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@ -44,7 +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">1.7.1.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
</span>
</div>
@ -174,13 +174,6 @@
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Survey
</a>
</li>
</ul>
</div>
@ -198,7 +191,7 @@
<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">17 August 2021</h4>
<h4 data-toc-skip class="date">29 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>
@ -207,7 +200,7 @@
<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 17 August 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 29 August 2021.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor" aria-hidden="true"></a>Introduction</h1>
@ -238,21 +231,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2021-08-17</td>
<td align="center">2021-08-29</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">2021-08-17</td>
<td align="center">2021-08-29</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">2021-08-17</td>
<td align="center">2021-08-29</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -349,68 +342,68 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-12-11</td>
<td align="center">B5</td>
<td align="center">Hospital D</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">M</td>
</tr>
<tr class="even">
<td align="center">2012-01-03</td>
<td align="center">D5</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">2013-03-20</td>
<td align="center">E3</td>
<td align="center">2012-06-29</td>
<td align="center">E6</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-02-14</td>
<td align="center">L5</td>
<td align="center">Hospital B</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">2010-04-27</td>
<td align="center">Y6</td>
<tr class="even">
<td align="center">2014-08-25</td>
<td align="center">D8</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2017-01-14</td>
<td align="center">V1</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">I</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">2011-08-04</td>
<td align="center">O2</td>
<td align="center">2010-10-15</td>
<td align="center">X2</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">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2011-04-05</td>
<td align="center">H6</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</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">2012-01-10</td>
<td align="center">Y7</td>
<td align="center">Hospital D</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">S</td>
<td align="center">F</td>
</tr>
@ -446,16 +439,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,443</td>
<td align="right">52.22%</td>
<td align="right">10,443</td>
<td align="right">52.22%</td>
<td align="right">10,326</td>
<td align="right">51.63%</td>
<td align="right">10,326</td>
<td align="right">51.63%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,557</td>
<td align="right">47.79%</td>
<td align="right">9,674</td>
<td align="right">48.37%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -510,9 +503,9 @@ 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 10,606 first weighted isolates (phenotype-based, 53.0% of total</span>
<span class="co"># =&gt; Found 10,571 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 53.0% 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>
@ -520,7 +513,7 @@ 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 10,606 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,571 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">
@ -559,27 +552,11 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2012-12-11</td>
<td align="center">B5</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">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2012-01-03</td>
<td align="center">D5</td>
<td align="center">Hospital B</td>
<td align="center">2012-06-29</td>
<td align="center">E6</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_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">S</td>
@ -589,14 +566,14 @@ 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">2017-02-14</td>
<td align="center">L5</td>
<td align="center">Hospital B</td>
<tr class="even">
<td align="left">2</td>
<td align="center">2014-08-25</td>
<td align="center">D8</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">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
@ -605,52 +582,68 @@ Longest: 1</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2012-03-07</td>
<td align="center">I8</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">9</td>
<td align="center">2010-12-20</td>
<td align="center">H10</td>
<td align="left">4</td>
<td align="center">2010-10-15</td>
<td align="center">X2</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">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">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">11</td>
<td align="center">2014-01-24</td>
<td align="center">M2</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="left">6</td>
<td align="center">2012-01-10</td>
<td align="center">Y7</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="odd">
<td align="left">8</td>
<td align="center">2016-02-07</td>
<td align="center">V2</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2016-11-08</td>
<td align="center">D4</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -674,8 +667,8 @@ 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: 10,606<br>
Available: 10,606 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,571<br>
Available: 10,571 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -692,33 +685,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,494</td>
<td align="right">42.37%</td>
<td align="right">4,494</td>
<td align="right">42.37%</td>
<td align="right">4,507</td>
<td align="right">42.64%</td>
<td align="right">4,507</td>
<td align="right">42.64%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,785</td>
<td align="right">26.26%</td>
<td align="right">7,279</td>
<td align="right">68.63%</td>
<td align="right">2,799</td>
<td align="right">26.48%</td>
<td align="right">7,306</td>
<td align="right">69.11%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,106</td>
<td align="right">19.86%</td>
<td align="right">9,385</td>
<td align="right">88.49%</td>
<td align="right">2,087</td>
<td align="right">19.74%</td>
<td align="right">9,393</td>
<td align="right">88.86%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,221</td>
<td align="right">11.51%</td>
<td align="right">10,606</td>
<td align="right">1,178</td>
<td align="right">11.14%</td>
<td align="right">10,571</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -765,8 +758,83 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-12-11</td>
<td align="center">B5</td>
<td align="center">2010-10-15</td>
<td align="center">X2</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-01-10</td>
<td align="center">Y7</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="odd">
<td align="center">2014-02-02</td>
<td align="center">K7</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">2011-08-05</td>
<td align="center">V3</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="center">2014-06-16</td>
<td align="center">Z8</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="even">
<td align="center">2017-08-23</td>
<td align="center">J10</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
@ -779,81 +847,6 @@ Longest: 24</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-06-11</td>
<td align="center">L7</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">2012-12-19</td>
<td align="center">A10</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">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">2014-12-05</td>
<td align="center">M6</td>
<td align="center">Hospital B</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">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-05-14</td>
<td align="center">L8</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">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2010-12-14</td>
<td align="center">Q1</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> function:</p>
@ -875,50 +868,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2137</td>
<td align="center">139</td>
<td align="center">2218</td>
<td align="center">4494</td>
<td align="center">2196</td>
<td align="center">119</td>
<td align="center">2192</td>
<td align="center">4507</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3298</td>
<td align="center">157</td>
<td align="center">1039</td>
<td align="center">4494</td>
<td align="center">3378</td>
<td align="center">151</td>
<td align="center">978</td>
<td align="center">4507</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3230</td>
<td align="center">3282</td>
<td align="center">0</td>
<td align="center">1264</td>
<td align="center">4494</td>
<td align="center">1225</td>
<td align="center">4507</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">3946</td>
<td align="center">3929</td>
<td align="center">0</td>
<td align="center">548</td>
<td align="center">4494</td>
<td align="center">578</td>
<td align="center">4507</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">1221</td>
<td align="center">1221</td>
<td align="center">1178</td>
<td align="center">1178</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">967</td>
<td align="center">44</td>
<td align="center">210</td>
<td align="center">1221</td>
<td align="center">930</td>
<td align="center">45</td>
<td align="center">203</td>
<td align="center">1178</td>
</tr>
</tbody>
</table>
@ -941,34 +934,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">3946</td>
<td align="center">3929</td>
<td align="center">0</td>
<td align="center">548</td>
<td align="center">4494</td>
<td align="center">578</td>
<td align="center">4507</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1088</td>
<td align="center">1052</td>
<td align="center">0</td>
<td align="center">133</td>
<td align="center">1221</td>
<td align="center">126</td>
<td align="center">1178</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2490</td>
<td align="center">2473</td>
<td align="center">0</td>
<td align="center">295</td>
<td align="center">2785</td>
<td align="center">326</td>
<td align="center">2799</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">2106</td>
<td align="center">2106</td>
<td align="center">2087</td>
<td align="center">2087</td>
</tr>
</tbody>
</table>
@ -982,7 +975,7 @@ 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] 0.5427117</span></code></pre></div>
<span class="co"># [1] 0.5403462</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>
@ -996,19 +989,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5356582</td>
<td align="center">0.5487147</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5408108</td>
<td align="center">0.5436519</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5371153</td>
<td align="center">0.5257549</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5614714</td>
<td align="center">0.5338095</td>
</tr>
</tbody>
</table>
@ -1027,23 +1020,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5356582</td>
<td align="center">3183</td>
<td align="center">0.5487147</td>
<td align="center">3151</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5408108</td>
<td align="center">3700</td>
<td align="center">0.5436519</td>
<td align="center">3631</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5371153</td>
<td align="center">1657</td>
<td align="center">0.5257549</td>
<td align="center">1689</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5614714</td>
<td align="center">2066</td>
<td align="center">0.5338095</td>
<td align="center">2100</td>
</tr>
</tbody>
</table>
@ -1064,27 +1057,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7688028</td>
<td align="center">0.8780596</td>
<td align="center">0.9815309</td>
<td align="center">0.7830042</td>
<td align="center">0.8717550</td>
<td align="center">0.9764810</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8280098</td>
<td align="center">0.8910729</td>
<td align="center">0.9754300</td>
<td align="center">0.8276740</td>
<td align="center">0.8930390</td>
<td align="center">0.9787776</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7921005</td>
<td align="center">0.8940754</td>
<td align="center">0.9795332</td>
<td align="center">0.7874241</td>
<td align="center">0.8835298</td>
<td align="center">0.9828510</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5351377</td>
<td align="center">0.5318639</td>
<td align="center">0.0000000</td>
<td align="center">0.5351377</td>
<td align="center">0.5318639</td>
</tr>
</tbody>
</table>
@ -1109,23 +1102,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">53.6%</td>
<td align="right">26.4%</td>
<td align="right">54.9%</td>
<td align="right">25.8%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.1%</td>
<td align="right">24.6%</td>
<td align="right">54.4%</td>
<td align="right">27.8%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">53.7%</td>
<td align="right">27.5%</td>
<td align="right">52.6%</td>
<td align="right">25.0%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">56.1%</td>
<td align="right">29.0%</td>
<td align="right">53.4%</td>
<td align="right">24.3%</td>
</tr>
</tbody>
</table>
@ -1209,16 +1202,16 @@ 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] 0.25 16 0.0625 32 0.025 1 256 64 0.002 0.005 </span>
<span class="co"># [11] 0.01 0.005 8 0.01 0.025 128 0.01 8 0.005 256 </span>
<span class="co"># [21] 0.005 8 0.0625 0.125 0.005 16 8 2 0.5 4 </span>
<span class="co"># [31] 2 32 0.25 0.25 8 0.025 0.25 8 64 1 </span>
<span class="co"># [41] 0.005 0.01 0.005 256 0.025 0.5 2 0.025 0.5 0.005 </span>
<span class="co"># [51] 0.0625 128 4 1 0.0625 0.002 16 0.002 8 0.005 </span>
<span class="co"># [61] 1 1 8 32 0.002 32 0.25 8 4 0.001 </span>
<span class="co"># [71] 2 16 16 0.025 0.005 0.0625 2 128 0.001 2 </span>
<span class="co"># [81] 64 0.025 16 64 2 128 8 0.5 4 256 </span>
<span class="co"># [91] 0.5 32 0.001 0.01 2 64 4 32 4 0.0625</span></code></pre></div>
<span class="co"># [1] 1 128 0.01 0.25 0.01 16 0.001 0.125 0.25 0.01 </span>
<span class="co"># [11] 0.005 16 0.0625 64 &gt;=256 0.5 0.01 16 0.5 0.0625</span>
<span class="co"># [21] 0.001 0.5 0.0625 4 2 8 0.5 0.0625 0.125 128 </span>
<span class="co"># [31] 0.002 0.25 2 8 0.125 0.0625 0.125 16 128 0.002 </span>
<span class="co"># [41] 1 0.005 2 32 0.01 0.0625 &gt;=256 64 16 0.005 </span>
<span class="co"># [51] 2 0.001 &gt;=256 32 64 &gt;=256 128 0.01 0.005 0.001 </span>
<span class="co"># [61] 0.01 0.125 2 0.125 &gt;=256 32 64 0.01 2 0.25 </span>
<span class="co"># [71] 0.01 64 0.5 128 0.001 64 128 0.002 &gt;=256 64 </span>
<span class="co"># [81] 0.01 8 0.5 4 16 0.025 0.025 0.001 0.125 0.025 </span>
<span class="co"># [91] 2 64 64 128 32 128 0.001 32 2 0.005</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>
@ -1247,10 +1240,10 @@ 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] 26 25 28 21 24 22 21 27 22 21 31 25 26 17 28 29 18 31 21 30 23 28 22 18 28</span>
<span class="co"># [26] 21 25 26 18 30 22 28 25 28 25 21 29 26 19 21 19 26 31 17 25 22 21 27 24 26</span>
<span class="co"># [51] 20 17 18 27 31 31 20 31 26 22 25 22 19 22 27 19 25 27 30 17 24 27 22 28 18</span>
<span class="co"># [76] 26 30 29 25 23 26 29 19 25 25 24 25 30 29 25 29 17 26 21 20 29 26 23 29 31</span></code></pre></div>
<span class="co"># [1] 30 29 25 23 27 18 23 21 31 26 17 30 18 31 30 25 22 19 18 26 31 19 21 25 29</span>
<span class="co"># [26] 22 26 30 20 20 18 19 18 29 22 17 27 21 24 18 17 23 27 18 19 31 18 29 30 25</span>
<span class="co"># [51] 27 23 21 20 31 19 19 25 25 23 23 19 17 25 21 30 20 31 26 23 29 27 30 29 24</span>
<span class="co"># [76] 20 23 23 27 20 24 19 28 24 31 29 26 23 20 29 23 18 17 27 21 28 28 17 23 17</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>