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@ -41,7 +41,7 @@
</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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9004</span>
</span>
</div>
@ -187,7 +187,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">11 December 2019</h4>
<h4 class="date">20 December 2019</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -196,10 +196,23 @@
<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 11 December 2019.</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 20 December 2019.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
<p>Conducting antimicrobial resistance analysis unfortunately requires in-depth knowledge from different scientific fields, which makes it hard to do right. At least, it requires:</p>
<ul>
<li>Good questions (always start with these!)</li>
<li>A thorough understanding of both (clinical) epidemiology and (clinical) microbiology, to understand the clinical and epidemiological relevance of results and their pharmaceutical implications</li>
<li>Experience with data analysis with microbiological tests and their results (MIC/RSI values)</li>
<li>Availability of the biological taxonomy of microorganisms</li>
<li>Available (inter-)national guidelines and methods to apply them</li>
</ul>
<p>Of course, we cannot instantly provide you with knowledge and experience. But with this <code>AMR</code> pacakge, we aimed at providing (1) tools to simplify antimicrobial resistance data cleaning/analysis, (2) methods to easily incorporate international guidelines and (3) scientifically reliable reference data. The <code>AMR</code> package enables standardised and reproducible antimicrobial resistance analyses, including the application of evidence-based rules, determination of first isolates, translation of various codes for microorganisms and antimicrobial agents, determination of (multi-drug) resistant microorganisms, and calculation of antimicrobial resistance, prevalence and future trends.</p>
</div>
<div id="preparation" class="section level1">
<h1 class="hasAnchor">
<a href="#preparation" class="anchor"></a>Preparation</h1>
<p>For this tutorial, we will create fake demonstration data to work with.</p>
<p>You can skip to <a href="#cleaning-the-data">Cleaning the data</a> if you already have your own data ready. If you start your analysis, try to make the structure of your data generally look like this:</p>
<table class="table">
@ -212,21 +225,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2019-12-11</td>
<td align="center">2019-12-20</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">2019-12-11</td>
<td align="center">2019-12-20</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">2019-12-11</td>
<td align="center">2019-12-20</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -321,71 +334,71 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-05-19</td>
<td align="center">J2</td>
<td align="center">2015-01-13</td>
<td align="center">Y8</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-07-09</td>
<td align="center">K4</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2014-05-10</td>
<td align="center">R6</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-06-29</td>
<td align="center">T4</td>
<td align="center">2010-04-08</td>
<td align="center">O8</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2012-02-11</td>
<td align="center">O10</td>
<td align="center">2010-05-11</td>
<td align="center">W2</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">I</td>
<td align="center">S</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">F</td>
</tr>
<tr class="even">
<td align="center">2017-04-09</td>
<td align="center">D3</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">2011-11-23</td>
<td align="center">I9</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">2011-03-28</td>
<td align="center">D3</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="even">
<td align="center">2013-11-16</td>
<td align="center">P8</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -406,8 +419,8 @@
#
# Item Count Percent Cum. Count Cum. Percent
# --- ----- ------- -------- ----------- -------------
# 1 M 10,408 52.04% 10,408 52.04%
# 2 F 9,592 47.96% 20,000 100.00%</code></pre>
# 1 M 10,341 51.71% 10,341 51.71%
# 2 F 9,659 48.30% 20,000 100.00%</code></pre>
<p>So, we can draw at least two conclusions immediately. From a data scientists perspective, the data looks clean: only values <code>M</code> and <code>F</code>. From a researchers perspective: there are slightly more men. Nothing we didn’t already know.</p>
<p>The data is already quite clean, but we still need to transform some variables. The <code>bacteria</code> column now consists of text, and we want to add more variables based on microbial IDs later on. So, we will transform this column to valid IDs. The <code><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> function of the <code>dplyr</code> package makes this really easy:</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span></a>
@ -422,8 +435,8 @@
<a class="sourceLine" id="cb14-3" data-line-number="3"><span class="co"># Other rules by this AMR package</span></a>
<a class="sourceLine" id="cb14-4" data-line-number="4"><span class="co"># Non-EUCAST: inherit amoxicillin results for unavailable ampicillin (no changes)</span></a>
<a class="sourceLine" id="cb14-5" data-line-number="5"><span class="co"># Non-EUCAST: inherit ampicillin results for unavailable amoxicillin (no changes)</span></a>
<a class="sourceLine" id="cb14-6" data-line-number="6"><span class="co"># Non-EUCAST: set amoxicillin/clav acid = S where ampicillin = S (2,997 values changed)</span></a>
<a class="sourceLine" id="cb14-7" data-line-number="7"><span class="co"># Non-EUCAST: set ampicillin = R where amoxicillin/clav acid = R (165 values changed)</span></a>
<a class="sourceLine" id="cb14-6" data-line-number="6"><span class="co"># Non-EUCAST: set amoxicillin/clav acid = S where ampicillin = S (2,942 values changed)</span></a>
<a class="sourceLine" id="cb14-7" data-line-number="7"><span class="co"># Non-EUCAST: set ampicillin = R where amoxicillin/clav acid = R (159 values changed)</span></a>
<a class="sourceLine" id="cb14-8" data-line-number="8"><span class="co"># Non-EUCAST: set piperacillin = R where piperacillin/tazobactam = R (no changes)</span></a>
<a class="sourceLine" id="cb14-9" data-line-number="9"><span class="co"># Non-EUCAST: set piperacillin/tazobactam = S where piperacillin = S (no changes)</span></a>
<a class="sourceLine" id="cb14-10" data-line-number="10"><span class="co"># Non-EUCAST: set trimethoprim = R where trimethoprim/sulfa = R (no changes)</span></a>
@ -448,14 +461,14 @@
<a class="sourceLine" id="cb14-29" data-line-number="29"><span class="co"># Pasteurella multocida (no changes)</span></a>
<a class="sourceLine" id="cb14-30" data-line-number="30"><span class="co"># Staphylococcus (no changes)</span></a>
<a class="sourceLine" id="cb14-31" data-line-number="31"><span class="co"># Streptococcus groups A, B, C, G (no changes)</span></a>
<a class="sourceLine" id="cb14-32" data-line-number="32"><span class="co"># Streptococcus pneumoniae (1,063 values changed)</span></a>
<a class="sourceLine" id="cb14-32" data-line-number="32"><span class="co"># Streptococcus pneumoniae (942 values changed)</span></a>
<a class="sourceLine" id="cb14-33" data-line-number="33"><span class="co"># Viridans group streptococci (no changes)</span></a>
<a class="sourceLine" id="cb14-34" data-line-number="34"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-35" data-line-number="35"><span class="co"># EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
<a class="sourceLine" id="cb14-36" data-line-number="36"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,242 values changed)</span></a>
<a class="sourceLine" id="cb14-36" data-line-number="36"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,222 values changed)</span></a>
<a class="sourceLine" id="cb14-37" data-line-number="37"><span class="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb14-38" data-line-number="38"><span class="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb14-39" data-line-number="39"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,782 values changed)</span></a>
<a class="sourceLine" id="cb14-39" data-line-number="39"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,709 values changed)</span></a>
<a class="sourceLine" id="cb14-40" data-line-number="40"><span class="co"># Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></a>
<a class="sourceLine" id="cb14-41" data-line-number="41"><span class="co"># Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></a>
<a class="sourceLine" id="cb14-42" data-line-number="42"><span class="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)</span></a>
@ -463,15 +476,15 @@
<a class="sourceLine" id="cb14-44" data-line-number="44"><span class="co"># Table 13: Interpretive rules for quinolones (no changes)</span></a>
<a class="sourceLine" id="cb14-45" data-line-number="45"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-46" data-line-number="46"><span class="co"># -------------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb14-47" data-line-number="47"><span class="co"># EUCAST rules affected 6,564 out of 20,000 rows, making a total of 8,249 edits</span></a>
<a class="sourceLine" id="cb14-47" data-line-number="47"><span class="co"># EUCAST rules affected 6,398 out of 20,000 rows, making a total of 7,974 edits</span></a>
<a class="sourceLine" id="cb14-48" data-line-number="48"><span class="co"># =&gt; added 0 test results</span></a>
<a class="sourceLine" id="cb14-49" data-line-number="49"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-50" data-line-number="50"><span class="co"># =&gt; changed 8,249 test results</span></a>
<a class="sourceLine" id="cb14-51" data-line-number="51"><span class="co"># - 102 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-52" data-line-number="52"><span class="co"># - 4,787 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-53" data-line-number="53"><span class="co"># - 1,224 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-54" data-line-number="54"><span class="co"># - 363 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-55" data-line-number="55"><span class="co"># - 1,773 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-50" data-line-number="50"><span class="co"># =&gt; changed 7,974 test results</span></a>
<a class="sourceLine" id="cb14-51" data-line-number="51"><span class="co"># - 95 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-52" data-line-number="52"><span class="co"># - 4,603 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-53" data-line-number="53"><span class="co"># - 1,165 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-54" data-line-number="54"><span class="co"># - 334 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-55" data-line-number="55"><span class="co"># - 1,777 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-56" data-line-number="56"><span class="co"># -------------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb14-57" data-line-number="57"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-58" data-line-number="58"><span class="co"># Use eucast_rules(..., verbose = TRUE) (on your original data) to get a data.frame with all specified edits instead.</span></a></code></pre></div>
@ -499,8 +512,8 @@
<a class="sourceLine" id="cb16-3" data-line-number="3"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `bacteria` as input for `col_mo`.</span></a>
<a class="sourceLine" id="cb16-4" data-line-number="4"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a>
<a class="sourceLine" id="cb16-5" data-line-number="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<a class="sourceLine" id="cb16-6" data-line-number="6"><span class="co"># =&gt; Found 5,656 first isolates (28.3% of total)</span></a></code></pre></div>
<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>
<a class="sourceLine" id="cb16-6" data-line-number="6"><span class="co"># =&gt; Found 5,647 first isolates (28.2% of total)</span></a></code></pre></div>
<p>So only 28.2% 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="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb17-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(first <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>)</a></code></pre></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>
@ -510,7 +523,7 @@
<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 D2, 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 T5, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -526,30 +539,30 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-02-23</td>
<td align="center">D2</td>
<td align="center">2010-02-25</td>
<td align="center">T5</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">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-03-20</td>
<td align="center">D2</td>
<td align="center">2010-03-02</td>
<td align="center">T5</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</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">2010-04-13</td>
<td align="center">D2</td>
<td align="center">2010-04-02</td>
<td align="center">T5</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -559,19 +572,19 @@
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-07-22</td>
<td align="center">D2</td>
<td align="center">2010-06-08</td>
<td align="center">T5</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">5</td>
<td align="center">2010-07-22</td>
<td align="center">D2</td>
<td align="center">2010-06-20</td>
<td align="center">T5</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -581,21 +594,21 @@
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-08-04</td>
<td align="center">D2</td>
<td align="center">2010-09-13</td>
<td align="center">T5</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">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-08-19</td>
<td align="center">D2</td>
<td align="center">2010-10-06</td>
<td align="center">T5</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>
@ -603,35 +616,35 @@
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-09-02</td>
<td align="center">D2</td>
<td align="center">2010-11-19</td>
<td align="center">T5</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">S</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">2010-09-04</td>
<td align="center">D2</td>
<td align="center">2010-12-06</td>
<td align="center">T5</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">10</td>
<td align="center">2010-09-18</td>
<td align="center">D2</td>
<td align="center">2010-12-07</td>
<td align="center">T5</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">S</td>
<td align="center">FALSE</td>
</tr>
</tbody>
@ -647,7 +660,7 @@
<a class="sourceLine" id="cb19-7" data-line-number="7"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<a class="sourceLine" id="cb19-8" data-line-number="8"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.</span></a>
<a class="sourceLine" id="cb19-9" data-line-number="9"><span class="co"># [Criterion] Inclusion based on key antibiotics, ignoring I</span></a>
<a class="sourceLine" id="cb19-10" data-line-number="10"><span class="co"># =&gt; Found 15,026 first weighted isolates (75.1% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb19-10" data-line-number="10"><span class="co"># =&gt; Found 15,050 first weighted isolates (75.3% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -664,23 +677,23 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-02-23</td>
<td align="center">D2</td>
<td align="center">2010-02-25</td>
<td align="center">T5</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">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-03-20</td>
<td align="center">D2</td>
<td align="center">2010-03-02</td>
<td align="center">T5</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
@ -688,8 +701,8 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-04-13</td>
<td align="center">D2</td>
<td align="center">2010-04-02</td>
<td align="center">T5</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -700,46 +713,46 @@
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-07-22</td>
<td align="center">D2</td>
<td align="center">2010-06-08</td>
<td align="center">T5</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="odd">
<td align="center">5</td>
<td align="center">2010-07-22</td>
<td align="center">D2</td>
<td align="center">2010-06-20</td>
<td align="center">T5</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">6</td>
<td align="center">2010-08-04</td>
<td align="center">D2</td>
<td align="center">2010-09-13</td>
<td align="center">T5</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">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-08-19</td>
<td align="center">D2</td>
<td align="center">2010-10-06</td>
<td align="center">T5</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>
@ -748,47 +761,47 @@
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-09-02</td>
<td align="center">D2</td>
<td align="center">2010-11-19</td>
<td align="center">T5</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">S</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">2010-09-04</td>
<td align="center">D2</td>
<td align="center">2010-12-06</td>
<td align="center">T5</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">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2010-09-18</td>
<td align="center">D2</td>
<td align="center">2010-12-07</td>
<td align="center">T5</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">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Instead of 1, now 9 isolates are flagged. In total, 75.1% 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>Instead of 1, now 7 isolates are flagged. In total, 75.3% of all isolates are marked ‘first weighted’ - 47.0% 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="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb20-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</a></code></pre></div>
<p>So we end up with 15,026 isolates for analysis.</p>
<p>So we end up with 15,050 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb21-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(first, keyab))</a></code></pre></div>
@ -796,6 +809,7 @@
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(data_1st)</a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th></th>
<th align="center">date</th>
<th align="center">patient_id</th>
<th align="center">hospital</th>
@ -812,57 +826,13 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-05-19</td>
<td align="center">J2</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">2016-07-09</td>
<td align="center">K4</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">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="odd">
<td align="center">2014-05-10</td>
<td align="center">R6</td>
<td align="center">Hospital C</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">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="center">2011-06-29</td>
<td align="center">T4</td>
<td>2</td>
<td align="center">2010-04-08</td>
<td align="center">O8</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
@ -871,14 +841,63 @@
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-02-11</td>
<td align="center">O10</td>
<tr class="even">
<td>3</td>
<td align="center">2010-05-11</td>
<td align="center">W2</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</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">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>4</td>
<td align="center">2011-11-23</td>
<td align="center">I9</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="even">
<td>5</td>
<td align="center">2011-03-28</td>
<td align="center">D3</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>6</td>
<td align="center">2013-11-16</td>
<td align="center">P8</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">F</td>
<td align="center">Gram-positive</td>
@ -887,15 +906,16 @@
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-04-09</td>
<td align="center">D3</td>
<td align="center">Hospital D</td>
<td>7</td>
<td align="center">2014-12-19</td>
<td align="center">Q5</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">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>
@ -920,7 +940,7 @@
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(genus, species)</a></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 15,026 (of which NA: 0 = 0%)<br>
Length: 15,050 (of which NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -937,33 +957,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,425</td>
<td align="right">49.41%</td>
<td align="right">7,425</td>
<td align="right">49.41%</td>
<td align="right">7,510</td>
<td align="right">49.90%</td>
<td align="right">7,510</td>
<td align="right">49.90%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,806</td>
<td align="right">25.33%</td>
<td align="right">11,231</td>
<td align="right">74.74%</td>
<td align="right">3,786</td>
<td align="right">25.16%</td>
<td align="right">11,296</td>
<td align="right">75.06%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,311</td>
<td align="right">15.38%</td>
<td align="right">13,542</td>
<td align="right">90.12%</td>
<td align="right">2,294</td>
<td align="right">15.24%</td>
<td align="right">13,590</td>
<td align="right">90.30%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,484</td>
<td align="right">9.88%</td>
<td align="right">15,026</td>
<td align="right">1,460</td>
<td align="right">9.70%</td>
<td align="right">15,050</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -975,7 +995,7 @@ 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="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/proportion.html">resistance</a></span>(AMX)</a>
<a class="sourceLine" id="cb25-2" data-line-number="2"><span class="co"># [1] 0.4631971</span></a></code></pre></div>
<a class="sourceLine" id="cb25-2" data-line-number="2"><span class="co"># [1] 0.4623256</span></a></code></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="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb26-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital) <span class="op">%&gt;%</span><span class="st"> </span></a>
@ -988,19 +1008,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4553786</td>
<td align="center">0.4637522</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4653638</td>
<td align="center">0.4602655</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4613043</td>
<td align="center">0.4760000</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4729412</td>
<td align="center">0.4536218</td>
</tr>
</tbody>
</table>
@ -1018,23 +1038,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4553786</td>
<td align="center">4583</td>
<td align="center">0.4637522</td>
<td align="center">4552</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4653638</td>
<td align="center">5168</td>
<td align="center">0.4602655</td>
<td align="center">5197</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4613043</td>
<td align="center">2300</td>
<td align="center">0.4760000</td>
<td align="center">2250</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4729412</td>
<td align="center">2975</td>
<td align="center">0.4536218</td>
<td align="center">3051</td>
</tr>
</tbody>
</table>
@ -1054,27 +1074,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.9248485</td>
<td align="center">0.8921212</td>
<td align="center">0.9936700</td>
<td align="center">0.9227696</td>
<td align="center">0.8909454</td>
<td align="center">0.9920107</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.9238544</td>
<td align="center">0.8928571</td>
<td align="center">0.9946092</td>
<td align="center">0.9191781</td>
<td align="center">0.9061644</td>
<td align="center">0.9917808</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.9224908</td>
<td align="center">0.9177614</td>
<td align="center">0.9923805</td>
<td align="center">0.9186476</td>
<td align="center">0.9199683</td>
<td align="center">0.9915478</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5962787</td>
<td align="center">0.6129032</td>
<td align="center">0.0000000</td>
<td align="center">0.5962787</td>
<td align="center">0.6129032</td>
</tr>
</tbody>
</table>
@ -1193,8 +1213,9 @@ Longest: 24</p>
<h2 class="hasAnchor">
<a href="#tocnav" class="anchor"></a>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li>
<a href="#introduction">Introduction</a><ul class="nav nav-pills nav-stacked">
<li><a href="#introduction">Introduction</a></li>
<li>
<a href="#preparation">Preparation</a><ul class="nav nav-pills nav-stacked">
<li><a href="#needed-r-packages">Needed R packages</a></li>
</ul>
</li>
@ -1230,7 +1251,7 @@ Longest: 24</p>
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<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N M Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
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