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rlang dependency, new fungi

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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">0.5.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</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 February 2019</h4>
<h4 class="date">28 February 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/">RMarkdown</a>. However, the methodology remains unchanged. This page was generated on 27 February 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/">RMarkdown</a>. However, the methodology remains unchanged. This page was generated on 28 February 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">2019-02-27</td>
<td align="center">2019-02-28</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">2019-02-27</td>
<td align="center">2019-02-28</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">2019-02-27</td>
<td align="center">2019-02-28</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -327,70 +327,70 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-02-27</td>
<td align="center">B4</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">2015-09-11</td>
<td align="center">C6</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-02-11</td>
<td align="center">T4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-04-14</td>
<td align="center">N3</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella 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">M</td>
</tr>
<tr class="even">
<td align="center">2017-03-09</td>
<td align="center">D1</td>
<td align="center">2015-05-10</td>
<td align="center">N2</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">I</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">M</td>
</tr>
<tr class="odd">
<td align="center">2013-10-22</td>
<td align="center">W9</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">2012-03-06</td>
<td align="center">C2</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">M</td>
</tr>
<tr class="even">
<td align="center">2011-11-09</td>
<td align="center">X3</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2017-02-01</td>
<td align="center">O6</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-08-12</td>
<td align="center">C10</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">2017-02-26</td>
<td align="center">X1</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
@ -411,8 +411,8 @@
#&gt;
#&gt; Item Count Percent Cum. Count Cum. Percent
#&gt; --- ----- ------- -------- ----------- -------------
#&gt; 1 M 10,333 51.7% 10,333 51.7%
#&gt; 2 F 9,667 48.3% 20,000 100.0%</code></pre>
#&gt; 1 M 10,244 51.2% 10,244 51.2%
#&gt; 2 F 9,756 48.8% 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>
@ -443,10 +443,10 @@
<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 (1264 changes)</span></a>
<a class="sourceLine" id="cb14-22" title="22"><span class="co">#&gt; Table 1: Intrinsic resistance in Enterobacteriaceae (1275 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 (2835 changes)</span></a>
<a class="sourceLine" id="cb14-25" title="25"><span class="co">#&gt; Table 4: Intrinsic resistance in Gram-positive bacteria (2727 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>
@ -462,9 +462,9 @@
<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 7,417 out of 20,000 rows</span></a>
<a class="sourceLine" id="cb14-41" title="41"><span class="co">#&gt; =&gt; EUCAST rules affected 7,427 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 4,099 test results (0 to S; 0 to I; 4,099 to R)</span></a></code></pre></div>
<a class="sourceLine" id="cb14-43" title="43"><span class="co">#&gt; -&gt; changed 4,002 test results (0 to S; 0 to I; 4,002 to R)</span></a></code></pre></div>
</div>
<div id="adding-new-variables" class="section level1">
<h1 class="hasAnchor">
@ -489,8 +489,8 @@
<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 5,647 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>
<a class="sourceLine" id="cb16-6" title="6"><span class="co">#&gt; =&gt; Found 5,650 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>
<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>
@ -516,43 +516,43 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-07</td>
<td align="center">E5</td>
<td align="center">2010-04-26</td>
<td align="center">H9</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">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-01-14</td>
<td align="center">E5</td>
<td align="center">2010-05-27</td>
<td align="center">H9</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">FALSE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-02-07</td>
<td align="center">E5</td>
<td align="center">2010-07-20</td>
<td align="center">H9</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">I</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">2010-03-28</td>
<td align="center">E5</td>
<td align="center">2010-11-25</td>
<td align="center">H9</td>
<td align="center">B_ESCHR_COL</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>
@ -560,54 +560,54 @@
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-05-25</td>
<td align="center">E5</td>
<td align="center">2011-01-19</td>
<td align="center">H9</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>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-07-23</td>
<td align="center">E5</td>
<td align="center">2011-01-24</td>
<td align="center">H9</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">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">2010-08-18</td>
<td align="center">E5</td>
<td align="center">2011-03-09</td>
<td align="center">H9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-11-19</td>
<td align="center">E5</td>
<td align="center">2011-06-07</td>
<td align="center">H9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-12-05</td>
<td align="center">E5</td>
<td align="center">2011-07-30</td>
<td align="center">H9</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>
@ -615,14 +615,14 @@
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-02-04</td>
<td align="center">E5</td>
<td align="center">2011-08-01</td>
<td align="center">H9</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">TRUE</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
</tbody>
</table>
@ -637,7 +637,7 @@
<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 15,867 first weighted isolates (79.3% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb19-10" title="10"><span class="co">#&gt; =&gt; Found 15,814 first weighted isolates (79.1% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -654,11 +654,11 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-07</td>
<td align="center">E5</td>
<td align="center">2010-04-26</td>
<td align="center">H9</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">TRUE</td>
@ -666,23 +666,23 @@
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-01-14</td>
<td align="center">E5</td>
<td align="center">2010-05-27</td>
<td align="center">H9</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">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-02-07</td>
<td align="center">E5</td>
<td align="center">2010-07-20</td>
<td align="center">H9</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">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
@ -690,70 +690,70 @@
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-03-28</td>
<td align="center">E5</td>
<td align="center">2010-11-25</td>
<td align="center">H9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-05-25</td>
<td align="center">E5</td>
<td align="center">2011-01-19</td>
<td align="center">H9</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="even">
<td align="center">6</td>
<td align="center">2010-07-23</td>
<td align="center">E5</td>
<td align="center">2011-01-24</td>
<td align="center">H9</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">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-08-18</td>
<td align="center">E5</td>
<td align="center">2011-03-09</td>
<td align="center">H9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">FALSE</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-11-19</td>
<td align="center">E5</td>
<td align="center">2011-06-07</td>
<td align="center">H9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-12-05</td>
<td align="center">E5</td>
<td align="center">2011-07-30</td>
<td align="center">H9</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>
@ -762,23 +762,23 @@
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-02-04</td>
<td align="center">E5</td>
<td align="center">2011-08-01</td>
<td align="center">H9</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">TRUE</td>
<td align="center">TRUE</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
</tbody>
</table>
<p>Instead of 2, now 7 isolates are flagged. In total, 79.3% of all isolates are marked ‘first weighted’ - 51.1% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>Instead of 2, now 6 isolates are flagged. In total, 79.1% of all isolates are marked ‘first weighted’ - 50.8% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>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 15,867 isolates for analysis.</p>
<p>So we end up with 15,814 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>
@ -803,63 +803,63 @@
</tr></thead>
<tbody>
<tr class="odd">
<td>2</td>
<td align="center">2014-02-11</td>
<td align="center">T4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COL</td>
<td>1</td>
<td align="center">2015-09-11</td>
<td align="center">C6</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AUR</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">Escherichia</td>
<td align="center">coli</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>3</td>
<td align="center">2015-04-14</td>
<td align="center">N3</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNE</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">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>4</td>
<td align="center">2017-03-09</td>
<td align="center">D1</td>
<td align="center">Hospital A</td>
<td align="center">2012-03-06</td>
<td align="center">C2</td>
<td align="center">Hospital C</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">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>5</td>
<td align="center">2013-10-22</td>
<td align="center">W9</td>
<tr class="odd">
<td>4</td>
<td align="center">2011-11-09</td>
<td align="center">X3</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AUR</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">TRUE</td>
</tr>
<tr class="even">
<td>6</td>
<td align="center">2017-02-26</td>
<td align="center">X1</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNE</td>
<td align="center">R</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">F</td>
<td align="center">Gram negative</td>
<td align="center">Klebsiella</td>
@ -867,10 +867,26 @@
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>6</td>
<td align="center">2012-08-12</td>
<td align="center">C10</td>
<td align="center">Hospital B</td>
<td>7</td>
<td align="center">2010-02-15</td>
<td align="center">P3</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="even">
<td>8</td>
<td align="center">2012-10-20</td>
<td align="center">H4</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">S</td>
<td align="center">S</td>
@ -882,22 +898,6 @@
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>7</td>
<td align="center">2012-05-06</td>
<td align="center">V7</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">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>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -915,9 +915,9 @@
<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> (15,867 x 13)</strong></p>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (15,814 x 13)</strong></p>
<p>Columns: 2<br>
Length: 15,867 (of which NA: 0 = 0.00%)<br>
Length: 15,814 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -934,33 +934,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,816</td>
<td align="right">49.3%</td>
<td align="right">7,816</td>
<td align="right">49.3%</td>
<td align="right">7,918</td>
<td align="right">50.1%</td>
<td align="right">7,918</td>
<td align="right">50.1%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">4,004</td>
<td align="right">25.2%</td>
<td align="right">11,820</td>
<td align="right">3,865</td>
<td align="right">24.4%</td>
<td align="right">11,783</td>
<td align="right">74.5%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,496</td>
<td align="right">15.7%</td>
<td align="right">14,316</td>
<td align="right">90.2%</td>
<td align="right">2,458</td>
<td align="right">15.5%</td>
<td align="right">14,241</td>
<td align="right">90.1%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,551</td>
<td align="right">9.8%</td>
<td align="right">15,867</td>
<td align="right">1,573</td>
<td align="right">9.9%</td>
<td align="right">15,814</td>
<td align="right">100.0%</td>
</tr>
</tbody>
@ -969,9 +969,9 @@ Longest: 24</p>
<div id="resistance-percentages" class="section level2">
<h2 class="hasAnchor">
<a href="#resistance-percentages" class="anchor"></a>Resistance percentages</h2>
<p>The functions <code>portion_R</code>, <code>portion_RI</code>, <code>portion_I</code>, <code>portion_IS</code> and <code>portion_S</code> can be used to determine the portion of a specific antimicrobial outcome. They can be used on their own:</p>
<p>The functions <code><a href="../reference/portion.html">portion_R()</a></code>, <code>portion_RI()</code>, <code><a href="../reference/portion.html">portion_I()</a></code>, <code>portion_IS()</code> and <code><a href="../reference/portion.html">portion_S()</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] 0.4757673</span></a></code></pre></div>
<a class="sourceLine" id="cb25-2" title="2"><span class="co">#&gt; [1] 0.4762868</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>
@ -984,19 +984,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4797111</td>
<td align="center">0.4752371</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4868636</td>
<td align="center">0.4825898</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4661747</td>
<td align="center">0.4705631</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4581512</td>
<td align="center">0.4711928</td>
</tr>
</tbody>
</table>
@ -1014,72 +1014,72 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4797111</td>
<td align="center">4707</td>
<td align="center">0.4752371</td>
<td align="center">4745</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4868636</td>
<td align="center">5519</td>
<td align="center">0.4825898</td>
<td align="center">5514</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4661747</td>
<td align="center">2439</td>
<td align="center">0.4705631</td>
<td align="center">2344</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4581512</td>
<td align="center">3202</td>
<td align="center">0.4711928</td>
<td align="center">3211</td>
</tr>
</tbody>
</table>
<p>These functions can also be used to get the portion of multiple antibiotics, to calculate co-resistance very easily:</p>
<p>These functions can also be used to get the portion of multiple antibiotics, to calculate empiric susceptibility of combination therapies very easily:</p>
<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb28-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(genus) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb28-3" title="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(<span class="dt">amoxicillin =</span> <span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl),</a>
<a class="sourceLine" id="cb28-3" title="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(<span class="dt">amoxiclav =</span> <span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl),</a>
<a class="sourceLine" id="cb28-4" title="4"> <span class="dt">gentamicin =</span> <span class="kw"><a href="../reference/portion.html">portion_S</a></span>(gent),</a>
<a class="sourceLine" id="cb28-5" title="5"> <span class="st">"amox + gent"</span> =<span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent))</a></code></pre></div>
<a class="sourceLine" id="cb28-5" title="5"> <span class="dt">amoxiclav_genta =</span> <span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent))</a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">genus</th>
<th align="center">amoxicillin</th>
<th align="center">amoxiclav</th>
<th align="center">gentamicin</th>
<th align="center">amox + gent</th>
<th align="center">amoxiclav_genta</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7345189</td>
<td align="center">0.8976459</td>
<td align="center">0.9721085</td>
<td align="center">0.7346552</td>
<td align="center">0.8993433</td>
<td align="center">0.9744885</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.7433914</td>
<td align="center">0.8949065</td>
<td align="center">0.9767892</td>
<td align="center">0.7406230</td>
<td align="center">0.9020979</td>
<td align="center">0.9726637</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7285215</td>
<td align="center">0.9153347</td>
<td align="center">0.9787712</td>
<td align="center">0.7322122</td>
<td align="center">0.9210867</td>
<td align="center">0.9785252</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.7315705</td>
<td align="center">0.7135883</td>
<td align="center">0.0000000</td>
<td align="center">0.7315705</td>
<td align="center">0.7135883</td>
</tr>
</tbody>
</table>
<p>To make a transition to the next part, let’s see how this difference could be plotted:</p>
<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb29-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(genus) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb29-3" title="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(<span class="st">"1. Amoxicillin"</span> =<span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl),</a>
<a class="sourceLine" id="cb29-3" title="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(<span class="st">"1. Amoxi/clav"</span> =<span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl),</a>
<a class="sourceLine" id="cb29-4" title="4"> <span class="st">"2. Gentamicin"</span> =<span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(gent),</a>
<a class="sourceLine" id="cb29-5" title="5"> <span class="st">"3. Amox + gent"</span> =<span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent)) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb29-5" title="5"> <span class="st">"3. Amoxi/clav + gent"</span> =<span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent)) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb29-6" title="6"><span class="st"> </span>tidyr<span class="op">::</span><span class="kw"><a href="https://tidyr.tidyverse.org/reference/gather.html">gather</a></span>(<span class="st">"Antibiotic"</span>, <span class="st">"S"</span>, <span class="op">-</span>genus) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb29-7" title="7"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span>(<span class="kw"><a href="https://ggplot2.tidyverse.org/reference/aes.html">aes</a></span>(<span class="dt">x =</span> genus,</a>
<a class="sourceLine" id="cb29-8" title="8"> <span class="dt">y =</span> S,</a>
@ -1100,9 +1100,9 @@ Longest: 24</p>
<a class="sourceLine" id="cb30-7" title="7"> <span class="dt">x =</span> <span class="st">"My X axis"</span>,</a>
<a class="sourceLine" id="cb30-8" title="8"> <span class="dt">y =</span> <span class="st">"My Y axis"</span>)</a>
<a class="sourceLine" id="cb30-9" title="9"></a>
<a class="sourceLine" id="cb30-10" title="10"><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span>(a_data_set,</a>
<a class="sourceLine" id="cb30-11" title="11"> <span class="kw"><a href="https://ggplot2.tidyverse.org/reference/aes.html">aes</a></span>(year, value) <span class="op">+</span></a>
<a class="sourceLine" id="cb30-12" title="12"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html">geom_bar</a></span>()</a></code></pre></div>
<a class="sourceLine" id="cb30-10" title="10"><span class="co"># or as short as:</span></a>
<a class="sourceLine" id="cb30-11" title="11"><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span>(a_data_set) <span class="op">+</span></a>
<a class="sourceLine" id="cb30-12" title="12"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html">geom_bar</a></span>(<span class="kw"><a href="https://ggplot2.tidyverse.org/reference/aes.html">aes</a></span>(year))</a></code></pre></div>
<p>The <code>AMR</code> package contains functions to extend this <code>ggplot2</code> package, for example <code><a href="../reference/ggplot_rsi.html">geom_rsi()</a></code>. It automatically transforms data with <code><a href="../reference/count.html">count_df()</a></code> or <code><a href="../reference/portion.html">portion_df()</a></code> and show results in stacked bars. Its simplest and shortest example:</p>
<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" title="1"><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span>(data_1st) <span class="op">+</span></a>
<a class="sourceLine" id="cb31-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/ggplot_rsi.html">geom_rsi</a></span>(<span class="dt">translate_ab =</span> <span class="ot">FALSE</span>)</a></code></pre></div>