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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9014</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">18 May 2020</h4>
<h4 class="date">19 May 2020</h4>
<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/AMR.Rmd"><code>vignettes/AMR.Rmd</code></a></small>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -195,7 +195,7 @@
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 18 May 2020.</p>
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 19 May 2020.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -226,21 +226,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2020-05-18</td>
<td align="center">2020-05-19</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">2020-05-18</td>
<td align="center">2020-05-19</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">2020-05-18</td>
<td align="center">2020-05-19</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -251,14 +251,15 @@
<div id="needed-r-packages" class="section level2">
<h2 class="hasAnchor">
<a href="#needed-r-packages" class="anchor"></a>Needed R packages</h2>
<p>As with many uses in R, we need some additional packages for AMR analysis. Our package works closely together with the <a href="https://www.tidyverse.org">tidyverse packages</a> <a href="https://dplyr.tidyverse.org/"><code>dplyr</code></a> and <a href="https://ggplot2.tidyverse.org"><code>ggplot2</code></a> by Dr Hadley Wickham. The tidyverse tremendously improves the way we conduct data science - it allows for a very natural way of writing syntaxes and creating beautiful plots in R.</p>
<p>Our <code>AMR</code> package depends on these packages and even extends their use and functions.</p>
<p>As with many uses in R, we need some additional packages for AMR analysis. Our package works closely together with the <a href="https://www.tidyverse.org">tidyverse packages</a> <a href="https://dplyr.tidyverse.org/"><code>dplyr</code></a> and <a href="https://ggplot2.tidyverse.org"><code>ggplot2</code></a> by RStudio. The tidyverse tremendously improves the way we conduct data science - it allows for a very natural way of writing syntaxes and creating beautiful plots in R.</p>
<p>We will also use the <code>cleaner</code> package, that can be used for cleaning data and creating frequency tables.</p>
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">ggplot2</span>)
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">AMR</span>)
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">cleaner</span>)
<span class="co"># (if not yet installed, install with:)</span>
<span class="co"># install.packages(c("dplyr", "ggplot2", "AMR"))</span></pre></body></html></div>
<span class="co"># install.packages(c("dplyr", "ggplot2", "AMR", "cleaner"))</span></pre></body></html></div>
</div>
</div>
<div id="creation-of-data" class="section level1">
@ -335,68 +336,68 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-06-23</td>
<td align="center">V9</td>
<td align="center">Hospital C</td>
<td align="center">2017-01-17</td>
<td align="center">W7</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-12-25</td>
<td align="center">S10</td>
<td align="center">Hospital D</td>
<td align="center">2017-01-15</td>
<td align="center">S1</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2011-01-27</td>
<td align="center">Z10</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">2014-03-03</td>
<td align="center">F8</td>
<td align="center">Hospital D</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">F</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-09-14</td>
<td align="center">N1</td>
<td align="center">2013-10-12</td>
<td align="center">K3</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">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2017-10-31</td>
<td align="center">W1</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">2017-07-30</td>
<td align="center">Y4</td>
<td align="center">Hospital B</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">F</td>
</tr>
<tr class="even">
<td align="center">2014-03-29</td>
<td align="center">L4</td>
<td align="center">Hospital B</td>
<td align="center">2011-01-18</td>
<td align="center">B4</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
@ -408,9 +409,9 @@
<div id="cleaning-the-data" class="section level1">
<h1 class="hasAnchor">
<a href="#cleaning-the-data" class="anchor"></a>Cleaning the data</h1>
<p>We also created a package dedicated to data cleaning and checking, called the <code>cleaner</code> package. It gets automatically installed with the <code>AMR</code> package. For its <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function to create frequency tables, you don’t even need to load it yourself as it is available through the <code>AMR</code> package as well.</p>
<p>We also created a package dedicated to data cleaning and checking, called the <code>cleaner</code> package. It <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function can be used to create frequency tables.</p>
<p>For example, for the <code>gender</code> variable:</p>
<div class="sourceCode" id="cb10"><html><body><pre class="r"><span class="no">data</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">gender</span>) <span class="co"># this would be the same: freq(data$gender)</span></pre></body></html></div>
<div class="sourceCode" id="cb10"><html><body><pre class="r"><span class="no">data</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">gender</span>)</pre></body></html></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 20,000<br>
@ -431,16 +432,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,293</td>
<td align="right">51.47%</td>
<td align="right">10,293</td>
<td align="right">51.47%</td>
<td align="right">10,336</td>
<td align="right">51.68%</td>
<td align="right">10,336</td>
<td align="right">51.68%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,707</td>
<td align="right">48.54%</td>
<td align="right">9,664</td>
<td align="right">48.32%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -480,7 +481,7 @@ Longest: 1</p>
<span class="co"># [34mNOTE: Using column `[1mbacteria[22m` as input for `col_mo`.[39m</span>
<span class="co"># [34mNOTE: Using column `[1mdate[22m` as input for `col_date`.[39m</span>
<span class="co"># [34mNOTE: Using column `[1mpatient_id[22m` as input for `col_patient_id`.[39m</span></pre></body></html></div>
<p>So only 28.6% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<p>So only 28.3% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb16"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">&lt;-</span> <span class="no">data</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="no">first</span> <span class="kw">==</span> <span class="fl">TRUE</span>)</pre></body></html></div>
<p>For future use, the above two syntaxes can be shortened with the <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> function:</p>
@ -490,7 +491,7 @@ Longest: 1</p>
<div id="first-weighted-isolates" class="section level2">
<h2 class="hasAnchor">
<a href="#first-weighted-isolates" class="anchor"></a>First <em>weighted</em> isolates</h2>
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient N1, sorted on date:</p>
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient T4, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -506,21 +507,21 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-03-16</td>
<td align="center">N1</td>
<td align="center">2010-02-08</td>
<td align="center">T4</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">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-04-19</td>
<td align="center">N1</td>
<td align="center">2010-03-28</td>
<td align="center">T4</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>
@ -528,8 +529,8 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-06-26</td>
<td align="center">N1</td>
<td align="center">2010-06-15</td>
<td align="center">T4</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -539,52 +540,30 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-07-17</td>
<td align="center">N1</td>
<td align="center">2010-07-21</td>
<td align="center">T4</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">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-09-14</td>
<td align="center">N1</td>
<td align="center">2011-01-20</td>
<td align="center">T4</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">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-09-23</td>
<td align="center">N1</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">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-12-14</td>
<td align="center">N1</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">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-07-30</td>
<td align="center">N1</td>
<td align="center">2011-04-24</td>
<td align="center">T4</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -593,24 +572,46 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-08-21</td>
<td align="center">N1</td>
<td align="center">7</td>
<td align="center">2011-06-20</td>
<td align="center">T4</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-06-23</td>
<td align="center">T4</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">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-09-20</td>
<td align="center">T4</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">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-09-09</td>
<td align="center">N1</td>
<td align="center">2011-10-08</td>
<td align="center">T4</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">S</td>
<td align="center">FALSE</td>
</tr>
@ -642,131 +643,131 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-03-16</td>
<td align="center">N1</td>
<td align="center">2010-02-08</td>
<td align="center">T4</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">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-04-19</td>
<td align="center">N1</td>
<td align="center">2010-03-28</td>
<td align="center">T4</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>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-06-26</td>
<td align="center">N1</td>
<td align="center">2010-06-15</td>
<td align="center">T4</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">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-07-17</td>
<td align="center">N1</td>
<td align="center">2010-07-21</td>
<td align="center">T4</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">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-09-14</td>
<td align="center">N1</td>
<td align="center">2011-01-20</td>
<td align="center">T4</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">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-09-23</td>
<td align="center">N1</td>
<td align="center">2011-04-24</td>
<td align="center">T4</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">FALSE</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-12-14</td>
<td align="center">N1</td>
<td align="center">2011-06-20</td>
<td align="center">T4</td>
<td align="center">B_ESCHR_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">S</td>
<td align="center">FALSE</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-07-30</td>
<td align="center">N1</td>
<td align="center">2011-06-23</td>
<td align="center">T4</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">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">R</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-08-21</td>
<td align="center">N1</td>
<td align="center">2011-09-20</td>
<td align="center">T4</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">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-09-09</td>
<td align="center">N1</td>
<td align="center">2011-10-08</td>
<td align="center">T4</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">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Instead of 2, now 4 isolates are flagged. In total, 75.4% of all isolates are marked ‘first weighted’ - 46.8% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>Instead of 2, now 10 isolates are flagged. In total, 75.2% of all isolates are marked ‘first weighted’ - 46.9% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>As with <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
<div class="sourceCode" id="cb19"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">&lt;-</span> <span class="no">data</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</pre></body></html></div>
<p>So we end up with 15,085 isolates for analysis.</p>
<p>So we end up with 15,048 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb20"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">&lt;-</span> <span class="no">data_1st</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(-<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">first</span>, <span class="no">keyab</span>))</pre></body></html></div>
@ -792,9 +793,9 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td>1</td>
<td align="center">2013-06-23</td>
<td align="center">V9</td>
<td align="center">Hospital C</td>
<td align="center">2017-01-17</td>
<td align="center">W7</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
@ -808,14 +809,14 @@ Longest: 1</p>
</tr>
<tr class="even">
<td>2</td>
<td align="center">2016-12-25</td>
<td align="center">S10</td>
<td align="center">Hospital D</td>
<td align="center">2017-01-15</td>
<td align="center">S1</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
@ -824,66 +825,66 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td>3</td>
<td align="center">2011-01-27</td>
<td align="center">Z10</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">2014-03-03</td>
<td align="center">F8</td>
<td align="center">Hospital D</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">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</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>
<tr class="even">
<td>4</td>
<td align="center">2010-09-14</td>
<td align="center">N1</td>
<td>5</td>
<td align="center">2017-07-30</td>
<td align="center">Y4</td>
<td align="center">Hospital B</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">R</td>
<td align="center">R</td>
<td align="center">M</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>5</td>
<td align="center">2017-10-31</td>
<td align="center">W1</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td>6</td>
<td align="center">2011-01-18</td>
<td align="center">B4</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">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>7</td>
<td align="center">2010-03-02</td>
<td align="center">W2</td>
<td align="center">2013-05-01</td>
<td align="center">G7</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">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -905,8 +906,8 @@ Longest: 1</p>
<div class="sourceCode" id="cb23"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">genus</span>, <span class="no">species</span>)</pre></body></html></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 15,085<br>
Available: 15,085 (100%, NA: 0 = 0%)<br>
Length: 15,048<br>
Available: 15,048 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -923,33 +924,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,418</td>
<td align="right">49.17%</td>
<td align="right">7,418</td>
<td align="right">49.17%</td>
<td align="right">7,376</td>
<td align="right">49.02%</td>
<td align="right">7,376</td>
<td align="right">49.02%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,716</td>
<td align="right">24.63%</td>
<td align="right">11,134</td>
<td align="right">73.81%</td>
<td align="right">3,819</td>
<td align="right">25.38%</td>
<td align="right">11,195</td>
<td align="right">74.40%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,404</td>
<td align="right">15.94%</td>
<td align="right">13,538</td>
<td align="right">89.74%</td>
<td align="right">2,330</td>
<td align="right">15.48%</td>
<td align="right">13,525</td>
<td align="right">89.88%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,547</td>
<td align="right">10.26%</td>
<td align="right">15,085</td>
<td align="right">1,523</td>
<td align="right">10.12%</td>
<td align="right">15,048</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -961,7 +962,7 @@ Longest: 24</p>
<p>The functions <code><a href="../reference/proportion.html">resistance()</a></code> and <code><a href="../reference/proportion.html">susceptibility()</a></code> can be used to calculate antimicrobial resistance or susceptibility. For more specific analyses, the functions <code><a href="../reference/proportion.html">proportion_S()</a></code>, <code><a href="../reference/proportion.html">proportion_SI()</a></code>, <code><a href="../reference/proportion.html">proportion_I()</a></code>, <code><a href="../reference/proportion.html">proportion_IR()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code> can be used to determine the proportion of a specific antimicrobial outcome.</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="cb24"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="no">AMX</span>)
<span class="co"># [1] 0.4658933</span></pre></body></html></div>
<span class="co"># [1] 0.4628522</span></pre></body></html></div>
<p>Or can be used in conjuction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb25"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="no">hospital</span>) <span class="kw">%&gt;%</span>
@ -974,19 +975,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4701310</td>
<td align="center">0.4566180</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4702970</td>
<td align="center">0.4606292</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4575579</td>
<td align="center">0.4775330</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4574359</td>
<td align="center">0.4650083</td>
</tr>
</tbody>
</table>
@ -1004,23 +1005,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4701310</td>
<td align="center">4503</td>
<td align="center">0.4566180</td>
<td align="center">4518</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4702970</td>
<td align="center">5454</td>
<td align="center">0.4606292</td>
<td align="center">5245</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4575579</td>
<td align="center">2203</td>
<td align="center">0.4775330</td>
<td align="center">2270</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4574359</td>
<td align="center">2925</td>
<td align="center">0.4650083</td>
<td align="center">3015</td>
</tr>
</tbody>
</table>
@ -1040,27 +1041,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.9207334</td>
<td align="center">0.8959288</td>
<td align="center">0.9936641</td>
<td align="center">0.9197397</td>
<td align="center">0.8889642</td>
<td align="center">0.9940347</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.9198449</td>
<td align="center">0.9004525</td>
<td align="center">0.9974144</td>
<td align="center">0.9277741</td>
<td align="center">0.8929744</td>
<td align="center">0.9954038</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.9203445</td>
<td align="center">0.9233046</td>
<td align="center">0.9938105</td>
<td align="center">0.9316575</td>
<td align="center">0.9279916</td>
<td align="center">0.9963341</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.6110649</td>
<td align="center">0.6253219</td>
<td align="center">0.0000000</td>
<td align="center">0.6110649</td>
<td align="center">0.6253219</td>
</tr>
</tbody>
</table>