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@ -187,13 +187,13 @@
</header><script src="AMR_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
</header><script src="AMR_files/header-attrs-2.3/header-attrs.js"></script><script src="AMR_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">30 September 2020</h4>
<h4 class="date">08 October 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd"><code>vignettes/AMR.Rmd</code></a></small>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -202,7 +202,7 @@
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 30 September 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 08 October 2020.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -233,21 +233,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2020-09-30</td>
<td align="center">2020-10-08</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">2020-09-30</td>
<td align="center">2020-10-08</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">2020-09-30</td>
<td align="center">2020-10-08</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -361,69 +361,69 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-08-26</td>
<td align="center">P9</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-09-24</td>
<td align="center">T6</td>
<td align="center">Hospital B</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">F</td>
</tr>
<tr class="odd">
<td align="center">2017-04-02</td>
<td align="center">X1</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella 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">2016-12-13</td>
<td align="center">F1</td>
<td align="center">2014-02-15</td>
<td align="center">Y9</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</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">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-05-11</td>
<td align="center">J4</td>
<td align="center">Hospital C</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">2012-02-05</td>
<td align="center">O8</td>
<td align="center">2013-06-10</td>
<td align="center">J1</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">M</td>
</tr>
<tr class="even">
<td align="center">2013-02-02</td>
<td align="center">U4</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="odd">
<td align="center">2015-12-04</td>
<td align="center">S10</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">2017-06-17</td>
<td align="center">K1</td>
<td align="center">2016-09-17</td>
<td align="center">G2</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
</tbody>
@ -459,16 +459,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,232</td>
<td align="right">51.16%</td>
<td align="right">10,232</td>
<td align="right">51.16%</td>
<td align="right">10,310</td>
<td align="right">51.55%</td>
<td align="right">10,310</td>
<td align="right">51.55%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,768</td>
<td align="right">48.84%</td>
<td align="right">9,690</td>
<td align="right">48.45%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -485,7 +485,7 @@ Longest: 1</p>
<span class="kw">data</span> <span class="op">&lt;-</span> <span class="kw">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(<span class="kw">AMX</span><span class="op">:</span><span class="kw">GEN</span>), <span class="kw">as.rsi</span>)
</pre></div>
<p>Finally, we will apply <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST rules</a> on our antimicrobial results. In Europe, most medical microbiological laboratories already apply these rules. Our package features their latest insights on intrinsic resistance and exceptional phenotypes. Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p>
<p>Finally, we will apply <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST rules</a> on our antimicrobial results. In Europe, most medical microbiological laboratories already apply these rules. Our package features their latest insights on intrinsic resistance and exceptional phenotypes. Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p>
<p>Because the amoxicillin (column <code>AMX</code>) and amoxicillin/clavulanic acid (column <code>AMC</code>) in our data were generated randomly, some rows will undoubtedly contain AMX = S and AMC = R, which is technically impossible. The <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> fixes this:</p>
<div class="sourceCode" id="cb13"><pre class="downlit">
<span class="kw">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="kw">data</span>, col_mo = <span class="st">"bacteria"</span>, rules = <span class="st">"all"</span>)
@ -506,7 +506,7 @@ Longest: 1</p>
<h2 class="hasAnchor">
<a href="#first-isolates" class="anchor"></a>First isolates</h2>
<p>We also need to know which isolates we can <em>actually</em> use for analysis.</p>
<p>To conduct an analysis of antimicrobial resistance, you must <a href="https://www.ncbi.nlm.nih.gov/pubmed/17304462">only include the first isolate of every patient per episode</a> (Hindler <em>et al.</em>, Clin Infect Dis. 2007). If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following weeks (yes, some countries like the Netherlands have these blood drawing policies). The resistance percentage of oxacillin of all isolates would be overestimated, because you included this MRSA more than once. It would clearly be <a href="https://en.wikipedia.org/wiki/Selection_bias">selection bias</a>.</p>
<p>To conduct an analysis of antimicrobial resistance, you must <a href="https:/pubmed.ncbi.nlm.nih.gov/17304462/">only include the first isolate of every patient per episode</a> (Hindler <em>et al.</em>, Clin Infect Dis. 2007). If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following weeks (yes, some countries like the Netherlands have these blood drawing policies). The resistance percentage of oxacillin of all isolates would be overestimated, because you included this MRSA more than once. It would clearly be <a href="https://en.wikipedia.org/wiki/Selection_bias">selection bias</a>.</p>
<p>The Clinical and Laboratory Standards Institute (CLSI) appoints this as follows:</p>
<blockquote>
<p><em>(…) When preparing a cumulative antibiogram to guide clinical decisions about empirical antimicrobial therapy of initial infections, <strong>only the first isolate of a given species per patient, per analysis period (eg, one year) should be included, irrespective of body site, antimicrobial susceptibility profile, or other phenotypical characteristics (eg, biotype)</strong>. The first isolate is easily identified, and cumulative antimicrobial susceptibility test data prepared using the first isolate are generally comparable to cumulative antimicrobial susceptibility test data calculated by other methods, providing duplicate isolates are excluded.</em> <br><a href="https://clsi.org/standards/products/microbiology/documents/m39/">M39-A4 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition. CLSI, 2014. Chapter 6.4</a></p>
@ -533,7 +533,7 @@ 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 Z5, 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 T8, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -549,74 +549,74 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-02-11</td>
<td align="center">Z5</td>
<td align="center">2010-04-04</td>
<td align="center">T8</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">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-04-11</td>
<td align="center">Z5</td>
<td align="center">2010-10-03</td>
<td align="center">T8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-05-31</td>
<td align="center">Z5</td>
<td align="center">2010-10-19</td>
<td align="center">T8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</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>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2011-03-29</td>
<td align="center">Z5</td>
<td align="center">2011-01-12</td>
<td align="center">T8</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">TRUE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2011-04-23</td>
<td align="center">Z5</td>
<td align="center">2011-02-03</td>
<td align="center">T8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-05-06</td>
<td align="center">Z5</td>
<td align="center">2011-04-04</td>
<td align="center">T8</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>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-09-05</td>
<td align="center">Z5</td>
<td align="center">2011-05-23</td>
<td align="center">T8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
@ -626,19 +626,19 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-09-29</td>
<td align="center">Z5</td>
<td align="center">2011-06-09</td>
<td align="center">T8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-11-16</td>
<td align="center">Z5</td>
<td align="center">2011-07-02</td>
<td align="center">T8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -648,13 +648,13 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-11-26</td>
<td align="center">Z5</td>
<td align="center">2011-12-05</td>
<td align="center">T8</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>
</tbody>
@ -687,133 +687,133 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-02-11</td>
<td align="center">Z5</td>
<td align="center">2010-04-04</td>
<td align="center">T8</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">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-04-11</td>
<td align="center">Z5</td>
<td align="center">2010-10-03</td>
<td align="center">T8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-05-31</td>
<td align="center">Z5</td>
<td align="center">2010-10-19</td>
<td align="center">T8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</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">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2011-03-29</td>
<td align="center">Z5</td>
<td align="center">2011-01-12</td>
<td align="center">T8</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">TRUE</td>
<td align="center">TRUE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2011-04-23</td>
<td align="center">Z5</td>
<td align="center">2011-02-03</td>
<td align="center">T8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-05-06</td>
<td align="center">Z5</td>
<td align="center">2011-04-04</td>
<td align="center">T8</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>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-09-05</td>
<td align="center">Z5</td>
<td align="center">2011-05-23</td>
<td align="center">T8</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">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-09-29</td>
<td align="center">Z5</td>
<td align="center">2011-06-09</td>
<td align="center">T8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-11-16</td>
<td align="center">Z5</td>
<td align="center">2011-07-02</td>
<td align="center">T8</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">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-11-26</td>
<td align="center">Z5</td>
<td align="center">2011-12-05</td>
<td align="center">T8</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 10 isolates are flagged. In total, 78.6% of all isolates are marked ‘first weighted’ - 50.1% 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 4 isolates are flagged. In total, 78.7% of all isolates are marked ‘first weighted’ - 50.2% 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"><pre class="downlit">
<span class="kw">data_1st</span> <span class="op">&lt;-</span> <span class="kw">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()
</pre></div>
<p>So we end up with 15,718 isolates for analysis.</p>
<p>So we end up with 15,741 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb20"><pre class="downlit">
<span class="kw">data_1st</span> <span class="op">&lt;-</span> <span class="kw">data_1st</span> <span class="op">%&gt;%</span>
@ -836,7 +836,7 @@ Longest: 1</p>
<col width="3%">
<col width="5%">
<col width="10%">
<col width="11%">
<col width="10%">
<col width="8%">
<col width="11%">
</colgroup>
@ -859,98 +859,98 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2016-08-26</td>
<td align="center">P9</td>
<td align="center">Hospital C</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">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2016-09-24</td>
<td align="center">T6</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">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2016-12-13</td>
<td align="center">F1</td>
<td align="center">2014-02-15</td>
<td align="center">Y9</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="center">2017-06-17</td>
<td align="center">K1</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">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">2012-05-11</td>
<td align="center">J4</td>
<td align="center">Hospital C</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2013-02-02</td>
<td align="center">U4</td>
<td align="center">Hospital B</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">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">2015-12-04</td>
<td align="center">S10</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">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">2011-02-20</td>
<td align="center">V8</td>
<td align="center">Hospital D</td>
<td align="left">6</td>
<td align="center">2016-09-17</td>
<td align="center">G2</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">S</td>
<td align="center">S</td>
<td align="center">F</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">9</td>
<td align="center">2016-09-22</td>
<td align="center">D3</td>
<td align="left">7</td>
<td align="center">2012-06-30</td>
<td align="center">V5</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</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">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">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -976,8 +976,8 @@ Longest: 1</p>
</pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 15,718<br>
Available: 15,718 (100%, NA: 0 = 0%)<br>
Length: 15,741<br>
Available: 15,741 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -994,33 +994,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,841</td>
<td align="right">49.89%</td>
<td align="right">7,841</td>
<td align="right">49.89%</td>
<td align="right">7,868</td>
<td align="right">49.98%</td>
<td align="right">7,868</td>
<td align="right">49.98%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,956</td>
<td align="right">25.17%</td>
<td align="right">11,797</td>
<td align="right">75.05%</td>
<td align="right">3,927</td>
<td align="right">24.95%</td>
<td align="right">11,795</td>
<td align="right">74.93%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,346</td>
<td align="right">14.93%</td>
<td align="right">14,143</td>
<td align="right">89.98%</td>
<td align="right">2,394</td>
<td align="right">15.21%</td>
<td align="right">14,189</td>
<td align="right">90.14%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,575</td>
<td align="right">10.02%</td>
<td align="right">15,718</td>
<td align="right">1,552</td>
<td align="right">9.86%</td>
<td align="right">15,741</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -1049,50 +1049,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">3793</td>
<td align="center">242</td>
<td align="center">3806</td>
<td align="center">7841</td>
<td align="center">3823</td>
<td align="center">237</td>
<td align="center">3808</td>
<td align="center">7868</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">6205</td>
<td align="center">301</td>
<td align="center">1335</td>
<td align="center">7841</td>
<td align="center">6210</td>
<td align="center">315</td>
<td align="center">1343</td>
<td align="center">7868</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">5980</td>
<td align="center">5984</td>
<td align="center">0</td>
<td align="center">1861</td>
<td align="center">7841</td>
<td align="center">1884</td>
<td align="center">7868</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">7075</td>
<td align="center">7078</td>
<td align="center">0</td>
<td align="center">766</td>
<td align="center">7841</td>
<td align="center">790</td>
<td align="center">7868</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">1575</td>
<td align="center">1575</td>
<td align="center">1552</td>
<td align="center">1552</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">1217</td>
<td align="center">77</td>
<td align="center">281</td>
<td align="center">1575</td>
<td align="center">1198</td>
<td align="center">63</td>
<td align="center">291</td>
<td align="center">1552</td>
</tr>
</tbody>
</table>
@ -1117,34 +1117,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">5980</td>
<td align="center">5984</td>
<td align="center">0</td>
<td align="center">1861</td>
<td align="center">7841</td>
<td align="center">1884</td>
<td align="center">7868</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">CIP</td>
<td align="center">1207</td>
<td align="center">1176</td>
<td align="center">0</td>
<td align="center">368</td>
<td align="center">1575</td>
<td align="center">376</td>
<td align="center">1552</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">CIP</td>
<td align="center">2971</td>
<td align="center">3037</td>
<td align="center">0</td>
<td align="center">985</td>
<td align="center">3956</td>
<td align="center">890</td>
<td align="center">3927</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">CIP</td>
<td align="center">1790</td>
<td align="center">1852</td>
<td align="center">0</td>
<td align="center">556</td>
<td align="center">2346</td>
<td align="center">542</td>
<td align="center">2394</td>
</tr>
</tbody>
</table>
@ -1157,7 +1157,7 @@ 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="cb28"><pre class="downlit">
<span class="kw">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="kw">AMX</span>)
<span class="co"># [1] 0.5318107</span>
<span class="co"># [1] 0.531923</span>
</pre></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="cb29"><pre class="downlit">
@ -1174,19 +1174,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5401506</td>
<td align="center">0.5240989</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5244014</td>
<td align="center">0.5326633</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5256917</td>
<td align="center">0.5554161</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5363864</td>
<td align="center">0.5248050</td>
</tr>
</tbody>
</table>
@ -1207,23 +1207,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5401506</td>
<td align="center">4782</td>
<td align="center">0.5240989</td>
<td align="center">4772</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5244014</td>
<td align="center">5471</td>
<td align="center">0.5326633</td>
<td align="center">5373</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5256917</td>
<td align="center">2277</td>
<td align="center">0.5554161</td>
<td align="center">2391</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5363864</td>
<td align="center">3188</td>
<td align="center">0.5248050</td>
<td align="center">3205</td>
</tr>
</tbody>
</table>
@ -1246,27 +1246,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.8297411</td>
<td align="center">0.9023084</td>
<td align="center">0.9858436</td>
<td align="center">0.8293086</td>
<td align="center">0.8995933</td>
<td align="center">0.9874174</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8215873</td>
<td align="center">0.9060317</td>
<td align="center">0.9879365</td>
<td align="center">0.8125000</td>
<td align="center">0.9085052</td>
<td align="center">0.9832474</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8276036</td>
<td align="center">0.9160768</td>
<td align="center">0.9848332</td>
<td align="center">0.8245480</td>
<td align="center">0.9238605</td>
<td align="center">0.9870130</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5392157</td>
<td align="center">0.5459482</td>
<td align="center">0.0000000</td>
<td align="center">0.5392157</td>
<td align="center">0.5459482</td>
</tr>
</tbody>
</table>