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@ -192,7 +192,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">16 May 2019</h4>
<h4 class="date">17 May 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 16 May 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 17 May 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">2019-05-16</td>
<td align="center">2019-05-17</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">2019-05-16</td>
<td align="center">2019-05-17</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">2019-05-16</td>
<td align="center">2019-05-17</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -327,69 +327,69 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-05-13</td>
<td align="center">X4</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2014-11-13</td>
<td align="center">S2</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">F</td>
</tr>
<tr class="even">
<td align="center">2013-01-01</td>
<td align="center">V1</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">2016-11-12</td>
<td align="center">G5</td>
<td align="center">Hospital A</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">M</td>
</tr>
<tr class="even">
<td align="center">2011-09-23</td>
<td align="center">U6</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-09-19</td>
<td align="center">G9</td>
<td align="center">Hospital A</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="odd">
<td align="center">2015-09-22</td>
<td align="center">L6</td>
<td align="center">2010-04-06</td>
<td align="center">C9</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</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">M</td>
</tr>
<tr class="even">
<td align="center">2017-09-13</td>
<td align="center">N3</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2015-12-01</td>
<td align="center">Z3</td>
<td align="center">Hospital A</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="even">
<td align="center">2011-02-25</td>
<td align="center">F10</td>
<td align="center">2012-04-11</td>
<td align="center">D2</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">R</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
</tbody>
@ -411,8 +411,8 @@
#&gt;
#&gt; Item Count Percent Cum. Count Cum. Percent
#&gt; --- ----- ------- -------- ----------- -------------
#&gt; 1 M 10,410 52.0% 10,410 52.0%
#&gt; 2 F 9,590 48.0% 20,000 100.0%</code></pre>
#&gt; 1 M 10,325 51.6% 10,325 51.6%
#&gt; 2 F 9,675 48.4% 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>
@ -442,14 +442,14 @@
<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 (1532 new changes)</span></a>
<a class="sourceLine" id="cb14-21" title="21"><span class="co">#&gt; Streptococcus pneumoniae (1508 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 (1341 new changes)</span></a>
<a class="sourceLine" id="cb14-25" title="25"><span class="co">#&gt; Table 01: Intrinsic resistance in Enterobacteriaceae (1335 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 (2834 new changes)</span></a>
<a class="sourceLine" id="cb14-28" title="28"><span class="co">#&gt; Table 04: Intrinsic resistance in Gram-positive bacteria (2792 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>
@ -457,24 +457,24 @@
<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 (2225 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 (109 new changes)</span></a>
<a class="sourceLine" id="cb14-36" title="36"><span class="co">#&gt; Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2206 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 (141 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 6,633 out of 20,000 rows, making a total of 8,041 edits</span></a>
<a class="sourceLine" id="cb14-44" title="44"><span class="co">#&gt; EUCAST rules affected 6,587 out of 20,000 rows, making a total of 7,982 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 8,041 test results</span></a>
<a class="sourceLine" id="cb14-48" title="48"><span class="co">#&gt; - 118 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-49" title="49"><span class="co">#&gt; - 4,906 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-50" title="50"><span class="co">#&gt; - 1,094 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-51" title="51"><span class="co">#&gt; - 326 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-52" title="52"><span class="co">#&gt; - 1,577 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-53" title="53"><span class="co">#&gt; - 20 test results changed from R to I</span></a>
<a class="sourceLine" id="cb14-47" title="47"><span class="co">#&gt; =&gt; changed 7,982 test results</span></a>
<a class="sourceLine" id="cb14-48" title="48"><span class="co">#&gt; - 102 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-49" title="49"><span class="co">#&gt; - 4,844 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-50" title="50"><span class="co">#&gt; - 1,047 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-51" title="51"><span class="co">#&gt; - 345 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-52" title="52"><span class="co">#&gt; - 1,615 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-53" title="53"><span class="co">#&gt; - 29 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>
@ -502,8 +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 5,706 first isolates (28.5% of total)</span></a></code></pre></div>
<p>So only 28.5% 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 5,711 first isolates (28.6% of total)</span></a></code></pre></div>
<p>So only 28.6% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<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>
@ -529,19 +529,19 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-31</td>
<td align="center">O3</td>
<td align="center">2010-02-03</td>
<td align="center">Q6</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">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-04-24</td>
<td align="center">O3</td>
<td align="center">2010-03-18</td>
<td align="center">Q6</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -551,10 +551,10 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-04-26</td>
<td align="center">O3</td>
<td align="center">2010-04-04</td>
<td align="center">Q6</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>
@ -562,8 +562,8 @@
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-05-07</td>
<td align="center">O3</td>
<td align="center">2010-04-12</td>
<td align="center">Q6</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -573,10 +573,10 @@
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-07-07</td>
<td align="center">O3</td>
<td align="center">2010-05-08</td>
<td align="center">Q6</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>
@ -584,10 +584,10 @@
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-07-28</td>
<td align="center">O3</td>
<td align="center">2010-08-03</td>
<td align="center">Q6</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>
@ -595,30 +595,30 @@
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-08-30</td>
<td align="center">O3</td>
<td align="center">2010-08-04</td>
<td align="center">Q6</td>
<td align="center">B_ESCHR_COL</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">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-09-08</td>
<td align="center">O3</td>
<td align="center">2010-11-02</td>
<td align="center">Q6</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">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-10-11</td>
<td align="center">O3</td>
<td align="center">2010-11-09</td>
<td align="center">Q6</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
@ -628,11 +628,11 @@
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2010-11-11</td>
<td align="center">O3</td>
<td align="center">2010-12-18</td>
<td align="center">Q6</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">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
@ -650,7 +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 15,027 first weighted isolates (75.1% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb19-10" title="10"><span class="co">#&gt; =&gt; Found 15,123 first weighted isolates (75.6% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -667,70 +667,70 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-31</td>
<td align="center">O3</td>
<td align="center">2010-02-03</td>
<td align="center">Q6</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">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-04-24</td>
<td align="center">O3</td>
<td align="center">2010-03-18</td>
<td align="center">Q6</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">FALSE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-04-26</td>
<td align="center">O3</td>
<td align="center">2010-04-04</td>
<td align="center">Q6</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>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-05-07</td>
<td align="center">O3</td>
<td align="center">2010-04-12</td>
<td align="center">Q6</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">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-07-07</td>
<td align="center">O3</td>
<td align="center">2010-05-08</td>
<td align="center">Q6</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>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-07-28</td>
<td align="center">O3</td>
<td align="center">2010-08-03</td>
<td align="center">Q6</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>
@ -739,11 +739,11 @@
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-08-30</td>
<td align="center">O3</td>
<td align="center">2010-08-04</td>
<td align="center">Q6</td>
<td align="center">B_ESCHR_COL</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">FALSE</td>
@ -751,20 +751,20 @@
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-09-08</td>
<td align="center">O3</td>
<td align="center">2010-11-02</td>
<td align="center">Q6</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">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-10-11</td>
<td align="center">O3</td>
<td align="center">2010-11-09</td>
<td align="center">Q6</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
@ -775,11 +775,11 @@
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2010-11-11</td>
<td align="center">O3</td>
<td align="center">2010-12-18</td>
<td align="center">Q6</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">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
@ -787,11 +787,11 @@
</tr>
</tbody>
</table>
<p>Instead of 1, now 10 isolates are flagged. In total, 75.1% of all isolates are marked ‘first weighted’ - 46.6% 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 6 isolates are flagged. In total, 75.6% of all isolates are marked ‘first weighted’ - 47.1% 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>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 15,027 isolates for analysis.</p>
<p>So we end up with 15,123 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>
@ -817,78 +817,78 @@
<tbody>
<tr class="odd">
<td>1</td>
<td align="center">2013-05-13</td>
<td align="center">X4</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">I</td>
<td align="center">2014-11-13</td>
<td align="center">S2</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 positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</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>2</td>
<td align="center">2016-09-19</td>
<td align="center">G9</td>
<td>3</td>
<td align="center">2016-11-12</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">B_KLBSL_PNE</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">Escherichia</td>
<td align="center">coli</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>3</td>
<td align="center">2015-09-22</td>
<td align="center">L6</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COL</td>
<td>4</td>
<td align="center">2011-09-23</td>
<td align="center">U6</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNE</td>
<td align="center">R</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">M</td>
<td align="center">F</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>5</td>
<td align="center">2015-12-01</td>
<td align="center">Z3</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">2010-04-06</td>
<td align="center">C9</td>
<td align="center">Hospital D</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">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">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>6</td>
<td align="center">2011-02-25</td>
<td align="center">F10</td>
<td align="center">2012-04-11</td>
<td align="center">D2</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AUR</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">R</td>
<td align="center">M</td>
<td align="center">Gram positive</td>
<td align="center">Staphylococcus</td>
@ -896,16 +896,16 @@
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>7</td>
<td align="center">2010-08-13</td>
<td align="center">G10</td>
<td>8</td>
<td align="center">2012-08-17</td>
<td align="center">Z4</td>
<td align="center">Hospital C</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
@ -928,9 +928,9 @@
<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> (15,027 x 13)</strong></p>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (15,123 x 13)</strong></p>
<p>Columns: 2<br>
Length: 15,027 (of which NA: 0 = 0.00%)<br>
Length: 15,123 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -947,33 +947,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,318</td>
<td align="right">48.7%</td>
<td align="right">7,318</td>
<td align="right">48.7%</td>
<td align="right">7,466</td>
<td align="right">49.4%</td>
<td align="right">7,466</td>
<td align="right">49.4%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,729</td>
<td align="right">24.8%</td>
<td align="right">11,047</td>
<td align="right">3,649</td>
<td align="right">24.1%</td>
<td align="right">11,115</td>
<td align="right">73.5%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,370</td>
<td align="right">15.8%</td>
<td align="right">13,417</td>
<td align="right">89.3%</td>
<td align="right">2,381</td>
<td align="right">15.7%</td>
<td align="right">13,496</td>
<td align="right">89.2%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,610</td>
<td align="right">10.7%</td>
<td align="right">15,027</td>
<td align="right">1,627</td>
<td align="right">10.8%</td>
<td align="right">15,123</td>
<td align="right">100.0%</td>
</tr>
</tbody>
@ -984,7 +984,7 @@ 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>(AMX)</a>
<a class="sourceLine" id="cb25-2" title="2"><span class="co">#&gt; [1] 0.4973714</span></a></code></pre></div>
<a class="sourceLine" id="cb25-2" title="2"><span class="co">#&gt; [1] 0.5012233</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>
@ -997,19 +997,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4993375</td>
<td align="center">0.5100641</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4931245</td>
<td align="center">0.4945632</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5068182</td>
<td align="center">0.4960457</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4949396</td>
<td align="center">0.5036765</td>
</tr>
</tbody>
</table>
@ -1027,23 +1027,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4993375</td>
<td align="center">4528</td>
<td align="center">0.5100641</td>
<td align="center">4521</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4931245</td>
<td align="center">5236</td>
<td align="center">0.4945632</td>
<td align="center">5334</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5068182</td>
<td align="center">2200</td>
<td align="center">0.4960457</td>
<td align="center">2276</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4949396</td>
<td align="center">3063</td>
<td align="center">0.5036765</td>
<td align="center">2992</td>
</tr>
</tbody>
</table>
@ -1063,27 +1063,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.8800219</td>
<td align="center">0.8938234</td>
<td align="center">0.9885215</td>
<td align="center">0.8775784</td>
<td align="center">0.8984731</td>
<td align="center">0.9910260</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.7136646</td>
<td align="center">0.9012422</td>
<td align="center">0.9732919</td>
<td align="center">0.7221881</td>
<td align="center">0.9053473</td>
<td align="center">0.9778734</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8806651</td>
<td align="center">0.9115044</td>
<td align="center">0.9895414</td>
<td align="center">0.8766785</td>
<td align="center">0.9188819</td>
<td align="center">0.9887640</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5751055</td>
<td align="center">0.5732885</td>
<td align="center">0.0000000</td>
<td align="center">0.5751055</td>
<td align="center">0.5732885</td>
</tr>
</tbody>
</table>