="right">56.2%</td>
<td align="right">28.5%</td>
</tr>
</tbody>
</table>
@ -1206,16 +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] 8 0.001 0.0625 0.025 128 0.005 16 64 &gt;=256 128 </span></span>
<span><span class="co"># [11] 128 0.5 0.005 0.005 &gt;=256 16 0.025 0.01 16 16 </span></span>
<span><span class="co"># [21] 2 32 0.01 &gt;=256 16 4 0.0625 8 128 1 </span></span>
<span><span class="co"># [31] 0.25 &gt;=256 8 64 0.01 32 0.25 32 0.25 8 </span></span>
<span><span class="co"># [41] 0.25 128 16 1 0.5 0.5 0.01 2 64 0.002 </span></span>
<span><span class="co"># [51] &gt;=256 2 0.001 8 0.0625 16 0.025 64 16 0.5 </span></span>
<span><span class="co"># [61] 128 16 0.025 16 8 128 0.001 &gt;=256 2 0.001 </span></span>
<span><span class="co"># [71] 16 1 32 16 16 0.25 0.025 32 0.0625 0.125 </span></span>
<span><span class="co"># [81] 0.25 16 128 0.001 1 0.25 0.001 0.01 8 4 </span></span>
<span><span class="co"># [91] 128 0.025 2 0.005 4 16 16 0.001 0.5 0.001</span></span></code></pre></div>
<span><span class="co"># [1] 0.002 &lt;=0.001 0.025 0.002 0.002 &gt;=256 8 4 0.5 </span></span>
<span><span class="co"># [10] &gt;=256 8 2 0.25 0.125 0.25 4 1 0.25 </span></span>
<span><span class="co"># [19] 32 32 0.25 0.01 0.125 1 128 32 0.5 </span></span>
<span><span class="co"># [28] 0.01 128 2 0.125 0.002 32 &gt;=256 64 0.005 </span></span>
<span><span class="co"># [37] 16 0.005 2 128 1 32 0.0625 0.005 2 </span></span>
<span><span class="co"># [46] 128 0.01 2 0.5 16 0.01 4 8 &lt;=0.001</span></span>
<span><span class="co"># [55] 0.25 32 0.125 0.002 &lt;=0.001 0.005 16 0.125 4 </span></span>
<span><span class="co"># [64] 32 32 0.01 0.002 64 0.01 0.0625 8 4 </span></span>
<span><span class="co"># [73] 64 &lt;=0.001 0.005 &lt;=0.001 16 0.5 2 2 &lt;=0.001</span></span>
<span><span class="co"># [82] 128 0.005 0.025 1 1 0.025 32 64 0.0625 </span></span>
<span><span class="co"># [91] 0.005 0.025 0.01 0.005 0.125 4 128 4 0.0625 </span></span>
<span><span class="co"># [100] 0.005</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>
@ -1242,10 +1244,10 @@ Longest: 24</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class &lt;disk&gt;</span></span>
<span><span class="co"># [1] 30 18 18 30 21 28 31 27 24 20 27 20 27 21 27 17 22 19 28 23 19 25 21 17 21</span></span>
<span><span class="co"># [26] 24 22 27 26 18 22 17 18 21 26 17 17 22 31 24 30 20 28 23 17 29 19 30 22 24</span></span>
<span><span class="co"># [51] 25 22 18 19 30 24 19 26 17 18 17 21 26 18 31 21 24 24 19 30 30 18 27 18 18</span></span>
<span><span class="co"># [76] 25 26 22 31 26 19 17 24 24 22 28 17 26 17 19 30 18 20 18 18 18 27 23 25 30</span></span></code></pre></div>
<span><span class="co"># [1] 26 17 18 21 22 21 20 25 25 26 25 19 19 27 21 29 19 31 20 31 18 26 26 25 26</span></span>
<span><span class="co"># [26] 30 27 29 22 27 29 29 20 17 22 31 24 23 29 24 24 28 27 24 26 30 21 23 28 19</span></span>
<span><span class="co"># [51] 18 30 23 27 24 30 26 29 30 19 19 17 24 30 23 29 23 18 19 29 23 28 21 28 19</span></span>
<span><span class="co"># [76] 27 26 22 26 18 20 22 20 23 23 28 18 26 19 24 22 17 19 26 20 19 24 18 28 21</span></span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>