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(v1.7.1.9023) Removed filter_ functions, new set_ab_names(), ATC code update, ab selector update, fixes #46 and fixed #47

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@ -21,6 +21,9 @@
<script src="../extra.js"></script><meta property="og:title" content="How to conduct AMR data analysis">
<meta property="og:description" content="AMR">
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
<meta name="twitter:card" content="summary_large_image">
<meta name="twitter:creator" content="@msberends">
<meta name="twitter:site" content="@univgroningen">
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@ -41,7 +44,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9023</span>
</span>
</div>
@ -195,7 +198,7 @@
<h1 data-toc-skip>How to conduct AMR data analysis</h1>
<h4 data-toc-skip class="author">Matthijs S. Berends</h4>
<h4 data-toc-skip class="date">23 July 2021</h4>
<h4 data-toc-skip class="date">16 August 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -204,7 +207,7 @@
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 23 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/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 16 August 2021.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor" aria-hidden="true"></a>Introduction</h1>
@ -235,21 +238,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2021-07-23</td>
<td align="center">2021-08-16</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">2021-07-23</td>
<td align="center">2021-08-16</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">2021-07-23</td>
<td align="center">2021-08-16</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -346,70 +349,70 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-03-31</td>
<td align="center">U1</td>
<td align="center">2016-06-21</td>
<td align="center">V8</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-09-19</td>
<td align="center">E6</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2013-10-17</td>
<td align="center">K4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</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">2013-09-11</td>
<td align="center">G5</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</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">2010-04-19</td>
<td align="center">Z2</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">2015-07-17</td>
<td align="center">M4</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2013-03-06</td>
<td align="center">B9</td>
<td align="center">Hospital C</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>
<tr class="even">
<td align="center">2016-10-06</td>
<td align="center">D8</td>
<td align="center">2014-03-08</td>
<td align="center">R1</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2013-05-12</td>
<td align="center">F10</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="even">
<td align="center">2016-07-15</td>
<td align="center">H7</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">M</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
@ -443,18 +446,18 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,388</td>
<td align="right">51.94%</td>
<td align="right">10,388</td>
<td align="right">51.94%</td>
<td align="right">10,300</td>
<td align="right">51.5%</td>
<td align="right">10,300</td>
<td align="right">51.5%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,612</td>
<td align="right">48.06%</td>
<td align="right">9,700</td>
<td align="right">48.5%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
<td align="right">100.0%</td>
</tr>
</tbody>
</table>
@ -507,9 +510,9 @@ Longest: 1</p>
<span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span>
<span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span>
<span class="co"># 2</span>
<span class="co"># =&gt; Found 10,659 first weighted isolates (phenotype-based, 53.3% of total</span>
<span class="co"># =&gt; Found 10,584 first weighted isolates (phenotype-based, 52.9% of total</span>
<span class="co"># where a microbial ID was available)</span></code></pre></div>
<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>
<p>So only 52.9% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
@ -517,7 +520,7 @@ Longest: 1</p>
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
<p>So we end up with 10,659 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,584 isolates for analysis. Now our data looks like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></code></pre></div>
<table style="width:100%;" class="table">
@ -555,46 +558,30 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">2</td>
<td align="center">2015-07-17</td>
<td align="center">M4</td>
<td align="center">Hospital B</td>
<td align="left">1</td>
<td align="center">2016-06-21</td>
<td align="center">V8</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</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">3</td>
<td align="center">2013-03-06</td>
<td align="center">B9</td>
<td align="left">2</td>
<td align="center">2017-09-19</td>
<td align="center">E6</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="center">2013-05-12</td>
<td align="center">F10</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">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
@ -602,27 +589,43 @@ Longest: 1</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2016-07-27</td>
<td align="center">E3</td>
<tr class="odd">
<td align="left">4</td>
<td align="center">2013-09-11</td>
<td align="center">G5</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">B_KLBSL_PNMN</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">Gram-positive</td>
<td align="center">Streptococcus</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">6</td>
<td align="center">2014-03-08</td>
<td align="center">R1</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">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">2015-02-09</td>
<td align="center">T6</td>
<td align="center">Hospital A</td>
<td align="left">7</td>
<td align="center">2015-07-22</td>
<td align="center">U6</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
@ -635,19 +638,19 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2017-08-22</td>
<td align="center">F8</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="left">8</td>
<td align="center">2015-07-26</td>
<td align="center">A1</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="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">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>
</tbody>
@ -671,8 +674,8 @@ Longest: 1</p>
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,659<br>
Available: 10,659 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,584<br>
Available: 10,584 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -689,33 +692,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,644</td>
<td align="right">43.57%</td>
<td align="right">4,644</td>
<td align="right">43.57%</td>
<td align="right">4,573</td>
<td align="right">43.21%</td>
<td align="right">4,573</td>
<td align="right">43.21%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,731</td>
<td align="right">25.62%</td>
<td align="right">7,375</td>
<td align="right">69.19%</td>
<td align="right">2,737</td>
<td align="right">25.86%</td>
<td align="right">7,310</td>
<td align="right">69.07%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,125</td>
<td align="right">19.94%</td>
<td align="right">9,500</td>
<td align="right">89.13%</td>
<td align="right">2,126</td>
<td align="right">20.09%</td>
<td align="right">9,436</td>
<td align="right">89.15%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,159</td>
<td align="right">10.87%</td>
<td align="right">10,659</td>
<td align="right">1,148</td>
<td align="right">10.85%</td>
<td align="right">10,584</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -734,14 +737,14 @@ 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="12%">
<col width="9%">
<col width="5%">
</colgroup>
@ -762,12 +765,12 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-03-06</td>
<td align="center">B9</td>
<td align="center">Hospital C</td>
<td align="center">2015-07-26</td>
<td align="center">A1</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="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>
@ -777,13 +780,43 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-07-27</td>
<td align="center">E3</td>
<td align="center">2016-04-15</td>
<td align="center">E1</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-12-17</td>
<td align="center">D8</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2010-04-23</td>
<td align="center">M6</td>
<td align="center">Hospital A</td>
<td align="center">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">M</td>
<td align="center">Gram-positive</td>
@ -792,63 +825,33 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-10-14</td>
<td align="center">X8</td>
<td align="center">2013-01-18</td>
<td align="center">O5</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-06-11</td>
<td align="center">V8</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">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="odd">
<td align="center">2013-09-03</td>
<td align="center">S3</td>
<td align="center">2012-12-05</td>
<td align="center">S7</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">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-05-16</td>
<td align="center">X5</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</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-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -872,50 +875,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2213</td>
<td align="center">141</td>
<td align="center">2290</td>
<td align="center">4644</td>
<td align="center">2169</td>
<td align="center">137</td>
<td align="center">2267</td>
<td align="center">4573</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3408</td>
<td align="center">175</td>
<td align="center">1061</td>
<td align="center">4644</td>
<td align="center">3389</td>
<td align="center">161</td>
<td align="center">1023</td>
<td align="center">4573</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3393</td>
<td align="center">3306</td>
<td align="center">0</td>
<td align="center">1251</td>
<td align="center">4644</td>
<td align="center">1267</td>
<td align="center">4573</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4060</td>
<td align="center">4004</td>
<td align="center">0</td>
<td align="center">584</td>
<td align="center">4644</td>
<td align="center">569</td>
<td align="center">4573</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">1159</td>
<td align="center">1159</td>
<td align="center">1148</td>
<td align="center">1148</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">215</td>
<td align="center">1159</td>
<td align="center">891</td>
<td align="center">44</td>
<td align="center">213</td>
<td align="center">1148</td>
</tr>
</tbody>
</table>
@ -938,34 +941,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4060</td>
<td align="center">4004</td>
<td align="center">0</td>
<td align="center">584</td>
<td align="center">4644</td>
<td align="center">569</td>
<td align="center">4573</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1052</td>
<td align="center">1048</td>
<td align="center">0</td>
<td align="center">107</td>
<td align="center">1159</td>
<td align="center">100</td>
<td align="center">1148</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2426</td>
<td align="center">2444</td>
<td align="center">0</td>
<td align="center">305</td>
<td align="center">2731</td>
<td align="center">293</td>
<td align="center">2737</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">2125</td>
<td align="center">2125</td>
<td align="center">2126</td>
<td align="center">2126</td>
</tr>
</tbody>
</table>
@ -979,7 +982,7 @@ Longest: 24</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>
<span class="co"># [1] 0.5388873</span></code></pre></div>
<span class="co"># [1] 0.5377929</span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span>
@ -993,19 +996,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5379610</td>
<td align="center">0.5389338</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5353400</td>
<td align="center">0.5440860</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5317705</td>
<td align="center">0.5516820</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5521531</td>
<td align="center">0.5145267</td>
</tr>
</tbody>
</table>
@ -1024,23 +1027,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5379610</td>
<td align="center">3227</td>
<td align="center">0.5389338</td>
<td align="center">3095</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5353400</td>
<td align="center">3721</td>
<td align="center">0.5440860</td>
<td align="center">3720</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5317705</td>
<td align="center">1621</td>
<td align="center">0.5516820</td>
<td align="center">1635</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5521531</td>
<td align="center">2090</td>
<td align="center">0.5145267</td>
<td align="center">2134</td>
</tr>
</tbody>
</table>
@ -1061,27 +1064,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7715332</td>
<td align="center">0.8742463</td>
<td align="center">0.9773902</td>
<td align="center">0.7762956</td>
<td align="center">0.8755740</td>
<td align="center">0.9781325</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8144953</td>
<td align="center">0.9076790</td>
<td align="center">0.9861950</td>
<td align="center">0.8144599</td>
<td align="center">0.9128920</td>
<td align="center">0.9782230</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8000732</td>
<td align="center">0.8883193</td>
<td align="center">0.9791285</td>
<td align="center">0.7939350</td>
<td align="center">0.8929485</td>
<td align="center">0.9839240</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5331765</td>
<td align="center">0.5352775</td>
<td align="center">0.0000000</td>
<td align="center">0.5331765</td>
<td align="center">0.5352775</td>
</tr>
</tbody>
</table>
@ -1100,29 +1103,29 @@ Longest: 24</p>
<table class="table">
<thead><tr class="header">
<th align="left">hospital</th>
<th align="right">amoxicillin</th>
<th align="right">amoxicillin_clavulanic_acid</th>
<th align="right">Amoxicillin</th>
<th align="right">Amoxicillin/clavulanic acid</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">53.8%</td>
<td align="right">26.0%</td>
<td align="right">53.9%</td>
<td align="right">25.8%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">53.5%</td>
<td align="right">26.9%</td>
<td align="right">54.4%</td>
<td align="right">27.2%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">53.2%</td>
<td align="right">26.3%</td>
<td align="right">55.2%</td>
<td align="right">27.8%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">55.2%</td>
<td align="right">26.2%</td>
<td align="right">51.5%</td>
<td align="right">24.6%</td>
</tr>
</tbody>
</table>
@ -1206,16 +1209,18 @@ Longest: 24</p>
<code class="sourceCode R"><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
<span class="va">mic_values</span>
<span class="co"># Class &lt;mic&gt;</span>
<span class="co"># [1] 0.125 128 0.25 16 0.125 32 0.125 0.0625 8 0.025 </span>
<span class="co"># [11] 0.125 128 0.01 16 1 8 0.005 0.005 64 0.005 </span>
<span class="co"># [21] 128 16 0.025 128 0.5 0.005 0.025 0.001 64 0.001 </span>
<span class="co"># [31] 32 2 256 8 128 32 256 0.5 0.125 1 </span>
<span class="co"># [41] 0.01 128 0.01 64 1 128 64 0.01 0.025 0.005 </span>
<span class="co"># [51] 128 0.0625 8 256 64 32 0.001 0.025 0.5 0.0625</span>
<span class="co"># [61] 0.5 0.002 0.002 0.01 0.0625 128 128 0.01 0.5 256 </span>
<span class="co"># [71] 0.0625 256 0.25 0.025 0.025 8 256 0.002 0.025 0.025 </span>
<span class="co"># [81] 0.002 1 0.005 32 128 256 256 0.005 16 0.025 </span>
<span class="co"># [91] 0.25 0.025 0.002 64 16 2 1 0.0625 16 256</span></code></pre></div>
<span class="co"># [1] 0.0625 256 32 0.002 &lt;=0.001 256 0.5 0.025 0.5 </span>
<span class="co"># [10] 2 0.002 0.005 0.005 1 32 0.01 0.002 64 </span>
<span class="co"># [19] 0.25 4 0.025 0.125 0.005 1 2 0.002 0.25 </span>
<span class="co"># [28] 0.25 32 2 0.25 0.25 0.005 0.5 0.002 0.002 </span>
<span class="co"># [37] 8 0.25 2 2 0.005 0.5 64 128 2 </span>
<span class="co"># [46] 64 0.0625 0.002 1 0.01 16 0.125 64 4 </span>
<span class="co"># [55] 16 2 32 0.025 256 16 1 0.005 32 </span>
<span class="co"># [64] 16 0.01 0.025 4 0.0625 0.125 0.025 0.5 0.5 </span>
<span class="co"># [73] 0.025 128 0.01 0.025 256 0.25 1 64 0.125 </span>
<span class="co"># [82] 2 &lt;=0.001 0.25 8 0.0625 4 16 0.025 64 </span>
<span class="co"># [91] 8 0.01 0.0625 8 128 0.5 4 0.002 0.5 </span>
<span class="co"># [100] 64</span></code></pre></div>
<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>
@ -1244,10 +1249,10 @@ 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] 28 23 25 19 26 25 18 26 28 20 17 17 27 22 22 22 26 28 21 19 30 22 17 30 30</span>
<span class="co"># [26] 22 29 17 21 20 17 29 22 21 29 30 26 30 18 17 24 20 20 31 31 22 22 22 27 28</span>
<span class="co"># [51] 23 19 21 19 24 20 27 29 18 21 24 24 29 20 21 22 21 25 26 24 27 31 17 23 29</span>
<span class="co"># [76] 31 21 29 31 24 23 26 26 25 22 26 28 26 22 25 17 29 21 21 30 18 18 23 31 27</span></code></pre></div>
<span class="co"># [1] 18 22 30 28 29 31 18 21 17 31 28 25 21 22 29 26 21 30 17 20 18 21 26 19 24</span>
<span class="co"># [26] 17 30 17 26 19 29 23 23 22 26 25 20 25 29 20 28 29 31 24 23 26 29 20 17 17</span>
<span class="co"># [51] 27 18 18 29 17 20 21 24 30 17 25 27 21 30 28 26 27 20 22 19 19 24 21 28 22</span>
<span class="co"># [76] 24 21 28 24 17 29 23 31 28 25 20 18 18 30 31 17 18 17 28 24 22 24 31 25 31</span></code></pre></div>
<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>