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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="">1.8.2.9141</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</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">
@ -187,7 +187,7 @@
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 22 February 2023.</p>
generated on 23 February 2023.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -243,21 +243,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2023-02-22</td>
<td align="center">2023-02-23</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">2023-02-22</td>
<td align="center">2023-02-23</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">2023-02-22</td>
<td align="center">2023-02-23</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -388,12 +388,12 @@ data set:</p>
<col width="13%">
<col width="13%">
<col width="13%">
<col width="28%">
<col width="26%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="8%">
<col width="9%">
</colgroup>
<thead><tr class="header">
<th align="center">date</th>
@ -408,69 +408,69 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-11-27</td>
<td align="center">L9</td>
<td align="center">Hospital B</td>
<td align="center">2014-03-08</td>
<td align="center">B5</td>
<td align="center">Hospital C</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-02-25</td>
<td align="center">S6</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">R</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-05-04</td>
<td align="center">M3</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">M</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2012-07-29</td>
<td align="center">M1</td>
<td align="center">2014-12-01</td>
<td align="center">P7</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-05-01</td>
<td align="center">F7</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">I</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-02-24</td>
<td align="center">R3</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-05-08</td>
<td align="center">I8</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">2014-04-25</td>
<td align="center">M9</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2010-05-05</td>
<td align="center">T6</td>
<td align="center">Hospital C</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">I</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-10-26</td>
<td align="center">B6</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">S</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
</tbody>
@ -507,16 +507,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,350</td>
<td align="right">51.75%</td>
<td align="right">10,350</td>
<td align="right">51.75%</td>
<td align="right">10,313</td>
<td align="right">51.57%</td>
<td align="right">10,313</td>
<td align="right">51.57%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,650</td>
<td align="right">48.25%</td>
<td align="right">9,687</td>
<td align="right">48.44%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -629,9 +629,9 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co">#&gt; Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co">#&gt; 2</span></span>
<span><span class="co">#&gt; Including isolates from ICU.</span></span>
<span><span class="co">#&gt; =&gt; Found 12,352 'phenotype-based' first isolates (61.8% of total where a</span></span>
<span><span class="co">#&gt; =&gt; Found 12,263 'phenotype-based' first isolates (61.3% of total where a</span></span>
<span><span class="co">#&gt; microbial ID was available)</span></span></code></pre></div>
<p>So only 61.8% is suitable for resistance analysis! We can now filter
<p>So only 61.3% 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">
@ -641,11 +641,11 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<div class="sourceCode" id="cb16"><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="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>So we end up with 12 352 isolates for analysis. Now our data looks
<p>So we end up with 12 263 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">
<table class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -658,7 +658,7 @@ like:</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="10%">
<col width="9%">
<col width="5%">
</colgroup>
@ -681,25 +681,25 @@ like:</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2017-11-27</td>
<td align="center">L9</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">R</td>
<td align="center">2014-03-08</td>
<td align="center">B5</td>
<td align="center">Hospital C</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</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">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2010-03-27</td>
<td align="center">Y9</td>
<td align="center">Hospital B</td>
<td align="left">3</td>
<td align="center">2014-12-01</td>
<td align="center">P7</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
@ -712,69 +712,69 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">8</td>
<td align="center">2012-08-01</td>
<td align="center">G7</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="left">5</td>
<td align="center">2010-05-05</td>
<td align="center">T6</td>
<td align="center">Hospital C</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">I</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">2011-10-26</td>
<td align="center">B6</td>
<td align="center">Hospital D</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-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</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">2014-09-23</td>
<td align="center">Q2</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</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="even">
<td align="left">10</td>
<td align="center">2015-05-06</td>
<td align="center">T1</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">I</td>
<td align="center">I</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">12</td>
<td align="center">2017-02-03</td>
<td align="center">I2</td>
<td align="center">Hospital A</td>
<td align="center">2011-08-26</td>
<td align="center">P9</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</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>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">14</td>
<td align="center">2014-02-20</td>
<td align="center">C1</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">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>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -808,8 +808,8 @@ readable:</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://msberends.github.io/cleaner/reference/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: 12,352<br>
Available: 12,352 (100%, NA: 0 = 0%)<br>
Length: 12,263<br>
Available: 12,263 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -834,33 +834,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">5,975</td>
<td align="right">48.37%</td>
<td align="right">5,975</td>
<td align="right">48.37%</td>
<td align="right">5,863</td>
<td align="right">47.81%</td>
<td align="right">5,863</td>
<td align="right">47.81%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,212</td>
<td align="right">26.00%</td>
<td align="right">9,187</td>
<td align="right">74.38%</td>
<td align="right">3,213</td>
<td align="right">26.20%</td>
<td align="right">9,076</td>
<td align="right">74.01%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,865</td>
<td align="right">15.10%</td>
<td align="right">11,052</td>
<td align="right">89.48%</td>
<td align="right">1,879</td>
<td align="right">15.32%</td>
<td align="right">10,955</td>
<td align="right">89.33%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,300</td>
<td align="right">10.52%</td>
<td align="right">12,352</td>
<td align="right">1,308</td>
<td align="right">10.67%</td>
<td align="right">12,263</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -909,42 +909,42 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-11-27</td>
<td align="center">L9</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">2011-10-26</td>
<td align="center">B6</td>
<td align="center">Hospital D</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-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</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">2012-08-01</td>
<td align="center">G7</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">I</td>
<td align="center">2014-09-23</td>
<td align="center">Q2</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</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">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</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">2015-05-06</td>
<td align="center">T1</td>
<td align="center">Hospital A</td>
<td align="center">2014-06-16</td>
<td align="center">S3</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
@ -954,28 +954,13 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-02-20</td>
<td align="center">C1</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">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-12-30</td>
<td align="center">K1</td>
<td align="center">2013-07-11</td>
<td align="center">L9</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -983,14 +968,14 @@ antibiotic class they are in:</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2010-03-10</td>
<td align="center">L3</td>
<tr class="odd">
<td align="center">2011-11-10</td>
<td align="center">N1</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">R</td>
<td align="center">I</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>
@ -998,6 +983,21 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-02-01</td>
<td align="center">H9</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>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in
@ -1020,50 +1020,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">2781</td>
<td align="center">1199</td>
<td align="center">1995</td>
<td align="center">5975</td>
<td align="center">2727</td>
<td align="center">1251</td>
<td align="center">1885</td>
<td align="center">5863</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">1545</td>
<td align="center">1253</td>
<td align="center">3177</td>
<td align="center">5975</td>
<td align="center">1482</td>
<td align="center">1242</td>
<td align="center">3139</td>
<td align="center">5863</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">1980</td>
<td align="center">1850</td>
<td align="center">2145</td>
<td align="center">5975</td>
<td align="center">2084</td>
<td align="center">1802</td>
<td align="center">1977</td>
<td align="center">5863</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2034</td>
<td align="center">1856</td>
<td align="center">2085</td>
<td align="center">5975</td>
<td align="center">1999</td>
<td align="center">1799</td>
<td align="center">2065</td>
<td align="center">5863</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">570</td>
<td align="center">266</td>
<td align="center">464</td>
<td align="center">1300</td>
<td align="center">546</td>
<td align="center">264</td>
<td align="center">498</td>
<td align="center">1308</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1300</td>
<td align="center">1300</td>
<td align="center">1308</td>
<td align="center">1308</td>
</tr>
</tbody>
</table>
@ -1085,34 +1085,34 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2034</td>
<td align="center">1856</td>
<td align="center">2085</td>
<td align="center">5975</td>
<td align="center">1999</td>
<td align="center">1799</td>
<td align="center">2065</td>
<td align="center">5863</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">443</td>
<td align="center">408</td>
<td align="center">449</td>
<td align="center">1300</td>
<td align="center">475</td>
<td align="center">389</td>
<td align="center">444</td>
<td align="center">1308</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1111</td>
<td align="center">988</td>
<td align="center">1113</td>
<td align="center">3212</td>
<td align="center">1105</td>
<td align="center">1034</td>
<td align="center">1074</td>
<td align="center">3213</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">1865</td>
<td align="center">1865</td>
<td align="center">1879</td>
<td align="center">1879</td>
</tr>
</tbody>
</table>
@ -1144,7 +1144,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb25"><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">#&gt; [1] 0.5845207</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 0.5849303</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="cb26"><pre class="downlit sourceCode r">
@ -1159,19 +1159,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5857797</td>
<td align="center">0.5897998</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5846154</td>
<td align="center">0.5851407</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5920836</td>
<td align="center">0.5656620</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5768763</td>
<td align="center">0.5919967</td>
</tr>
</tbody>
</table>
@ -1196,23 +1196,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5857797</td>
<td align="center">3713</td>
<td align="center">0.5897998</td>
<td align="center">3647</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5846154</td>
<td align="center">4355</td>
<td align="center">0.5851407</td>
<td align="center">4334</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5920836</td>
<td align="center">1819</td>
<td align="center">0.5656620</td>
<td align="center">1858</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5768763</td>
<td align="center">2465</td>
<td align="center">0.5919967</td>
<td align="center">2424</td>
</tr>
</tbody>
</table>
@ -1237,27 +1237,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6661088</td>
<td align="center">0.6510460</td>
<td align="center">0.8816736</td>
<td align="center">0.6784922</td>
<td align="center">0.6477912</td>
<td align="center">0.8882824</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6430769</td>
<td align="center">0.6546154</td>
<td align="center">0.8792308</td>
<td align="center">0.6192661</td>
<td align="center">0.6605505</td>
<td align="center">0.8631498</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6634496</td>
<td align="center">0.6534869</td>
<td align="center">0.8826276</td>
<td align="center">0.6616869</td>
<td align="center">0.6657330</td>
<td align="center">0.8882664</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4734584</td>
<td align="center">0.4827036</td>
<td align="center">0.0000000</td>
<td align="center">0.4734584</td>
<td align="center">0.4827036</td>
</tr>
</tbody>
</table>
@ -1285,23 +1285,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">58.6%</td>
<td align="right">37.9%</td>
<td align="right">59.0%</td>
<td align="right">36.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">58.5%</td>
<td align="right">34.9%</td>
<td align="right">35.8%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">59.2%</td>
<td align="right">38.1%</td>
<td align="right">56.6%</td>
<td align="right">34.6%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">57.7%</td>
<td align="right">36.7%</td>
<td align="right">59.2%</td>
<td align="right">37.3%</td>
</tr>
</tbody>
</table>
@ -1417,18 +1417,18 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</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">#&gt; Class 'mic'</span></span>
<span><span class="co">#&gt; [1] 4 0.002 16 1 0.125 &lt;=0.001 64 0.5 2 </span></span>
<span><span class="co">#&gt; [10] &lt;=0.001 0.0625 1 2 0.5 0.01 0.002 0.0625 &gt;=256 </span></span>
<span><span class="co">#&gt; [19] &gt;=256 0.5 &lt;=0.001 8 64 0.025 0.005 0.025 &gt;=256 </span></span>
<span><span class="co">#&gt; [28] 128 0.125 0.125 0.25 64 32 128 0.01 0.0625 </span></span>
<span><span class="co">#&gt; [37] 64 0.5 &gt;=256 0.025 0.0625 &gt;=256 0.25 0.0625 8 </span></span>
<span><span class="co">#&gt; [46] &lt;=0.001 16 0.125 &lt;=0.001 &lt;=0.001 &lt;=0.001 &lt;=0.001 2 0.5 </span></span>
<span><span class="co">#&gt; [55] 0.005 &lt;=0.001 &gt;=256 0.0625 2 0.0625 0.025 64 &lt;=0.001</span></span>
<span><span class="co">#&gt; [64] 0.025 128 0.25 2 64 128 &gt;=256 0.025 2 </span></span>
<span><span class="co">#&gt; [73] 0.005 0.5 &lt;=0.001 4 16 1 &lt;=0.001 0.005 0.125 </span></span>
<span><span class="co">#&gt; [82] 0.005 1 0.125 32 32 0.25 8 16 0.025 </span></span>
<span><span class="co">#&gt; [91] 0.005 0.005 0.002 0.005 128 0.5 0.002 32 4 </span></span>
<span><span class="co">#&gt; [100] 8</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 1 &gt;=256 32 128 &gt;=256 0.025 &gt;=256 0.025 2 </span></span>
<span><span class="co">#&gt; [10] 64 8 1 128 0.0625 0.01 1 128 &lt;=0.001</span></span>
<span><span class="co">#&gt; [19] 8 32 32 0.0625 128 8 0.125 128 0.25 </span></span>
<span><span class="co">#&gt; [28] 0.25 &lt;=0.001 4 128 16 32 0.01 4 &lt;=0.001</span></span>
<span><span class="co">#&gt; [37] &lt;=0.001 16 0.01 0.25 8 32 0.25 &gt;=256 0.0625 </span></span>
<span><span class="co">#&gt; [46] 16 0.002 &gt;=256 0.25 0.025 0.0625 4 0.005 4 </span></span>
<span><span class="co">#&gt; [55] 128 0.125 0.0625 32 0.002 4 8 0.002 0.005 </span></span>
<span><span class="co">#&gt; [64] 0.0625 &gt;=256 0.25 0.01 1 0.5 0.01 0.125 16 </span></span>
<span><span class="co">#&gt; [73] 128 16 1 0.25 0.0625 1 &gt;=256 1 8 </span></span>
<span><span class="co">#&gt; [82] 0.5 32 32 &lt;=0.001 64 0.5 0.5 0.5 0.025 </span></span>
<span><span class="co">#&gt; [91] 16 0.5 &lt;=0.001 1 2 64 &gt;=256 1 0.25 </span></span>
<span><span class="co">#&gt; [100] 2</span></span></code></pre></div>
<div class="sourceCode" id="cb36"><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>
@ -1462,10 +1462,10 @@ plotting:</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">#&gt; Class 'disk'</span></span>
<span><span class="co">#&gt; [1] 21 17 22 25 18 19 27 23 26 29 23 21 31 23 18 23 19 21 28 24 22 19 19 28 17</span></span>
<span><span class="co">#&gt; [26] 18 29 29 21 26 25 29 17 26 31 28 22 17 31 28 21 21 30 25 20 30 27 19 21 18</span></span>
<span><span class="co">#&gt; [51] 23 18 27 23 18 19 24 27 21 20 25 27 18 17 23 23 31 23 22 26 20 29 28 21 26</span></span>
<span><span class="co">#&gt; [76] 17 18 18 19 19 17 21 20 18 25 21 23 28 25 18 18 28 18 27 18 22 23 18 19 24</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 28 24 26 18 22 19 28 20 30 27 21 31 21 17 18 30 27 23 20 24 29 29 24 30 26</span></span>
<span><span class="co">#&gt; [26] 21 19 18 25 26 17 17 18 28 26 27 21 21 25 20 18 31 27 21 25 19 22 25 27 20</span></span>
<span><span class="co">#&gt; [51] 31 19 28 28 24 24 31 30 29 30 27 21 22 28 30 22 28 31 31 29 20 31 27 19 28</span></span>
<span><span class="co">#&gt; [76] 25 22 20 28 22 23 26 24 23 27 20 31 19 22 30 27 24 17 27 17 29 23 17 29 26</span></span></code></pre></div>
<div class="sourceCode" id="cb42"><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>