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@ -39,7 +39,7 @@
</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">1.7.1.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9014</span>
</span>
</div>
@ -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">04 July 2021</h4>
<h4 class="date">06 July 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 04 July 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 06 July 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">2021-07-04</td>
<td align="center">2021-07-06</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">2021-07-04</td>
<td align="center">2021-07-06</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">2021-07-04</td>
<td align="center">2021-07-06</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -344,32 +344,32 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-09-28</td>
<td align="center">A1</td>
<td align="center">Hospital A</td>
<td align="center">2016-02-04</td>
<td align="center">V9</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">R</td>
<td align="center">M</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-09-28</td>
<td align="center">J9</td>
<td align="center">2011-09-24</td>
<td align="center">D2</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">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2011-10-02</td>
<td align="center">S7</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">2014-06-20</td>
<td align="center">Z9</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -377,9 +377,9 @@
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-11-15</td>
<td align="center">U6</td>
<td align="center">Hospital A</td>
<td align="center">2018-01-01</td>
<td align="center">P4</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
@ -388,26 +388,26 @@
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-12-08</td>
<td align="center">B10</td>
<td align="center">2014-12-14</td>
<td align="center">W2</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">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-05-10</td>
<td align="center">M2</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">2016-07-27</td>
<td align="center">R6</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
@ -441,16 +441,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,434</td>
<td align="right">52.17%</td>
<td align="right">10,434</td>
<td align="right">52.17%</td>
<td align="right">10,365</td>
<td align="right">51.83%</td>
<td align="right">10,365</td>
<td align="right">51.83%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,566</td>
<td align="right">47.83%</td>
<td align="right">9,635</td>
<td align="right">48.18%</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 10,702 first weighted isolates (phenotype-based, 53.5% of total</span>
<span class="co"># =&gt; Found 10,656 first weighted isolates (phenotype-based, 53.3% 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 53.3% 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 10,702 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,656 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">
@ -531,7 +531,7 @@ Longest: 1</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="13%">
<col width="9%">
<col width="5%">
</colgroup>
@ -553,73 +553,25 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2016-09-28</td>
<td align="center">A1</td>
<td align="center">Hospital A</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">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">2</td>
<td align="center">2012-09-28</td>
<td align="center">J9</td>
<td align="center">2011-09-24</td>
<td align="center">D2</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>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center"><em>Streptococcus</em></td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="center">2016-12-08</td>
<td align="center">B10</td>
<td align="center">Hospital A</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="even">
<td align="left">7</td>
<td align="center">2015-04-29</td>
<td align="center">W8</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">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">TRUE</td>
</tr>
<tr class="odd">
<td align="left">8</td>
<td align="center">2010-06-19</td>
<td align="center">Q5</td>
<td align="left">3</td>
<td align="center">2014-06-20</td>
<td align="center">Z9</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
@ -628,26 +580,74 @@ Longest: 1</p>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center"><em>Staphylococcus</em></td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">2016-07-27</td>
<td align="center">R6</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">F</td>
<td align="center">Gram-positive</td>
<td align="center"><em>Staphylococcus</em></td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2010-08-20</td>
<td align="center">A8</td>
<td align="center">Hospital B</td>
<td align="left">7</td>
<td align="center">2011-07-24</td>
<td align="center">W2</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</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"><em>Escherichia</em></td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">9</td>
<td align="center">2012-01-12</td>
<td align="center">K9</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"><em>Escherichia</em></td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">11</td>
<td align="center">2013-03-11</td>
<td align="center">B6</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center"><em>Klebsiella</em></td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -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: 10,702<br>
Available: 10,702 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,656<br>
Available: 10,656 (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">4,661</td>
<td align="right">43.55%</td>
<td align="right">4,661</td>
<td align="right">43.55%</td>
<td align="right">4,664</td>
<td align="right">43.77%</td>
<td align="right">4,664</td>
<td align="right">43.77%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,697</td>
<td align="right">25.20%</td>
<td align="right">7,358</td>
<td align="right">68.75%</td>
<td align="right">2,730</td>
<td align="right">25.62%</td>
<td align="right">7,394</td>
<td align="right">69.39%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,145</td>
<td align="right">20.04%</td>
<td align="right">9,503</td>
<td align="right">88.80%</td>
<td align="right">2,093</td>
<td align="right">19.64%</td>
<td align="right">9,487</td>
<td align="right">89.03%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,199</td>
<td align="right">11.20%</td>
<td align="right">10,702</td>
<td align="right">1,169</td>
<td align="right">10.97%</td>
<td align="right">10,656</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -732,14 +732,14 @@ Longest: 24</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="11%">
<col width="10%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="13%">
<col width="9%">
<col width="5%">
</colgroup>
@ -760,23 +760,38 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-09-28</td>
<td align="center">A1</td>
<td align="center">2011-09-24</td>
<td align="center">D2</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</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">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">Gram-positive</td>
<td align="center"><em>Streptococcus</em></td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-09-28</td>
<td align="center">J9</td>
<td align="center">2011-07-24</td>
<td align="center">W2</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center"><em>Escherichia</em></td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-03-17</td>
<td align="center">D5</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
@ -785,67 +800,52 @@ Longest: 24</p>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center"><em>Streptococcus</em></td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-04-29</td>
<td align="center">W8</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">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">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-02-20</td>
<td align="center">P2</td>
<td align="center">Hospital C</td>
<td align="center">2011-06-13</td>
<td align="center">X10</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center"><em>Streptococcus</em></td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2010-09-14</td>
<td align="center">T8</td>
<td align="center">Hospital A</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">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="center">2011-01-26</td>
<td align="center">K8</td>
<td align="center">2010-04-12</td>
<td align="center">Z4</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">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center"><em>Streptococcus</em></td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-02-25</td>
<td align="center">B5</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</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>
<td align="center">Streptococcus</td>
<td align="center"><em>Streptococcus</em></td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
@ -868,52 +868,52 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center"><em>E. coli</em></td>
<td align="center">AMX</td>
<td align="center">2209</td>
<td align="center">123</td>
<td align="center">2329</td>
<td align="center">4661</td>
<td align="center">2180</td>
<td align="center">145</td>
<td align="center">2339</td>
<td align="center">4664</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center"><em>E. coli</em></td>
<td align="center">AMC</td>
<td align="center">3406</td>
<td align="center">165</td>
<td align="center">1090</td>
<td align="center">4661</td>
<td align="center">3360</td>
<td align="center">176</td>
<td align="center">1128</td>
<td align="center">4664</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center"><em>E. coli</em></td>
<td align="center">CIP</td>
<td align="center">3416</td>
<td align="center">3405</td>
<td align="center">0</td>
<td align="center">1245</td>
<td align="center">4661</td>
<td align="center">1259</td>
<td align="center">4664</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center"><em>E. coli</em></td>
<td align="center">GEN</td>
<td align="center">4086</td>
<td align="center">4078</td>
<td align="center">0</td>
<td align="center">575</td>
<td align="center">4661</td>
<td align="center">586</td>
<td align="center">4664</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center"><em>K. pneumoniae</em></td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1199</td>
<td align="center">1199</td>
<td align="center">1169</td>
<td align="center">1169</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center"><em>K. pneumoniae</em></td>
<td align="center">AMC</td>
<td align="center">933</td>
<td align="center">39</td>
<td align="center">227</td>
<td align="center">1199</td>
<td align="center">924</td>
<td align="center">49</td>
<td align="center">196</td>
<td align="center">1169</td>
</tr>
</tbody>
</table>
@ -934,36 +934,36 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center"><em>E. coli</em></td>
<td align="center">GEN</td>
<td align="center">4086</td>
<td align="center">4078</td>
<td align="center">0</td>
<td align="center">575</td>
<td align="center">4661</td>
<td align="center">586</td>
<td align="center">4664</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center"><em>K. pneumoniae</em></td>
<td align="center">GEN</td>
<td align="center">1068</td>
<td align="center">1042</td>
<td align="center">0</td>
<td align="center">131</td>
<td align="center">1199</td>
<td align="center">127</td>
<td align="center">1169</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center"><em>S. aureus</em></td>
<td align="center">GEN</td>
<td align="center">2407</td>
<td align="center">2440</td>
<td align="center">0</td>
<td align="center">290</td>
<td align="center">2697</td>
<td align="center">2730</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center"><em>S. pneumoniae</em></td>
<td align="center">GEN</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">2145</td>
<td align="center">2145</td>
<td align="center">2093</td>
<td align="center">2093</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] 0.5418613</span></code></pre></div>
<span class="co"># [1] 0.5442005</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">0.5276730</td>
<td align="center">0.5512301</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5422819</td>
<td align="center">0.5383792</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5609308</td>
<td align="center">0.5587121</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5475970</td>
<td align="center">0.5329877</td>
</tr>
</tbody>
</table>
@ -1022,23 +1022,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5276730</td>
<td align="center">3180</td>
<td align="center">0.5512301</td>
<td align="center">3211</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5422819</td>
<td align="center">3725</td>
<td align="center">0.5383792</td>
<td align="center">3739</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5609308</td>
<td align="center">1633</td>
<td align="center">0.5587121</td>
<td align="center">1584</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5475970</td>
<td align="center">2164</td>
<td align="center">0.5329877</td>
<td align="center">2122</td>
</tr>
</tbody>
</table>
@ -1058,28 +1058,28 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7661446</td>
<td align="center">0.8766359</td>
<td align="center">0.9759708</td>
<td align="center"><em>Escherichia</em></td>
<td align="center">0.7581475</td>
<td align="center">0.8743568</td>
<td align="center">0.9762007</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8106756</td>
<td align="center">0.8907423</td>
<td align="center">0.9833194</td>
<td align="center"><em>Klebsiella</em></td>
<td align="center">0.8323353</td>
<td align="center">0.8913601</td>
<td align="center">0.9760479</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7942158</td>
<td align="center">0.8924731</td>
<td align="center">0.9818317</td>
<td align="center"><em>Staphylococcus</em></td>
<td align="center">0.7945055</td>
<td align="center">0.8937729</td>
<td align="center">0.9831502</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5501166</td>
<td align="center"><em>Streptococcus</em></td>
<td align="center">0.5351171</td>
<td align="center">0.0000000</td>
<td align="center">0.5501166</td>
<td align="center">0.5351171</td>
</tr>
</tbody>
</table>
@ -1104,23 +1104,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">52.8%</td>
<td align="right">26.0%</td>
<td align="right">55.1%</td>
<td align="right">27.0%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.2%</td>
<td align="right">26.5%</td>
<td align="right">53.8%</td>
<td align="right">26.2%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">56.1%</td>
<td align="right">26.7%</td>
<td align="right">55.9%</td>
<td align="right">27.7%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">54.8%</td>
<td align="right">27.1%</td>
<td align="right">53.3%</td>
<td align="right">27.0%</td>
</tr>
</tbody>
</table>
@ -1204,19 +1204,16 @@ 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] 32 2 4 &gt;=128 8 1 &lt;=0.0625 &gt;=128 </span>
<span class="co"># [9] &lt;=0.0625 &lt;=0.0625 64 2 0.125 8 &lt;=0.0625 0.125 </span>
<span class="co"># [17] 64 &gt;=128 &gt;=128 16 32 2 8 32 </span>
<span class="co"># [25] 0.5 0.5 16 8 &gt;=128 2 16 &gt;=128 </span>
<span class="co"># [33] 0.5 2 64 64 16 &lt;=0.0625 1 4 </span>
<span class="co"># [41] 0.125 16 &lt;=0.0625 0.125 0.25 0.125 8 4 </span>
<span class="co"># [49] &lt;=0.0625 32 1 &lt;=0.0625 1 0.5 0.5 64 </span>
<span class="co"># [57] 2 &lt;=0.0625 8 &lt;=0.0625 32 4 32 64 </span>
<span class="co"># [65] 0.125 0.5 4 0.125 0.5 4 8 8 </span>
<span class="co"># [73] 0.5 64 &gt;=128 32 0.25 32 4 4 </span>
<span class="co"># [81] 0.25 64 0.125 &lt;=0.0625 2 1 2 &lt;=0.0625</span>
<span class="co"># [89] 1 &gt;=128 0.125 2 64 16 1 64 </span>
<span class="co"># [97] 32 64 0.125 &lt;=0.0625</span></code></pre></div>
<span class="co"># [1] 1 16 8 0.5 64 0.125 4 2 0.25 16 </span>
<span class="co"># [11] 8 64 0.25 64 0.25 0.25 0.125 1 0.5 4 </span>
<span class="co"># [21] 64 0.0625 &gt;=128 0.5 0.5 &gt;=128 0.25 0.125 16 32 </span>
<span class="co"># [31] 16 0.0625 4 8 4 &gt;=128 4 0.25 0.0625 0.5 </span>
<span class="co"># [41] 2 0.125 0.25 1 16 2 0.125 1 2 2 </span>
<span class="co"># [51] 0.25 0.5 8 4 8 1 4 64 2 32 </span>
<span class="co"># [61] 0.5 2 1 8 8 32 64 4 2 32 </span>
<span class="co"># [71] &gt;=128 1 64 4 64 8 8 64 0.125 0.0625</span>
<span class="co"># [81] 8 &gt;=128 0.0625 0.0625 0.25 8 8 0.0625 32 0.25 </span>
<span class="co"># [91] 32 0.0625 0.125 1 &gt;=128 16 0.0625 8 0.0625 2</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>
@ -1245,10 +1242,10 @@ 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] 23 19 31 23 17 26 25 27 18 29 30 27 25 23 28 27 28 26 20 22 28 21 22 25 23</span>
<span class="co"># [26] 18 20 22 19 30 22 20 23 21 20 24 28 25 31 29 24 21 31 21 23 24 30 17 27 23</span>
<span class="co"># [51] 18 24 27 27 22 17 20 26 22 28 28 26 27 26 21 17 28 27 19 21 22 26 17 21 18</span>
<span class="co"># [76] 28 22 25 30 29 19 17 29 29 24 29 30 28 17 23 25 28 17 27 28 25 23 22 19 24</span></code></pre></div>
<span class="co"># [1] 25 19 26 17 25 27 22 17 29 29 27 28 21 18 26 29 21 27 24 17 18 19 23 19 21</span>
<span class="co"># [26] 18 23 21 27 29 18 25 24 17 31 18 22 25 30 19 29 26 27 22 22 28 21 23 22 20</span>
<span class="co"># [51] 30 19 23 21 30 17 19 22 18 25 29 28 25 31 20 23 20 22 27 24 21 21 24 19 31</span>
<span class="co"># [76] 19 18 27 20 27 21 25 26 29 27 29 21 27 27 25 20 22 25 26 29 19 19 23 19 20</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>