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new EUCAST rules algorithm

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dr. M.S. (Matthijs) Berends
2019-04-05 18:47:39 +02:00
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@ -40,7 +40,7 @@
</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="Released version">0.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">27 March 2019</h4>
<h4 class="date">05 April 2019</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -201,7 +201,7 @@
<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 27 March 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 05 April 2019.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -217,21 +217,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2019-03-27</td>
<td align="center">2019-04-05</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">2019-03-27</td>
<td align="center">2019-04-05</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">2019-03-27</td>
<td align="center">2019-04-05</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -327,30 +327,19 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-10-28</td>
<td align="center">A4</td>
<td align="center">2015-03-05</td>
<td align="center">Z5</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">M</td>
</tr>
<tr class="even">
<td align="center">2011-07-22</td>
<td align="center">Y8</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-09-30</td>
<td align="center">N3</td>
<tr class="even">
<td align="center">2017-08-05</td>
<td align="center">K5</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
@ -359,38 +348,49 @@
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-08-31</td>
<td align="center">V4</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</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">2013-02-14</td>
<td align="center">Z6</td>
<td align="center">2013-07-07</td>
<td align="center">G5</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2015-09-03</td>
<td align="center">O2</td>
<td align="center">Hospital A</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-02-01</td>
<td align="center">D5</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-12-28</td>
<td align="center">V6</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">2014-03-20</td>
<td align="center">K9</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
@ -411,8 +411,8 @@
#&gt;
#&gt; Item Count Percent Cum. Count Cum. Percent
#&gt; --- ----- ------- -------- ----------- -------------
#&gt; 1 M 10,344 51.7% 10,344 51.7%
#&gt; 2 F 9,656 48.3% 20,000 100.0%</code></pre>
#&gt; 1 M 10,405 52.0% 10,405 52.0%
#&gt; 2 F 9,595 48.0% 20,000 100.0%</code></pre>
<p>So, we can draw at least two conclusions immediately. From a data scientist perspective, the data looks clean: only values <code>M</code> and <code>F</code>. From a researcher 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" title="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span></a>
@ -425,46 +425,59 @@
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1">data &lt;-<span class="st"> </span><span class="kw"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(data, <span class="dt">col_mo =</span> <span class="st">"bacteria"</span>)</a>
<a class="sourceLine" id="cb14-2" title="2"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-3" title="3"><span class="co">#&gt; Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)</span></a>
<a class="sourceLine" id="cb14-4" title="4"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-5" title="5"><span class="co">#&gt; EUCAST Clinical Breakpoints (v9.0, 2019)</span></a>
<a class="sourceLine" id="cb14-6" title="6"><span class="co">#&gt; Enterobacteriales (Order) (no changes)</span></a>
<a class="sourceLine" id="cb14-7" title="7"><span class="co">#&gt; Staphylococcus (no changes)</span></a>
<a class="sourceLine" id="cb14-8" title="8"><span class="co">#&gt; Enterococcus (no changes)</span></a>
<a class="sourceLine" id="cb14-9" title="9"><span class="co">#&gt; Streptococcus groups A, B, C, G (no changes)</span></a>
<a class="sourceLine" id="cb14-10" title="10"><span class="co">#&gt; Streptococcus pneumoniae (no changes)</span></a>
<a class="sourceLine" id="cb14-11" title="11"><span class="co">#&gt; Viridans group streptococci (no changes)</span></a>
<a class="sourceLine" id="cb14-12" title="12"><span class="co">#&gt; Haemophilus influenzae (no changes)</span></a>
<a class="sourceLine" id="cb14-13" title="13"><span class="co">#&gt; Moraxella catarrhalis (no changes)</span></a>
<a class="sourceLine" id="cb14-14" title="14"><span class="co">#&gt; Anaerobic Gram positives (no changes)</span></a>
<a class="sourceLine" id="cb14-15" title="15"><span class="co">#&gt; Anaerobic Gram negatives (no changes)</span></a>
<a class="sourceLine" id="cb14-16" title="16"><span class="co">#&gt; Pasteurella multocida (no changes)</span></a>
<a class="sourceLine" id="cb14-17" title="17"><span class="co">#&gt; Campylobacter jejuni and C. coli (no changes)</span></a>
<a class="sourceLine" id="cb14-18" title="18"><span class="co">#&gt; Aerococcus sanguinicola and A. urinae (no changes)</span></a>
<a class="sourceLine" id="cb14-19" title="19"><span class="co">#&gt; Kingella kingae (no changes)</span></a>
<a class="sourceLine" id="cb14-20" title="20"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-21" title="21"><span class="co">#&gt; EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
<a class="sourceLine" id="cb14-22" title="22"><span class="co">#&gt; Table 1: Intrinsic resistance in Enterobacteriaceae (1342 changes)</span></a>
<a class="sourceLine" id="cb14-23" title="23"><span class="co">#&gt; Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb14-24" title="24"><span class="co">#&gt; Table 3: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb14-25" title="25"><span class="co">#&gt; Table 4: Intrinsic resistance in Gram-positive bacteria (2726 changes)</span></a>
<a class="sourceLine" id="cb14-26" title="26"><span class="co">#&gt; Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></a>
<a class="sourceLine" id="cb14-27" title="27"><span class="co">#&gt; Table 9: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></a>
<a class="sourceLine" id="cb14-28" title="28"><span class="co">#&gt; Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb14-29" title="29"><span class="co">#&gt; Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)</span></a>
<a class="sourceLine" id="cb14-30" title="30"><span class="co">#&gt; Table 12: Interpretive rules for aminoglycosides (no changes)</span></a>
<a class="sourceLine" id="cb14-31" title="31"><span class="co">#&gt; Table 13: Interpretive rules for quinolones (no changes)</span></a>
<a class="sourceLine" id="cb14-32" title="32"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-33" title="33"><span class="co">#&gt; Other rules</span></a>
<a class="sourceLine" id="cb14-34" title="34"><span class="co">#&gt; Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (no changes)</span></a>
<a class="sourceLine" id="cb14-35" title="35"><span class="co">#&gt; Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no changes)</span></a>
<a class="sourceLine" id="cb14-36" title="36"><span class="co">#&gt; Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no changes)</span></a>
<a class="sourceLine" id="cb14-37" title="37"><span class="co">#&gt; Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (no changes)</span></a>
<a class="sourceLine" id="cb14-38" title="38"><span class="co">#&gt; Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)</span></a>
<a class="sourceLine" id="cb14-39" title="39"><span class="co">#&gt; Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)</span></a>
<a class="sourceLine" id="cb14-40" title="40"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-41" title="41"><span class="co">#&gt; =&gt; EUCAST rules affected 7,400 out of 20,000 rows</span></a>
<a class="sourceLine" id="cb14-42" title="42"><span class="co">#&gt; -&gt; added 0 test results</span></a>
<a class="sourceLine" id="cb14-43" title="43"><span class="co">#&gt; -&gt; changed 4,068 test results (0 to S; 0 to I; 4,068 to R)</span></a></code></pre></div>
<a class="sourceLine" id="cb14-4" title="4"><span class="co">#&gt; http://eucast.org/</span></a>
<a class="sourceLine" id="cb14-5" title="5"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-6" title="6"><span class="co">#&gt; EUCAST Clinical Breakpoints (v9.0, 2019)</span></a>
<a class="sourceLine" id="cb14-7" title="7"><span class="co">#&gt; Aerococcus sanguinicola (no new changes)</span></a>
<a class="sourceLine" id="cb14-8" title="8"><span class="co">#&gt; Aerococcus urinae (no new changes)</span></a>
<a class="sourceLine" id="cb14-9" title="9"><span class="co">#&gt; Anaerobic Gram negatives (no new changes)</span></a>
<a class="sourceLine" id="cb14-10" title="10"><span class="co">#&gt; Anaerobic Gram positives (no new changes)</span></a>
<a class="sourceLine" id="cb14-11" title="11"><span class="co">#&gt; Campylobacter coli (no new changes)</span></a>
<a class="sourceLine" id="cb14-12" title="12"><span class="co">#&gt; Campylobacter jejuni (no new changes)</span></a>
<a class="sourceLine" id="cb14-13" title="13"><span class="co">#&gt; Enterobacteriales (Order) (no new changes)</span></a>
<a class="sourceLine" id="cb14-14" title="14"><span class="co">#&gt; Enterococcus (no new changes)</span></a>
<a class="sourceLine" id="cb14-15" title="15"><span class="co">#&gt; Haemophilus influenzae (no new changes)</span></a>
<a class="sourceLine" id="cb14-16" title="16"><span class="co">#&gt; Kingella kingae (no new changes)</span></a>
<a class="sourceLine" id="cb14-17" title="17"><span class="co">#&gt; Moraxella catarrhalis (no new changes)</span></a>
<a class="sourceLine" id="cb14-18" title="18"><span class="co">#&gt; Pasteurella multocida (no new changes)</span></a>
<a class="sourceLine" id="cb14-19" title="19"><span class="co">#&gt; Staphylococcus (no new changes)</span></a>
<a class="sourceLine" id="cb14-20" title="20"><span class="co">#&gt; Streptococcus groups A, B, C, G (no new changes)</span></a>
<a class="sourceLine" id="cb14-21" title="21"><span class="co">#&gt; Streptococcus pneumoniae (1476 new changes)</span></a>
<a class="sourceLine" id="cb14-22" title="22"><span class="co">#&gt; Viridans group streptococci (no new changes)</span></a>
<a class="sourceLine" id="cb14-23" title="23"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-24" title="24"><span class="co">#&gt; EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
<a class="sourceLine" id="cb14-25" title="25"><span class="co">#&gt; Table 01: Intrinsic resistance in Enterobacteriaceae (1290 new changes)</span></a>
<a class="sourceLine" id="cb14-26" title="26"><span class="co">#&gt; Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no new changes)</span></a>
<a class="sourceLine" id="cb14-27" title="27"><span class="co">#&gt; Table 03: Intrinsic resistance in other Gram-negative bacteria (no new changes)</span></a>
<a class="sourceLine" id="cb14-28" title="28"><span class="co">#&gt; Table 04: Intrinsic resistance in Gram-positive bacteria (2758 new changes)</span></a>
<a class="sourceLine" id="cb14-29" title="29"><span class="co">#&gt; Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no new changes)</span></a>
<a class="sourceLine" id="cb14-30" title="30"><span class="co">#&gt; Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no new changes)</span></a>
<a class="sourceLine" id="cb14-31" title="31"><span class="co">#&gt; Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no new changes)</span></a>
<a class="sourceLine" id="cb14-32" title="32"><span class="co">#&gt; Table 12: Interpretive rules for aminoglycosides (no new changes)</span></a>
<a class="sourceLine" id="cb14-33" title="33"><span class="co">#&gt; Table 13: Interpretive rules for quinolones (no new changes)</span></a>
<a class="sourceLine" id="cb14-34" title="34"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-35" title="35"><span class="co">#&gt; Other rules</span></a>
<a class="sourceLine" id="cb14-36" title="36"><span class="co">#&gt; Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2311 new changes)</span></a>
<a class="sourceLine" id="cb14-37" title="37"><span class="co">#&gt; Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (107 new changes)</span></a>
<a class="sourceLine" id="cb14-38" title="38"><span class="co">#&gt; Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no new changes)</span></a>
<a class="sourceLine" id="cb14-39" title="39"><span class="co">#&gt; Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no new changes)</span></a>
<a class="sourceLine" id="cb14-40" title="40"><span class="co">#&gt; Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no new changes)</span></a>
<a class="sourceLine" id="cb14-41" title="41"><span class="co">#&gt; Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no new changes)</span></a>
<a class="sourceLine" id="cb14-42" title="42"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-43" title="43"><span class="co">#&gt; --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb14-44" title="44"><span class="co">#&gt; EUCAST rules affected 6,584 out of 20,000 rows, making a total of 7,942 edits</span></a>
<a class="sourceLine" id="cb14-45" title="45"><span class="co">#&gt; =&gt; added 0 test results</span></a>
<a class="sourceLine" id="cb14-46" title="46"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-47" title="47"><span class="co">#&gt; =&gt; changed 7,942 test results</span></a>
<a class="sourceLine" id="cb14-48" title="48"><span class="co">#&gt; - 125 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-49" title="49"><span class="co">#&gt; - 4,719 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-50" title="50"><span class="co">#&gt; - 1,093 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-51" title="51"><span class="co">#&gt; - 299 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-52" title="52"><span class="co">#&gt; - 1,682 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-53" title="53"><span class="co">#&gt; - 24 test results changed from R to I</span></a>
<a class="sourceLine" id="cb14-54" title="54"><span class="co">#&gt; --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb14-55" title="55"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-56" title="56"><span class="co">#&gt; Use verbose = TRUE to get a data.frame with all specified edits instead.</span></a></code></pre></div>
</div>
<div id="adding-new-variables" class="section level1">
<h1 class="hasAnchor">
@ -489,8 +502,8 @@
<a class="sourceLine" id="cb16-3" title="3"><span class="co">#&gt; </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" title="4"><span class="co">#&gt; </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" title="5"><span class="co">#&gt; </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" title="6"><span class="co">#&gt; =&gt; Found 5,665 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" title="6"><span class="co">#&gt; =&gt; Found 5,681 first isolates (28.4% of total)</span></a></code></pre></div>
<p>So only 28.4% 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" title="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" title="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>
@ -516,87 +529,87 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-09-11</td>
<td align="center">L7</td>
<td align="center">2010-01-24</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-11-07</td>
<td align="center">L7</td>
<td align="center">2010-07-22</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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">3</td>
<td align="center">2011-01-16</td>
<td align="center">L7</td>
<td align="center">2010-07-29</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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="even">
<td align="center">4</td>
<td align="center">2011-02-25</td>
<td align="center">L7</td>
<td align="center">2010-09-17</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2011-08-07</td>
<td align="center">L7</td>
<td align="center">2011-02-27</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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">6</td>
<td align="center">2011-08-16</td>
<td align="center">L7</td>
<td align="center">B_ESCHR_COL</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">7</td>
<td align="center">2011-10-08</td>
<td align="center">L7</td>
<td align="center">B_ESCHR_COL</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">8</td>
<td align="center">2011-10-26</td>
<td align="center">L7</td>
<td align="center">6</td>
<td align="center">2011-04-25</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-04-30</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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">2011-05-27</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -604,23 +617,23 @@
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2012-01-15</td>
<td align="center">L7</td>
<td align="center">2011-06-24</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">I</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="even">
<td align="center">10</td>
<td align="center">2012-02-08</td>
<td align="center">L7</td>
<td align="center">2011-10-29</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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>
</tr>
@ -637,7 +650,7 @@
<a class="sourceLine" id="cb19-7" title="7"><span class="co">#&gt; </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" title="8"><span class="co">#&gt; </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" title="9"><span class="co">#&gt; [Criterion] Inclusion based on key antibiotics, ignoring I.</span></a>
<a class="sourceLine" id="cb19-10" title="10"><span class="co">#&gt; =&gt; Found 15,729 first weighted isolates (78.6% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb19-10" title="10"><span class="co">#&gt; =&gt; Found 15,059 first weighted isolates (75.3% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -654,11 +667,11 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-09-11</td>
<td align="center">L7</td>
<td align="center">2010-01-24</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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">TRUE</td>
@ -666,119 +679,119 @@
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-11-07</td>
<td align="center">L7</td>
<td align="center">2010-07-22</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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">3</td>
<td align="center">2011-01-16</td>
<td align="center">L7</td>
<td align="center">2010-07-29</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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="even">
<td align="center">4</td>
<td align="center">2011-02-25</td>
<td align="center">L7</td>
<td align="center">2010-09-17</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2011-08-07</td>
<td align="center">L7</td>
<td align="center">2011-02-27</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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="even">
<td align="center">6</td>
<td align="center">2011-08-16</td>
<td align="center">L7</td>
<td align="center">2011-04-25</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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">7</td>
<td align="center">2011-10-08</td>
<td align="center">L7</td>
<td align="center">2011-04-30</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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">8</td>
<td align="center">2011-10-26</td>
<td align="center">L7</td>
<td align="center">B_ESCHR_COL</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">2011-05-27</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2012-01-15</td>
<td align="center">L7</td>
<td align="center">2011-06-24</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">I</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="even">
<td align="center">10</td>
<td align="center">2012-02-08</td>
<td align="center">L7</td>
<td align="center">2011-10-29</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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">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’ - 50.3% 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 5 isolates are flagged. In total, 75.3% 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="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="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" title="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 15,729 isolates for analysis.</p>
<p>So we end up with 15,059 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" title="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" title="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://www.rdocumentation.org/packages/base/topics/c">c</a></span>(first, keyab))</a></code></pre></div>
@ -802,13 +815,58 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-10-28</td>
<td align="center">A4</td>
<td align="center">2015-03-05</td>
<td align="center">Z5</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COL</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="even">
<td align="center">2017-08-05</td>
<td align="center">K5</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-08-31</td>
<td align="center">V4</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNE</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-07-07</td>
<td align="center">G5</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram negative</td>
@ -816,44 +874,14 @@
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-07-22</td>
<td align="center">Y8</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-09-30</td>
<td align="center">N3</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-02-14</td>
<td align="center">Z6</td>
<td align="center">2015-09-03</td>
<td align="center">O2</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COL</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">F</td>
<td align="center">Gram negative</td>
@ -861,34 +889,19 @@
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-02-01</td>
<td align="center">D5</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<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">2013-12-28</td>
<td align="center">V6</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">R</td>
<td align="center">2014-03-20</td>
<td align="center">K9</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COL</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 positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</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>
</tbody>
@ -908,9 +921,9 @@
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1"><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste</a></span>(data_1st<span class="op">$</span>genus, data_1st<span class="op">$</span>species))</a></code></pre></div>
<p>Or can be used like the <code>dplyr</code> way, which is easier readable:</p>
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus, species)</a></code></pre></div>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (15,729 x 13)</strong></p>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (15,059 x 13)</strong></p>
<p>Columns: 2<br>
Length: 15,729 (of which NA: 0 = 0.00%)<br>
Length: 15,059 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -927,33 +940,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,807</td>
<td align="right">49.6%</td>
<td align="right">7,807</td>
<td align="right">49.6%</td>
<td align="right">7,494</td>
<td align="right">49.8%</td>
<td align="right">7,494</td>
<td align="right">49.8%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,919</td>
<td align="right">24.9%</td>
<td align="right">11,726</td>
<td align="right">74.6%</td>
<td align="right">3,673</td>
<td align="right">24.4%</td>
<td align="right">11,167</td>
<td align="right">74.2%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,426</td>
<td align="right">2,325</td>
<td align="right">15.4%</td>
<td align="right">14,152</td>
<td align="right">90.0%</td>
<td align="right">13,492</td>
<td align="right">89.6%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,577</td>
<td align="right">10.0%</td>
<td align="right">15,729</td>
<td align="right">1,567</td>
<td align="right">10.4%</td>
<td align="right">15,059</td>
<td align="right">100.0%</td>
</tr>
</tbody>
@ -964,7 +977,7 @@ Longest: 24</p>
<a href="#resistance-percentages" class="anchor"></a>Resistance percentages</h2>
<p>The functions <code><a href="../reference/portion.html">portion_S()</a></code>, <code><a href="../reference/portion.html">portion_SI()</a></code>, <code><a href="../reference/portion.html">portion_I()</a></code>, <code><a href="../reference/portion.html">portion_IR()</a></code> and <code><a href="../reference/portion.html">portion_R()</a></code> can be used to determine the portion of a specific antimicrobial outcome. They 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" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_IR</a></span>(amox)</a>
<a class="sourceLine" id="cb25-2" title="2"><span class="co">#&gt; [1] 0.4796236</span></a></code></pre></div>
<a class="sourceLine" id="cb25-2" title="2"><span class="co">#&gt; [1] 0.4999668</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" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb26-2" title="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>
@ -977,19 +990,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4841779</td>
<td align="center">0.5037963</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4800215</td>
<td align="center">0.5007457</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4663419</td>
<td align="center">0.5111524</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4815057</td>
<td align="center">0.4851550</td>
</tr>
</tbody>
</table>
@ -1007,23 +1020,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4841779</td>
<td align="center">4835</td>
<td align="center">0.5037963</td>
<td align="center">4478</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4800215</td>
<td align="center">5581</td>
<td align="center">0.5007457</td>
<td align="center">5364</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4663419</td>
<td align="center">2258</td>
<td align="center">0.5111524</td>
<td align="center">2152</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4815057</td>
<td align="center">3055</td>
<td align="center">0.4851550</td>
<td align="center">3065</td>
</tr>
</tbody>
</table>
@ -1043,27 +1056,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7376713</td>
<td align="center">0.8986807</td>
<td align="center">0.9754067</td>
<td align="center">0.8796370</td>
<td align="center">0.8973846</td>
<td align="center">0.9902589</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.7305010</td>
<td align="center">0.8953710</td>
<td align="center">0.9727330</td>
<td align="center">0.7172942</td>
<td align="center">0.9081047</td>
<td align="center">0.9821315</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7305435</td>
<td align="center">0.9275325</td>
<td align="center">0.9793315</td>
<td align="center">0.8829295</td>
<td align="center">0.9221345</td>
<td align="center">0.9918323</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.7320692</td>
<td align="center">0.5767742</td>
<td align="center">0.0000000</td>
<td align="center">0.7320692</td>
<td align="center">0.5767742</td>
</tr>
</tbody>
</table>