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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>

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</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 apply EUCAST rules</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>EUCAST.Rmd</code></div>

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<span class="navbar-brand">
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<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 use the <em>G</em>-test</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>G_test.Rmd</code></div>

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<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>
@ -218,16 +218,16 @@
</li>
<li>
<p><strong>R is extremely flexible.</strong></p>
<p>Because you write the syntax yourself, you can do anything you want. The flexibility in transforming, gathering, grouping, summarising and drawing plots is endless - with SPSS, SAS or Stata you are bound to their algorithms and styles. It may be a bit flexible, but you can never create that very specific publication-ready plot without using other (paid) software.</p>
<p>Because you write the syntax yourself, you can do anything you want. The flexibility in transforming, gathering, grouping, summarising and drawing plots is endless - with SPSS, SAS or Stata you are bound to their algorithms and styles. They may be a bit flexible, but you can probably never create that very specific publication-ready plot without using other (paid) software.</p>
</li>
<li>
<p><strong>R can be easily automated.</strong></p>
<p>Over the last years, <a href="https://rmarkdown.rstudio.com/">R Markdown</a> has really made an interesting development. With R Markdown, you can very easily reproduce your reports, whether it’s to Word, Powerpoint, a website, a PDF document or just the raw data to Excel. I use this a lot to generate monthly reports automatically. Just write the code once and enjoy the automatically updated reports at any interval you like.</p>
<p>For an even more professional environment, you could create <a href="https://shiny.rstudio.com/">Shiny apps</a>: live manipulation of data using a custom made website. The webdesign knowledge needed (Javascript, CSS, HTML) is almost <em>zero</em>.</p>
<p>For an even more professional environment, you could create <a href="https://shiny.rstudio.com/">Shiny apps</a>: live manipulation of data using a custom made website. The webdesign knowledge needed (JavaScript, CSS, HTML) is almost <em>zero</em>.</p>
</li>
<li>
<p><strong>R has a huge community.</strong></p>
<p>Many R users just ask questions on website like <a href="https://stackoverflow.com">stackoverflow.com</a>, the largest online community for programmers. At the time of writing, around <a href="https://stackoverflow.com/questions/tagged/r?sort=votes">275,000 R questions</a> have been asked on this platform (which covers questions and answer for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, more than <a href="https://stackoverflow.com/questions/tagged/r?sort=votes">275,000 R-related questions</a> have already been asked on this platform (which covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
</li>
<li>
<p><strong>R understands any data type, including SPSS/SAS/Stata.</strong></p>

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<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 work with WHONET data</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>WHONET.Rmd</code></div>

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<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 get properties of an antibiotic</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>atc_property.Rmd</code></div>

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</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>Benchmarks</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>benchmarks.Rmd</code></div>
@ -217,14 +217,14 @@
<a class="sourceLine" id="cb2-8" title="8"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb2-9" title="9"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb2-10" title="10"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb2-11" title="11"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb2-12" title="12"><span class="co">#&gt; as.mo("sau") 16.70 16.80 21.50 16.8 17.50 56.6 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#&gt; as.mo("stau") 33.70 34.00 46.60 40.2 50.50 83.7 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#&gt; as.mo("staaur") 16.70 16.80 28.60 17.3 41.90 59.7 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#&gt; as.mo("STAAUR") 16.60 16.70 21.90 17.1 20.00 56.6 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#&gt; as.mo("S. aureus") 24.50 24.90 25.40 25.2 26.10 26.7 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#&gt; as.mo("S. aureus") 24.60 25.00 31.30 25.1 25.30 85.1 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#&gt; as.mo("Staphylococcus aureus") 7.37 7.42 8.17 7.5 8.27 11.8 10</span></a></code></pre></div>
<a class="sourceLine" id="cb2-11" title="11"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb2-12" title="12"><span class="co">#&gt; as.mo("sau") 16.70 16.80 17.10 16.90 17.20 18.4 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#&gt; as.mo("stau") 31.70 31.80 48.90 31.90 73.00 117.0 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#&gt; as.mo("staaur") 16.70 16.80 23.10 16.90 17.90 76.0 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#&gt; as.mo("STAAUR") 16.80 17.00 33.20 18.20 56.00 58.6 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#&gt; as.mo("S. aureus") 24.60 24.70 29.00 24.70 25.30 65.8 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#&gt; as.mo("S. aureus") 24.60 24.70 29.20 24.80 25.10 67.4 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#&gt; as.mo("Staphylococcus aureus") 7.02 7.11 7.73 7.26 7.33 11.9 10</span></a></code></pre></div>
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.</p>
<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Thermus islandicus</em> (<code>B_THERMS_ISL</code>), a bug probably never found before in humans:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">T.islandicus &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"theisl"</span>),</a>
@ -235,13 +235,13 @@
<a class="sourceLine" id="cb3-6" title="6"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb3-7" title="7"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(T.islandicus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb3-9" title="9"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co">#&gt; as.mo("theisl") 289.0 291.0 314.0 312.0 336.0 343 10</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co">#&gt; as.mo("THEISL") 290.0 293.0 319.0 331.0 337.0 344 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#&gt; as.mo("T. islandicus") 73.5 73.8 90.6 75.1 114.0 118 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#&gt; as.mo("T. islandicus") 73.7 73.9 78.5 74.6 74.7 115 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#&gt; as.mo("Thermus islandicus") 66.5 67.3 80.3 69.5 107.0 108 10</span></a></code></pre></div>
<p>That takes 6.7 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
<a class="sourceLine" id="cb3-9" title="9"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co">#&gt; as.mo("theisl") 262.0 292.0 296.0 304.0 310 312 10</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co">#&gt; as.mo("THEISL") 261.0 263.0 286.0 288.0 307 311 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#&gt; as.mo("T. islandicus") 142.0 143.0 164.0 165.0 184 187 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#&gt; as.mo("T. islandicus") 142.0 143.0 170.0 163.0 192 229 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#&gt; as.mo("Thermus islandicus") 67.7 68.1 94.3 89.4 117 132 10</span></a></code></pre></div>
<p>That takes 7.5 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
<p>In the figure below, we compare <em>Escherichia coli</em> (which is very common) with <em>Prevotella brevis</em> (which is moderately common) and with <em>Thermus islandicus</em> (which is very uncommon):</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/par">par</a></span>(<span class="dt">mar =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">5</span>, <span class="dv">16</span>, <span class="dv">4</span>, <span class="dv">2</span>)) <span class="co"># set more space for left margin text (16)</span></a>
<a class="sourceLine" id="cb4-2" title="2"></a>
@ -260,7 +260,7 @@
<div id="repetitive-results" class="section level3">
<h3 class="hasAnchor">
<a href="#repetitive-results" class="anchor"></a>Repetitive results</h3>
<p>Repetitive results mean that unique values are present more than once. Unique values will only be calculated once by <code><a href="../reference/as.mo.html">as.mo()</a></code>. We will use <code><a href="../reference/mo_property.html">mo_fullname()</a></code> for this test - a helper function that returns the full microbial name (genus, species and possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()</a></code> internally.</p>
<p>Repetitive results are unique values that are present more than once. Unique values will only be calculated once by <code><a href="../reference/as.mo.html">as.mo()</a></code>. We will use <code><a href="../reference/mo_property.html">mo_fullname()</a></code> for this test - a helper function that returns the full microbial name (genus, species and possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()</a></code> internally.</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(dplyr)</a>
<a class="sourceLine" id="cb5-2" title="2"><span class="co"># take all MO codes from the septic_patients data set</span></a>
<a class="sourceLine" id="cb5-3" title="3">x &lt;-<span class="st"> </span>septic_patients<span class="op">$</span>mo <span class="op">%&gt;%</span></a>
@ -286,9 +286,9 @@
<a class="sourceLine" id="cb5-23" title="23"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb5-24" title="24"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb5-25" title="25"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb5-26" title="26"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb5-27" title="27"><span class="co">#&gt; mo_fullname(x) 732 768 800 794 799 949 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.79 seconds (793 ms). You only lose time on your unique input values.</p>
<a class="sourceLine" id="cb5-26" title="26"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb5-27" title="27"><span class="co">#&gt; mo_fullname(x) 732 739 818 819 837 1040 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.82 seconds (818 ms). You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -301,10 +301,10 @@
<a class="sourceLine" id="cb6-5" title="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb6-6" title="6"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb6-7" title="7"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb6-8" title="8"><span class="co">#&gt; A 10.900 11.300 11.900 11.500 11.700 15.200 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co">#&gt; B 22.000 22.600 26.900 22.600 22.800 62.400 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co">#&gt; C 0.311 0.502 0.531 0.533 0.577 0.765 10</span></a></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0005 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<a class="sourceLine" id="cb6-8" title="8"><span class="co">#&gt; A 11.100 11.300 11.500 11.500 11.600 11.700 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co">#&gt; B 22.200 22.500 22.800 22.900 23.000 23.500 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co">#&gt; C 0.325 0.566 0.571 0.579 0.599 0.704 10</span></a></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0006 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
<a class="sourceLine" id="cb7-2" title="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
<a class="sourceLine" id="cb7-3" title="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
@ -317,14 +317,14 @@
<a class="sourceLine" id="cb7-10" title="10"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb7-11" title="11"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb7-12" title="12"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb7-13" title="13"><span class="co">#&gt; A 0.274 0.333 0.417 0.412 0.481 0.611 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co">#&gt; B 0.337 0.353 0.403 0.411 0.438 0.461 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co">#&gt; C 0.336 0.362 0.530 0.528 0.682 0.755 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co">#&gt; D 0.263 0.316 0.340 0.331 0.360 0.474 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co">#&gt; E 0.252 0.326 0.326 0.329 0.345 0.389 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co">#&gt; F 0.250 0.300 0.319 0.327 0.351 0.351 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co">#&gt; G 0.240 0.246 0.288 0.277 0.325 0.351 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co">#&gt; H 0.242 0.257 0.304 0.294 0.332 0.395 10</span></a></code></pre></div>
<a class="sourceLine" id="cb7-13" title="13"><span class="co">#&gt; A 0.308 0.392 0.419 0.406 0.478 0.524 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co">#&gt; B 0.377 0.406 0.424 0.418 0.442 0.486 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co">#&gt; C 0.359 0.516 0.580 0.574 0.664 0.730 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co">#&gt; D 0.266 0.326 0.337 0.342 0.350 0.383 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co">#&gt; E 0.254 0.281 0.332 0.336 0.359 0.446 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co">#&gt; F 0.237 0.315 0.329 0.340 0.360 0.374 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co">#&gt; G 0.261 0.295 0.318 0.323 0.341 0.390 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co">#&gt; H 0.271 0.290 0.321 0.317 0.343 0.403 10</span></a></code></pre></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> too, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
</div>
<div id="results-in-other-languages" class="section level3">
@ -351,13 +351,13 @@
<a class="sourceLine" id="cb8-18" title="18"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
<a class="sourceLine" id="cb8-19" title="19"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb8-20" title="20"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb8-21" title="21"><span class="co">#&gt; en 14.68 15.11 15.28 15.27 15.34 16.21 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co">#&gt; de 23.53 23.65 24.04 23.82 24.63 24.88 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co">#&gt; nl 23.36 23.53 27.76 23.81 23.87 63.45 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co">#&gt; es 23.59 23.83 23.94 23.96 24.07 24.22 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co">#&gt; it 23.30 23.76 27.92 23.83 24.18 64.01 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co">#&gt; fr 23.47 23.78 31.80 23.84 24.90 63.25 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co">#&gt; pt 23.28 23.69 27.97 23.85 24.42 64.14 10</span></a></code></pre></div>
<a class="sourceLine" id="cb8-21" title="21"><span class="co">#&gt; en 15.06 15.54 22.29 15.71 31.46 40.83 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co">#&gt; de 23.57 23.91 28.72 24.04 26.24 47.77 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co">#&gt; nl 23.46 23.87 33.14 24.71 45.69 68.77 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co">#&gt; es 23.76 23.98 37.40 24.72 46.85 90.39 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co">#&gt; it 23.98 24.07 30.76 24.49 25.18 67.52 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co">#&gt; fr 24.03 24.04 27.06 24.14 26.51 47.08 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co">#&gt; pt 23.66 24.00 30.90 24.17 25.84 65.76 10</span></a></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
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<h1>How to create frequency tables</h1>
<h4 class="author">Matthijs S. Berends</h4>
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<h1>How to get properties of a microorganism</h1>
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<h1>How to predict antimicrobial resistance</h1>
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