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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="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
@ -162,7 +162,7 @@
<img src="../logo.svg" class="logo" alt=""><h1>How to conduct AMR data analysis</h1>
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
<h4 data-toc-skip class="date">21 October 2022</h4>
<h4 data-toc-skip class="date">22 October 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="d-none name"><code>AMR.Rmd</code></div>
@ -170,7 +170,7 @@
<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 21 October 2022.</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 22 October 2022.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -201,21 +201,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-10-21</td>
<td align="center">2022-10-22</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">2022-10-21</td>
<td align="center">2022-10-22</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">2022-10-21</td>
<td align="center">2022-10-22</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -325,71 +325,71 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-06-09</td>
<td align="center">Z9</td>
<td align="center">Hospital A</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">F</td>
</tr>
<tr class="even">
<td align="center">2010-11-06</td>
<td align="center">Z5</td>
<td align="center">Hospital D</td>
<td align="center">2013-03-10</td>
<td align="center">E9</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2013-05-18</td>
<td align="center">R5</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2015-05-02</td>
<td align="center">R2</td>
<td align="center">Hospital B</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">F</td>
</tr>
<tr class="odd">
<td align="center">2015-07-14</td>
<td align="center">P2</td>
<td align="center">Hospital B</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">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-09-28</td>
<td align="center">G7</td>
<td align="center">Hospital D</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">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-04-01</td>
<td align="center">U4</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2013-08-12</td>
<td align="center">S7</td>
<td align="center">Hospital B</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">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-05-02</td>
<td align="center">K4</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-07-08</td>
<td align="center">E6</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="even">
<td align="center">2016-10-16</td>
<td align="center">Q1</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -422,16 +422,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,457</td>
<td align="right">52.29%</td>
<td align="right">10,457</td>
<td align="right">52.29%</td>
<td align="right">10,416</td>
<td align="right">52.08%</td>
<td align="right">10,416</td>
<td align="right">52.08%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,543</td>
<td align="right">47.72%</td>
<td align="right">9,584</td>
<td align="right">47.92%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -488,9 +488,9 @@ Longest: 1</p>
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,731 'phenotype-based' first isolates (53.7% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,729 'phenotype-based' first isolates (53.6% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.7% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<p>So only 53.6% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
@ -499,10 +499,10 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,731 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,729 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%">
@ -516,7 +516,7 @@ Longest: 1</p>
<col width="6%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="7%">
<col width="5%">
</colgroup>
<thead><tr class="header">
@ -537,41 +537,25 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2012-06-09</td>
<td align="center">Z9</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="left">2</td>
<td align="center">2013-04-01</td>
<td align="center">U4</td>
<td align="center">Hospital D</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">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="left">4</td>
<td align="center">2015-05-02</td>
<td align="center">R2</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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="left">5</td>
<td align="center">2015-07-14</td>
<td align="center">P2</td>
<td align="left">3</td>
<td align="center">2013-08-12</td>
<td align="center">S7</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
@ -584,14 +568,30 @@ Longest: 1</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2014-05-02</td>
<td align="center">K4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2012-06-15</td>
<td align="center">G7</td>
<td align="left">5</td>
<td align="center">2016-07-08</td>
<td align="center">E6</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</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">S</td>
<td align="center">M</td>
@ -601,35 +601,35 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">10</td>
<td align="center">2016-01-05</td>
<td align="center">N3</td>
<td align="left">7</td>
<td align="center">2017-02-23</td>
<td align="center">B4</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</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">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</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">11</td>
<td align="center">2017-09-24</td>
<td align="center">T7</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="left">9</td>
<td align="center">2016-11-10</td>
<td align="center">V1</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-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -653,8 +653,8 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,731<br>
Available: 10,731 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,729<br>
Available: 10,729 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -671,33 +671,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,682</td>
<td align="right">43.63%</td>
<td align="right">4,682</td>
<td align="right">43.63%</td>
<td align="right">4,633</td>
<td align="right">43.18%</td>
<td align="right">4,633</td>
<td align="right">43.18%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,733</td>
<td align="right">25.47%</td>
<td align="right">7,415</td>
<td align="right">69.10%</td>
<td align="right">2,796</td>
<td align="right">26.06%</td>
<td align="right">7,429</td>
<td align="right">69.24%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,132</td>
<td align="right">19.87%</td>
<td align="right">9,547</td>
<td align="right">88.97%</td>
<td align="right">2,137</td>
<td align="right">19.92%</td>
<td align="right">9,566</td>
<td align="right">89.16%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,184</td>
<td align="right">11.03%</td>
<td align="right">10,731</td>
<td align="right">1,163</td>
<td align="right">10.84%</td>
<td align="right">10,729</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -716,14 +716,14 @@ 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>
@ -744,43 +744,43 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-06-09</td>
<td align="center">Z9</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">S</td>
<td align="center">2017-02-23</td>
<td align="center">B4</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">F</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-05-02</td>
<td align="center">R2</td>
<td align="center">2016-01-27</td>
<td align="center">M1</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">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">2010-11-28</td>
<td align="center">Q9</td>
<td align="center">Hospital C</td>
<td align="center">2012-07-10</td>
<td align="center">U10</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">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@ -789,12 +789,12 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-11-10</td>
<td align="center">V1</td>
<td align="center">Hospital B</td>
<td align="center">2017-03-06</td>
<td align="center">X10</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">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
@ -804,30 +804,30 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-06-17</td>
<td align="center">Y3</td>
<td align="center">Hospital A</td>
<td align="center">2017-08-29</td>
<td align="center">F1</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-06-19</td>
<td align="center">H1</td>
<td align="center">Hospital D</td>
<td align="center">2014-05-24</td>
<td align="center">N8</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
@ -854,50 +854,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2224</td>
<td align="center">132</td>
<td align="center">2326</td>
<td align="center">4682</td>
<td align="center">2202</td>
<td align="center">119</td>
<td align="center">2312</td>
<td align="center">4633</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3427</td>
<td align="center">152</td>
<td align="center">1103</td>
<td align="center">4682</td>
<td align="center">3411</td>
<td align="center">175</td>
<td align="center">1047</td>
<td align="center">4633</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3453</td>
<td align="center">3383</td>
<td align="center">0</td>
<td align="center">1229</td>
<td align="center">4682</td>
<td align="center">1250</td>
<td align="center">4633</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4086</td>
<td align="center">4044</td>
<td align="center">0</td>
<td align="center">596</td>
<td align="center">4682</td>
<td align="center">589</td>
<td align="center">4633</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">1184</td>
<td align="center">1184</td>
<td align="center">1163</td>
<td align="center">1163</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">950</td>
<td align="center">43</td>
<td align="center">191</td>
<td align="center">1184</td>
<td align="center">917</td>
<td align="center">41</td>
<td align="center">205</td>
<td align="center">1163</td>
</tr>
</tbody>
</table>
@ -920,34 +920,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4086</td>
<td align="center">4044</td>
<td align="center">0</td>
<td align="center">596</td>
<td align="center">4682</td>
<td align="center">589</td>
<td align="center">4633</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1083</td>
<td align="center">1035</td>
<td align="center">0</td>
<td align="center">101</td>
<td align="center">1184</td>
<td align="center">128</td>
<td align="center">1163</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2453</td>
<td align="center">2484</td>
<td align="center">0</td>
<td align="center">280</td>
<td align="center">2733</td>
<td align="center">312</td>
<td align="center">2796</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">2132</td>
<td align="center">2132</td>
<td align="center">2137</td>
<td align="center">2137</td>
</tr>
</tbody>
</table>
@ -961,7 +961,7 @@ Longest: 24</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5461746</span></span></code></pre></div>
<span><span class="co"># [1] 0.5444123</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@ -975,19 +975,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5456783</td>
<td align="center">0.5464199</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5524140</td>
<td align="center">0.5451604</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5469820</td>
<td align="center">0.5317705</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5353107</td>
<td align="center">0.5496909</td>
</tr>
</tbody>
</table>
@ -1008,23 +1008,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5456783</td>
<td align="center">3251</td>
<td align="center">0.5464199</td>
<td align="center">3296</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5524140</td>
<td align="center">3749</td>
<td align="center">0.5451604</td>
<td align="center">3709</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5469820</td>
<td align="center">1607</td>
<td align="center">0.5317705</td>
<td align="center">1621</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5353107</td>
<td align="center">2124</td>
<td align="center">0.5496909</td>
<td align="center">2103</td>
</tr>
</tbody>
</table>
@ -1047,27 +1047,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7644169</td>
<td align="center">0.8727040</td>
<td align="center">0.9769329</td>
<td align="center">0.7740125</td>
<td align="center">0.8728686</td>
<td align="center">0.9769048</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8386824</td>
<td align="center">0.9146959</td>
<td align="center">0.9831081</td>
<td align="center">0.8237317</td>
<td align="center">0.8899398</td>
<td align="center">0.9724850</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7969265</td>
<td align="center">0.8975485</td>
<td align="center">0.9849982</td>
<td align="center">0.7914878</td>
<td align="center">0.8884120</td>
<td align="center">0.9846209</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5323640</td>
<td align="center">0.5297146</td>
<td align="center">0.0000000</td>
<td align="center">0.5323640</td>
<td align="center">0.5297146</td>
</tr>
</tbody>
</table>
@ -1093,22 +1093,22 @@ Longest: 24</p>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.6%</td>
<td align="right">25.6%</td>
<td align="right">27.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">55.2%</td>
<td align="right">27.5%</td>
<td align="right">54.5%</td>
<td align="right">26.0%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">54.7%</td>
<td align="right">26.1%</td>
<td align="right">53.2%</td>
<td align="right">25.6%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">53.5%</td>
<td align="right">26.5%</td>
<td align="right">55.0%</td>
<td align="right">26.9%</td>
</tr>
</tbody>
</table>
@ -1206,16 +1206,18 @@ Longest: 24</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 0.0625 0.0625 0.25 0.025 16 256 8 4 16 0.125 </span></span>
<span><span class="co"># [11] 16 0.0625 128 64 0.025 2 2 0.0625 0.25 0.025 </span></span>
<span><span class="co"># [21] 256 0.125 0.125 4 8 16 4 1 0.002 4 </span></span>
<span><span class="co"># [31] 1 8 1 0.001 16 0.002 64 16 32 0.002 </span></span>
<span><span class="co"># [41] 0.002 0.25 0.25 1 0.5 0.005 0.125 0.0625 4 8 </span></span>
<span><span class="co"># [51] 0.002 0.025 16 2 4 0.025 0.0625 256 64 4 </span></span>
<span><span class="co"># [61] 0.25 0.5 64 128 16 2 0.025 0.002 64 0.0625</span></span>
<span><span class="co"># [71] 64 0.5 0.001 0.025 2 0.5 8 64 0.25 256 </span></span>
<span><span class="co"># [81] 0.025 0.001 0.25 0.125 64 256 256 0.5 0.002 8 </span></span>
<span><span class="co"># [91] 64 64 0.5 4 0.5 0.125 2 32 0.01 0.25</span></span></code></pre></div>
<span><span class="co"># [1] &lt;=0.001 2 0.25 0.002 0.0625 1 0.002 32 1 </span></span>
<span><span class="co"># [10] 0.5 1 0.025 0.5 &lt;=0.001 0.005 4 &gt;=256 4 </span></span>
<span><span class="co"># [19] 8 1 16 0.002 &lt;=0.001 0.002 4 0.025 8 </span></span>
<span><span class="co"># [28] 16 16 1 0.25 &lt;=0.001 16 0.005 0.005 &lt;=0.001</span></span>
<span><span class="co"># [37] &lt;=0.001 16 &gt;=256 16 128 0.0625 1 0.25 0.005 </span></span>
<span><span class="co"># [46] 0.01 0.002 0.5 128 64 0.01 8 128 1 </span></span>
<span><span class="co"># [55] &gt;=256 &gt;=256 1 0.125 &lt;=0.001 0.25 64 2 0.002 </span></span>
<span><span class="co"># [64] &gt;=256 16 1 &gt;=256 0.5 8 &gt;=256 &gt;=256 0.005 </span></span>
<span><span class="co"># [73] 0.002 2 0.25 0.25 &lt;=0.001 0.0625 0.01 0.125 1 </span></span>
<span><span class="co"># [82] 0.005 0.125 0.25 2 0.025 0.025 32 1 0.25 </span></span>
<span><span class="co"># [91] 0.005 0.01 1 0.5 1 0.0625 0.5 4 1 </span></span>
<span><span class="co"># [100] 64</span></span></code></pre></div>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1242,10 +1244,10 @@ Longest: 24</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 30 27 25 26 26 30 31 29 25 26 25 22 17 25 18 20 18 30 31 28 22 29 26 17 21</span></span>
<span><span class="co"># [26] 27 30 26 29 28 22 21 26 20 24 26 30 27 25 26 30 17 20 18 20 21 24 20 18 21</span></span>
<span><span class="co"># [51] 27 23 23 26 24 20 29 21 22 26 31 28 26 25 18 26 21 19 21 18 23 30 19 27 25</span></span>
<span><span class="co"># [76] 31 31 21 30 24 28 28 26 29 25 23 19 20 29 20 18 17 28 21 28 27 17 21 18 25</span></span></code></pre></div>
<span><span class="co"># [1] 27 30 17 21 31 26 25 21 24 31 20 28 23 26 30 22 30 17 23 29 24 30 23 26 19</span></span>
<span><span class="co"># [26] 29 24 23 19 19 30 27 23 31 27 26 24 27 26 20 17 22 29 17 23 20 19 26 28 30</span></span>
<span><span class="co"># [51] 21 30 23 30 30 17 26 25 30 20 24 27 24 20 28 23 22 22 29 18 20 27 22 22 17</span></span>
<span><span class="co"># [76] 30 19 27 27 23 19 23 31 19 26 30 25 22 23 27 28 19 29 19 19 26 26 17 23 17</span></span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>