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memory for as.mo()

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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">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">05 March 2019</h4>
<h4 class="date">15 March 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 05 March 2019.</p>
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">RMarkdown</a>. However, the methodology remains unchanged. This page was generated on 15 March 2019.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -217,21 +217,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2019-03-05</td>
<td align="center">2019-03-15</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2019-03-05</td>
<td align="center">2019-03-15</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2019-03-05</td>
<td align="center">2019-03-15</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -327,21 +327,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-01-23</td>
<td align="center">E2</td>
<td align="center">2011-03-23</td>
<td align="center">H4</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-12-07</td>
<td align="center">L8</td>
<td align="center">2016-02-07</td>
<td align="center">A10</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -349,49 +349,49 @@
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-07-19</td>
<td align="center">W5</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2017-05-30</td>
<td align="center">Q9</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-11-26</td>
<td align="center">L7</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-01-24</td>
<td align="center">M7</td>
<td align="center">2016-09-19</td>
<td align="center">U5</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-11-13</td>
<td align="center">V10</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<tr class="odd">
<td align="center">2016-03-20</td>
<td align="center">X10</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-07-29</td>
<td align="center">D10</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -411,15 +411,15 @@
#&gt;
#&gt; Item Count Percent Cum. Count Cum. Percent
#&gt; --- ----- ------- -------- ----------- -------------
#&gt; 1 M 10,562 52.8% 10,562 52.8%
#&gt; 2 F 9,438 47.2% 20,000 100.0%</code></pre>
#&gt; 1 M 10,422 52.1% 10,422 52.1%
#&gt; 2 F 9,578 47.9% 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>
<a class="sourceLine" id="cb12-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">bacteria =</span> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(bacteria))</a></code></pre></div>
<p>We also want to transform the antibiotics, because in real life data we don’t know if they are really clean. The <code><a href="../reference/as.rsi.html">as.rsi()</a></code> function ensures reliability and reproducibility in these kind of variables. The <code><a href="https://dplyr.tidyverse.org/reference/summarise_all.html">mutate_at()</a></code> will run the <code><a href="../reference/as.rsi.html">as.rsi()</a></code> function on defined variables:</p>
<p>We also want to transform the antibiotics, because in real life data we don’t know if they are really clean. The <code><a href="../reference/as.rsi.html">as.rsi()</a></code> function ensures reliability and reproducibility in these kind of variables. The <code><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at()</a></code> will run the <code><a href="../reference/as.rsi.html">as.rsi()</a></code> function on defined variables:</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb13-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html">mutate_at</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(amox<span class="op">:</span>gent), as.rsi)</a></code></pre></div>
<a class="sourceLine" id="cb13-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(amox<span class="op">:</span>gent), as.rsi)</a></code></pre></div>
<p>Finally, we will apply <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST rules</a> on our antimicrobial results. In Europe, most medical microbiological laboratories already apply these rules. Our package features their latest insights on intrinsic resistance and exceptional phenotypes. Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p>
<p>Because the amoxicillin (column <code>amox</code>) and amoxicillin/clavulanic acid (column <code>amcl</code>) in our data were generated randomly, some rows will undoubtedly contain amox = S and amcl = R, which is technically impossible. The <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> fixes this:</p>
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1">data &lt;-<span class="st"> </span><span class="kw"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(data, <span class="dt">col_mo =</span> <span class="st">"bacteria"</span>)</a>
@ -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 (1344 changes)</span></a>
<a class="sourceLine" id="cb14-22" title="22"><span class="co">#&gt; Table 1: Intrinsic resistance in Enterobacteriaceae (1315 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 (2767 changes)</span></a>
<a class="sourceLine" id="cb14-25" title="25"><span class="co">#&gt; Table 4: Intrinsic resistance in Gram-positive bacteria (2799 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 7,383 out of 20,000 rows</span></a>
<a class="sourceLine" id="cb14-41" title="41"><span class="co">#&gt; =&gt; EUCAST rules affected 7,488 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 4,111 test results (0 to S; 0 to I; 4,111 to R)</span></a></code></pre></div>
<a class="sourceLine" id="cb14-43" title="43"><span class="co">#&gt; -&gt; changed 4,114 test results (0 to S; 0 to I; 4,114 to R)</span></a></code></pre></div>
</div>
<div id="adding-new-variables" class="section level1">
<h1 class="hasAnchor">
@ -489,7 +489,7 @@
<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 5,676 first isolates (28.4% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb16-6" title="6"><span class="co">#&gt; =&gt; Found 5,688 first isolates (28.4% of total)</span></a></code></pre></div>
<p>So only 28.4% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb17-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(first <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>)</a></code></pre></div>
@ -516,19 +516,19 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-20</td>
<td align="center">L10</td>
<td align="center">2010-04-01</td>
<td align="center">K1</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">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-03-26</td>
<td align="center">L10</td>
<td align="center">2010-04-30</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
@ -538,10 +538,10 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-05-05</td>
<td align="center">L10</td>
<td align="center">2010-10-12</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -549,19 +549,19 @@
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-06-20</td>
<td align="center">L10</td>
<td align="center">2010-12-05</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-07-10</td>
<td align="center">L10</td>
<td align="center">2011-01-19</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -571,21 +571,21 @@
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-08-01</td>
<td align="center">L10</td>
<td align="center">2011-04-07</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-08-27</td>
<td align="center">L10</td>
<td align="center">2011-06-16</td>
<td align="center">K1</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>
@ -593,19 +593,19 @@
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-09-09</td>
<td align="center">L10</td>
<td align="center">2011-07-16</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-09-26</td>
<td align="center">L10</td>
<td align="center">2011-08-25</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
@ -615,18 +615,18 @@
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2010-10-11</td>
<td align="center">L10</td>
<td align="center">2011-09-11</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">FALSE</td>
</tr>
</tbody>
</table>
<p>Only 1 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>Only 2 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>If a column exists with a name like ‘key(…)ab’ the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> function will automatically use it and determine the first weighted isolates. Mind the NOTEs in below output:</p>
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb19-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">keyab =</span> <span class="kw"><a href="../reference/key_antibiotics.html">key_antibiotics</a></span>(.)) <span class="op">%&gt;%</span><span class="st"> </span></a>
@ -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 15,767 first weighted isolates (78.8% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb19-10" title="10"><span class="co">#&gt; =&gt; Found 15,948 first weighted isolates (79.7% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -654,56 +654,80 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-20</td>
<td align="center">L10</td>
<td align="center">2010-04-01</td>
<td align="center">K1</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">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-03-26</td>
<td align="center">L10</td>
<td align="center">2010-04-30</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-05-05</td>
<td align="center">L10</td>
<td align="center">2010-10-12</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-06-20</td>
<td align="center">L10</td>
<td align="center">2010-12-05</td>
<td align="center">K1</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">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2011-01-19</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-04-07</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-07-10</td>
<td align="center">L10</td>
<td align="center">7</td>
<td align="center">2011-06-16</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -713,21 +737,21 @@
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-08-01</td>
<td align="center">L10</td>
<td align="center">8</td>
<td align="center">2011-07-16</td>
<td align="center">K1</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">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-08-27</td>
<td align="center">L10</td>
<td align="center">9</td>
<td align="center">2011-08-25</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
@ -737,48 +761,24 @@
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-09-09</td>
<td align="center">L10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-09-26</td>
<td align="center">L10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2010-10-11</td>
<td align="center">L10</td>
<td align="center">2011-09-11</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Instead of 1, now 4 isolates are flagged. In total, 78.8% of all isolates are marked ‘first weighted’ - 50.5% 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 7 isolates are flagged. In total, 79.7% of all isolates are marked ‘first weighted’ - 51.3% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>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 15,767 isolates for analysis.</p>
<p>So we end up with 15,948 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>
@ -786,6 +786,7 @@
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(data_1st)</a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th></th>
<th align="center">date</th>
<th align="center">patient_id</th>
<th align="center">hospital</th>
@ -802,90 +803,96 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-01-23</td>
<td align="center">E2</td>
<td>1</td>
<td align="center">2011-03-23</td>
<td align="center">H4</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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>2</td>
<td align="center">2016-02-07</td>
<td align="center">A10</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>5</td>
<td align="center">2016-03-20</td>
<td align="center">X10</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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>7</td>
<td align="center">2015-08-01</td>
<td align="center">Q4</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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 align="center">2017-12-07</td>
<td align="center">L8</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">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="odd">
<td align="center">2012-07-19</td>
<td align="center">W5</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AUR</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 positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-11-26</td>
<td align="center">L7</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-01-24</td>
<td align="center">M7</td>
<td align="center">Hospital B</td>
<td>8</td>
<td align="center">2012-03-10</td>
<td align="center">Z10</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-11-13</td>
<td align="center">V10</td>
<td align="center">Hospital A</td>
<td>11</td>
<td align="center">2014-10-21</td>
<td align="center">G8</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
@ -908,9 +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> (15,767 x 13)</strong></p>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (15,948 x 13)</strong></p>
<p>Columns: 2<br>
Length: 15,767 (of which NA: 0 = 0.00%)<br>
Length: 15,948 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -927,33 +934,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,762</td>
<td align="right">49.2%</td>
<td align="right">7,762</td>
<td align="right">49.2%</td>
<td align="right">7,952</td>
<td align="right">49.9%</td>
<td align="right">7,952</td>
<td align="right">49.9%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">4,014</td>
<td align="right">25.5%</td>
<td align="right">11,776</td>
<td align="right">74.7%</td>
<td align="right">3,886</td>
<td align="right">24.4%</td>
<td align="right">11,838</td>
<td align="right">74.2%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,450</td>
<td align="right">15.5%</td>
<td align="right">14,226</td>
<td align="right">90.2%</td>
<td align="right">2,509</td>
<td align="right">15.7%</td>
<td align="right">14,347</td>
<td align="right">90.0%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,541</td>
<td align="right">9.8%</td>
<td align="right">15,767</td>
<td align="right">1,601</td>
<td align="right">10.0%</td>
<td align="right">15,948</td>
<td align="right">100.0%</td>
</tr>
</tbody>
@ -964,7 +971,7 @@ Longest: 24</p>
<a href="#resistance-percentages" class="anchor"></a>Resistance percentages</h2>
<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] 0.4762479</span></a></code></pre></div>
<a class="sourceLine" id="cb25-2" title="2"><span class="co">#&gt; [1] 0.4812516</span></a></code></pre></div>
<p>Or can be used in conjuction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb26-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital) <span class="op">%&gt;%</span><span class="st"> </span></a>
@ -977,19 +984,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4717496</td>
<td align="center">0.4801481</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4754662</td>
<td align="center">0.4811895</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4748170</td>
<td align="center">0.4707087</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4854430</td>
<td align="center">0.4915144</td>
</tr>
</tbody>
</table>
@ -1007,23 +1014,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4717496</td>
<td align="center">4761</td>
<td align="center">0.4801481</td>
<td align="center">4861</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4754662</td>
<td align="center">5523</td>
<td align="center">0.4811895</td>
<td align="center">5582</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4748170</td>
<td align="center">2323</td>
<td align="center">0.4707087</td>
<td align="center">2441</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4854430</td>
<td align="center">3160</td>
<td align="center">0.4915144</td>
<td align="center">3064</td>
</tr>
</tbody>
</table>
@ -1043,27 +1050,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7333162</td>
<td align="center">0.9035043</td>
<td align="center">0.9748776</td>
<td align="center">0.7282445</td>
<td align="center">0.9031690</td>
<td align="center">0.9756036</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.7352369</td>
<td align="center">0.9104478</td>
<td align="center">0.9733939</td>
<td align="center">0.7270456</td>
<td align="center">0.9000625</td>
<td align="center">0.9787633</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7416542</td>
<td align="center">0.9160438</td>
<td align="center">0.9763328</td>
<td align="center">0.7220793</td>
<td align="center">0.9184251</td>
<td align="center">0.9796706</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.7473469</td>
<td align="center">0.7182144</td>
<td align="center">0.0000000</td>
<td align="center">0.7473469</td>
<td align="center">0.7182144</td>
</tr>
</tbody>
</table>

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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">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">05 March 2019</h4>
<h4 class="date">15 March 2019</h4>
<div class="hidden name"><code>EUCAST.Rmd</code></div>

4
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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">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</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">05 March 2019</h4>
<h4 class="date">15 March 2019</h4>
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@ -192,7 +192,7 @@
<h1>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">09 March 2019</h4>
<h4 class="date">15 March 2019</h4>
<div class="hidden name"><code>SPSS.Rmd</code></div>

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@ -192,7 +192,7 @@
<h1>How to work with WHONET data</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">05 March 2019</h4>
<h4 class="date">15 March 2019</h4>
<div class="hidden name"><code>WHONET.Rmd</code></div>
@ -227,17 +227,17 @@
<a class="sourceLine" id="cb3-3" title="3"><span class="st"> </span><span class="co"># get microbial ID based on given organism</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">mo =</span> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(Organism)) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="st"> </span><span class="co"># transform everything from "AMP_ND10" to "CIP_EE" to the new `rsi` class</span></a>
<a class="sourceLine" id="cb3-6" title="6"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html">mutate_at</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(AMP_ND10<span class="op">:</span>CIP_EE), as.rsi)</a></code></pre></div>
<a class="sourceLine" id="cb3-6" title="6"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(AMP_ND10<span class="op">:</span>CIP_EE), as.rsi)</a></code></pre></div>
<p>No errors or warnings, so all values are transformed succesfully. Let’s check it though, with a couple of frequency tables:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="co"># our newly created `mo` variable</span></a>
<a class="sourceLine" id="cb4-2" title="2">data <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(mo, <span class="dt">nmax =</span> <span class="dv">10</span>)</a></code></pre></div>
<p><strong>Frequency table of <code>mo</code> from a <code>data.frame</code> (500 x 54)</strong></p>
<p>Class: <code>mo</code> (<code>character</code>)<br>
Length: 500 (of which NA: 0 = 0.00%)<br>
Unique: 39</p>
<p>Families: 9<br>
Genera: 16<br>
Species: 36</p>
Unique: 37</p>
<p>Families: 10<br>
Genera: 17<br>
Species: 35</p>
<table class="table">
<thead><tr class="header">
<th align="left"></th>
@ -258,7 +258,7 @@ Species: 36</p>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">B_STPHY_CNS</td>
<td align="left">B_STPHY</td>
<td align="right">74</td>
<td align="right">14.8%</td>
<td align="right">319</td>
@ -314,23 +314,23 @@ Species: 36</p>
</tr>
<tr class="odd">
<td align="left">9</td>
<td align="left">B_ENTRB_CLO</td>
<td align="right">5</td>
<td align="right">1.0%</td>
<td align="right">439</td>
<td align="right">87.8%</td>
<td align="left">B_STRPT</td>
<td align="right">8</td>
<td align="right">1.6%</td>
<td align="right">442</td>
<td align="right">88.4%</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="left">B_ENTRC</td>
<td align="right">4</td>
<td align="right">0.8%</td>
<td align="right">443</td>
<td align="right">88.6%</td>
<td align="left">B_ENTRB_CLO</td>
<td align="right">5</td>
<td align="right">1.0%</td>
<td align="right">447</td>
<td align="right">89.4%</td>
</tr>
</tbody>
</table>
<p>(omitted 29 entries, n = 57 [11.4%])</p>
<p>(omitted 27 entries, n = 53 [10.6%])</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"></a>
<a class="sourceLine" id="cb5-2" title="2"><span class="co"># our transformed antibiotic columns</span></a>
<a class="sourceLine" id="cb5-3" title="3"><span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span></a>

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@ -192,7 +192,7 @@
<h1>How to get properties of an antibiotic</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">05 March 2019</h4>
<h4 class="date">15 March 2019</h4>
<div class="hidden name"><code>atc_property.Rmd</code></div>

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@ -40,7 +40,7 @@
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<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">0.5.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">12 March 2019</h4>
<h4 class="date">15 March 2019</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -215,33 +215,33 @@
<a class="sourceLine" id="cb2-6" title="6"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. aureus"</span>),</a>
<a class="sourceLine" id="cb2-7" title="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
<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="cb2-9" 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">2</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 16.8 25.70 17.00 19.60 59.7 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#&gt; as.mo("stau") 39.10 39.2 43.70 39.30 40.60 80.4 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#&gt; as.mo("staaur") 16.70 16.8 24.60 17.00 18.20 58.9 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#&gt; as.mo("STAAUR") 16.70 16.7 22.70 16.80 17.20 74.5 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#&gt; as.mo("S. aureus") 29.70 29.7 46.70 29.80 71.30 110.0 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#&gt; as.mo("S. aureus") 29.60 29.7 36.10 29.70 33.10 83.7 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#&gt; as.mo("Staphylococcus aureus") 7.03 7.1 7.14 7.14 7.17 7.3 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") 17.0 17.0 22.0 17.0 19.0 59.0 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#&gt; as.mo("stau") 41.0 41.0 46.0 41.0 44.0 83.0 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#&gt; as.mo("staaur") 17.0 17.0 26.0 17.0 18.0 74.0 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#&gt; as.mo("STAAUR") 17.0 17.0 29.0 17.0 52.0 62.0 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#&gt; as.mo("S. aureus") 31.0 31.0 32.0 31.0 32.0 32.0 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#&gt; as.mo("S. aureus") 31.0 31.0 48.0 32.0 73.0 110.0 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#&gt; as.mo("Staphylococcus aureus") 7.4 7.4 7.7 7.4 8.2 8.6 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>
<a class="sourceLine" id="cb3-2" title="2"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"THEISL"</span>),</a>
<a class="sourceLine" id="cb3-3" title="3"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"T. islandicus"</span>),</a>
<a class="sourceLine" id="cb3-4" title="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"T. islandicus"</span>),</a>
<a class="sourceLine" id="cb3-5" title="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Thermus islandicus"</span>),</a>
<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="cb3-2" title="2"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"THEISL"</span>),</a>
<a class="sourceLine" id="cb3-3" title="3"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"T. islandicus"</span>),</a>
<a class="sourceLine" id="cb3-4" title="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"T. islandicus"</span>),</a>
<a class="sourceLine" id="cb3-5" title="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Thermus islandicus"</span>),</a>
<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">2</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") 417.0 419.0 450.0 460.0 464.0 474 10</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co">#&gt; as.mo("THEISL") 415.0 416.0 443.0 458.0 460.0 468 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#&gt; as.mo("T. islandicus") 281.0 281.0 299.0 285.0 325.0 352 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#&gt; as.mo("T. islandicus") 292.0 298.0 341.0 336.0 340.0 495 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#&gt; as.mo("Thermus islandicus") 66.2 66.5 75.5 66.9 68.2 112 10</span></a></code></pre></div>
<p>That takes 10.9 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") 420 430 450 470 470 470 10</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co">#&gt; as.mo("THEISL") 420 440 480 470 480 680 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#&gt; as.mo("T. islandicus") 290 290 310 300 330 350 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#&gt; as.mo("T. islandicus") 300 300 330 330 350 350 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#&gt; as.mo("Thermus islandicus") 67 67 86 68 110 120 10</span></a></code></pre></div>
<p>That takes 11 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>
@ -251,12 +251,15 @@
<a class="sourceLine" id="cb4-6" title="6"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"T. islandicus"</span>),</a>
<a class="sourceLine" id="cb4-7" title="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"P. brevis"</span>),</a>
<a class="sourceLine" id="cb4-8" title="8"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>),</a>
<a class="sourceLine" id="cb4-9" title="9"> <span class="dt">times =</span> <span class="dv">50</span>),</a>
<a class="sourceLine" id="cb4-9" title="9"> <span class="dt">times =</span> <span class="dv">10</span>),</a>
<a class="sourceLine" id="cb4-10" title="10"> <span class="dt">horizontal =</span> <span class="ot">TRUE</span>, <span class="dt">las =</span> <span class="dv">1</span>, <span class="dt">unit =</span> <span class="st">"s"</span>, <span class="dt">log =</span> <span class="ot">FALSE</span>,</a>
<a class="sourceLine" id="cb4-11" title="11"> <span class="dt">xlab =</span> <span class="st">""</span>, <span class="dt">ylab =</span> <span class="st">"Time in seconds"</span>,</a>
<a class="sourceLine" id="cb4-11" title="11"> <span class="dt">xlab =</span> <span class="st">""</span>, <span class="dt">ylab =</span> <span class="st">"Time in seconds"</span>, <span class="dt">ylim =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="fl">0.5</span>),</a>
<a class="sourceLine" id="cb4-12" title="12"> <span class="dt">main =</span> <span class="st">"Benchmarks per prevalence"</span>)</a></code></pre></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-5-1.png" width="720"></p>
<p>Uncommon microorganisms take a lot more time than common microorganisms. To relieve this pitfall and further improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
<p>In reality, the <code><a href="../reference/as.mo.html">as.mo()</a></code> functions <strong>learns from its own output to speed up determinations for next times</strong>. In above figure, this effect was disabled to show the difference with the boxplot below - when you would use <code><a href="../reference/as.mo.html">as.mo()</a></code> yourself:</p>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-6-1.png" width="720"></p>
<p>The highest outliers are the first times. All next determinations were done in only thousands of seconds.</p>
<p>Still, uncommon microorganisms take a lot more time than common microorganisms, especially the first time. To relieve this pitfall and further improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
<div id="repetitive-results" class="section level3">
<h3 class="hasAnchor">
<a href="#repetitive-results" class="anchor"></a>Repetitive results</h3>
@ -286,9 +289,9 @@
<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) 794 834 863 844 876 1050 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.84 seconds (844 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) 738 813 847 819 921 975 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">
@ -301,9 +304,9 @@
<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 11.100 11.200 11.200 11.300 11.400 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co">#&gt; B 27.300 27.900 28.300 28.000 28.100 31.500 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co">#&gt; C 0.319 0.326 0.472 0.563 0.568 0.579 10</span></a></code></pre></div>
<a class="sourceLine" id="cb6-8" title="8"><span class="co">#&gt; A 11.000 11.100 15.700 11.300 11.400 52.900 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co">#&gt; B 28.700 28.900 29.400 29.200 29.500 30.500 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co">#&gt; C 0.322 0.556 0.523 0.568 0.581 0.586 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>
@ -317,14 +320,14 @@
<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 0.308 0.332 0.396 0.393 0.457 0.498 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co">#&gt; B 0.349 0.376 0.419 0.444 0.462 0.467 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co">#&gt; C 0.351 0.398 0.529 0.555 0.628 0.702 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co">#&gt; D 0.302 0.330 0.378 0.381 0.424 0.465 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co">#&gt; E 0.282 0.329 0.371 0.374 0.384 0.539 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co">#&gt; F 0.281 0.354 0.364 0.366 0.402 0.444 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co">#&gt; G 0.275 0.309 0.347 0.351 0.380 0.420 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co">#&gt; H 0.279 0.306 0.356 0.363 0.404 0.411 10</span></a></code></pre></div>
<a class="sourceLine" id="cb7-13" title="13"><span class="co">#&gt; A 0.314 0.339 0.399 0.380 0.460 0.507 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co">#&gt; B 0.347 0.387 0.455 0.402 0.493 0.684 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co">#&gt; C 0.429 0.505 0.566 0.588 0.656 0.660 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co">#&gt; D 0.321 0.340 0.383 0.367 0.412 0.490 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co">#&gt; E 0.303 0.328 0.369 0.379 0.403 0.449 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co">#&gt; F 0.251 0.323 0.346 0.348 0.391 0.400 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co">#&gt; G 0.286 0.305 0.345 0.338 0.389 0.398 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co">#&gt; H 0.272 0.297 0.355 0.338 0.427 0.450 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 +354,13 @@
<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 16.61 17.17 17.23 17.28 17.38 17.56 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co">#&gt; de 28.83 28.85 29.31 29.50 29.63 29.67 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co">#&gt; nl 29.08 29.44 33.71 29.65 29.72 71.15 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co">#&gt; es 28.86 29.52 38.07 29.70 30.60 72.14 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co">#&gt; it 28.71 29.48 34.04 29.63 31.28 71.09 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co">#&gt; fr 29.32 29.47 41.44 29.53 62.86 73.16 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co">#&gt; pt 29.05 29.43 33.93 29.62 30.93 71.00 10</span></a></code></pre></div>
<a class="sourceLine" id="cb8-21" title="21"><span class="co">#&gt; en 18.05 18.11 19.33 18.25 18.65 25.12 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co">#&gt; de 30.15 30.84 43.57 31.08 72.47 73.96 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co">#&gt; nl 30.30 30.63 34.96 30.71 30.73 73.40 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co">#&gt; es 30.24 30.49 31.39 30.97 32.20 33.68 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co">#&gt; it 30.53 30.71 31.18 30.83 31.71 32.38 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co">#&gt; fr 29.64 30.49 35.32 30.84 32.25 73.00 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co">#&gt; pt 30.73 30.81 39.47 31.09 32.29 73.25 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>
<h4 class="date">05 March 2019</h4>
<h4 class="date">15 March 2019</h4>
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</span>
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@ -192,7 +192,7 @@
<h1>How to get properties of a microorganism</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">05 March 2019</h4>
<h4 class="date">15 March 2019</h4>
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<h1>How to predict antimicrobial resistance</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">05 March 2019</h4>
<h4 class="date">15 March 2019</h4>
<div class="hidden name"><code>resistance_predict.Rmd</code></div>