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Catalogue of Life, replaces ITIS

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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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">14 February 2019</h4>
<h4 class="date">18 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 14 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 18 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">2019-02-14</td>
<td align="center">2019-02-18</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">2019-02-14</td>
<td align="center">2019-02-18</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">2019-02-14</td>
<td align="center">2019-02-18</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">2017-12-27</td>
<td align="center">C5</td>
<td align="center">2011-01-25</td>
<td align="center">V6</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</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">M</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-11-20</td>
<td align="center">Y5</td>
<td align="center">2013-07-31</td>
<td align="center">A8</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">F</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2011-06-25</td>
<td align="center">I4</td>
<td align="center">2016-10-12</td>
<td align="center">Y3</td>
<td align="center">Hospital D</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">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-12-31</td>
<td align="center">B4</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">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-10-16</td>
<td align="center">N10</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-09-01</td>
<td align="center">L1</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">2014-08-10</td>
<td align="center">F9</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">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-12-14</td>
<td align="center">Z3</td>
<td align="center">2017-12-05</td>
<td align="center">H7</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</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">F</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
@ -411,8 +411,8 @@
#&gt;
#&gt; Item Count Percent Cum. Count Cum. Percent
#&gt; --- ----- ------- -------- ----------- -------------
#&gt; 1 M 10,432 52.2% 10,432 52.2%
#&gt; 2 F 9,568 47.8% 20,000 100.0%</code></pre>
#&gt; 1 M 10,283 51.4% 10,283 51.4%
#&gt; 2 F 9,717 48.6% 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 (1241 changes)</span></a>
<a class="sourceLine" id="cb14-22" title="22"><span class="co">#&gt; Table 1: Intrinsic resistance in Enterobacteriaceae (1294 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 (2713 changes)</span></a>
<a class="sourceLine" id="cb14-25" title="25"><span class="co">#&gt; Table 4: Intrinsic resistance in Gram-positive bacteria (2822 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 7,301 out of 20,000 rows</span></a>
<a class="sourceLine" id="cb14-41" title="41"><span class="co">#&gt; =&gt; EUCAST rules affected 7,463 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 3,954 test results (0 to S; 0 to I; 3,954 to R)</span></a></code></pre></div>
<a class="sourceLine" id="cb14-43" title="43"><span class="co">#&gt; -&gt; changed 4,116 test results (0 to S; 0 to I; 4,116 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 5,669 first isolates (28.3% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb16-6" title="6"><span class="co">#&gt; =&gt; Found 5,654 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>
@ -516,43 +516,43 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-04</td>
<td align="center">M1</td>
<td align="center">2010-04-05</td>
<td align="center">Q7</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">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-01-27</td>
<td align="center">M1</td>
<td align="center">2010-05-10</td>
<td align="center">Q7</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">3</td>
<td align="center">2010-05-07</td>
<td align="center">M1</td>
<td align="center">2010-06-22</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-06-09</td>
<td align="center">M1</td>
<td align="center">2010-06-25</td>
<td align="center">Q7</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>
@ -560,10 +560,10 @@
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-07-23</td>
<td align="center">M1</td>
<td align="center">2010-10-03</td>
<td align="center">Q7</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>
@ -571,30 +571,30 @@
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-09-29</td>
<td align="center">M1</td>
<td align="center">2010-10-08</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-10-14</td>
<td align="center">M1</td>
<td align="center">2011-03-24</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-10-15</td>
<td align="center">M1</td>
<td align="center">2011-03-27</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -604,21 +604,21 @@
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-10-16</td>
<td align="center">M1</td>
<td align="center">2011-05-11</td>
<td align="center">Q7</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">R</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2010-11-16</td>
<td align="center">M1</td>
<td align="center">2011-07-22</td>
<td align="center">Q7</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>
@ -626,7 +626,7 @@
</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 15,859 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 15,805 first weighted isolates (79.0% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -654,23 +654,23 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-04</td>
<td align="center">M1</td>
<td align="center">2010-04-05</td>
<td align="center">Q7</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">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-01-27</td>
<td align="center">M1</td>
<td align="center">2010-05-10</td>
<td align="center">Q7</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>
@ -678,34 +678,34 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-05-07</td>
<td align="center">M1</td>
<td align="center">2010-06-22</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-06-09</td>
<td align="center">M1</td>
<td align="center">2010-06-25</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-07-23</td>
<td align="center">M1</td>
<td align="center">2010-10-03</td>
<td align="center">Q7</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>
@ -714,58 +714,58 @@
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-09-29</td>
<td align="center">M1</td>
<td align="center">2010-10-08</td>
<td align="center">Q7</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="odd">
<td align="center">7</td>
<td align="center">2010-10-14</td>
<td align="center">M1</td>
<td align="center">2011-03-24</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-10-15</td>
<td align="center">M1</td>
<td align="center">2011-03-27</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-10-16</td>
<td align="center">M1</td>
<td align="center">2011-05-11</td>
<td align="center">Q7</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">R</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2010-11-16</td>
<td align="center">M1</td>
<td align="center">2011-07-22</td>
<td align="center">Q7</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>
@ -774,11 +774,11 @@
</tr>
</tbody>
</table>
<p>Instead of 1, now 9 isolates are flagged. In total, 79.3% of all isolates are marked ‘first weighted’ - 51% 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 4 isolates are flagged. In total, 79% 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 15,859 isolates for analysis.</p>
<p>So we end up with 15,805 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>
@ -803,30 +803,62 @@
</tr></thead>
<tbody>
<tr class="odd">
<td>4</td>
<td align="center">2016-10-16</td>
<td align="center">N10</td>
<td align="center">Hospital A</td>
<td>2</td>
<td align="center">2013-07-31</td>
<td align="center">A8</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>5</td>
<td align="center">2015-09-01</td>
<td align="center">L1</td>
<td>3</td>
<td align="center">2016-10-12</td>
<td align="center">Y3</td>
<td align="center">Hospital D</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">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>
<tr class="odd">
<td>5</td>
<td align="center">2014-08-10</td>
<td align="center">F9</td>
<td align="center">Hospital A</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">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>6</td>
<td align="center">2017-12-05</td>
<td align="center">H7</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram negative</td>
@ -835,69 +867,37 @@
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>6</td>
<td align="center">2013-12-14</td>
<td align="center">Z3</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNE</td>
<td>7</td>
<td align="center">2014-02-06</td>
<td align="center">D7</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">R</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">F</td>
<td align="center">Gram negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</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>7</td>
<td align="center">2011-09-19</td>
<td align="center">U9</td>
<td>8</td>
<td align="center">2013-05-11</td>
<td align="center">A5</td>
<td align="center">Hospital A</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">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>8</td>
<td align="center">2016-02-23</td>
<td align="center">H1</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">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>9</td>
<td align="center">2016-08-02</td>
<td align="center">I4</td>
<td align="center">Hospital B</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">M</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</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> (15,859 x 13)</strong></p>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (15,805 x 13)</strong></p>
<p>Columns: 2<br>
Length: 15,859 (of which NA: 0 = 0.00%)<br>
Length: 15,805 (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">7,917</td>
<td align="right">49.9%</td>
<td align="right">7,917</td>
<td align="right">49.9%</td>
<td align="right">7,815</td>
<td align="right">49.4%</td>
<td align="right">7,815</td>
<td align="right">49.4%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,901</td>
<td align="right">24.6%</td>
<td align="right">11,818</td>
<td align="right">74.5%</td>
<td align="right">3,988</td>
<td align="right">25.2%</td>
<td align="right">11,803</td>
<td align="right">74.7%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,478</td>
<td align="right">15.6%</td>
<td align="right">14,296</td>
<td align="right">90.1%</td>
<td align="right">2,476</td>
<td align="right">15.7%</td>
<td align="right">14,279</td>
<td align="right">90.3%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,563</td>
<td align="right">9.9%</td>
<td align="right">15,859</td>
<td align="right">1,526</td>
<td align="right">9.7%</td>
<td align="right">15,805</td>
<td align="right">100.0%</td>
</tr>
</tbody>
@ -971,7 +971,7 @@ Longest: 24</p>
<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>
<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] 0.4776468</span></a></code></pre></div>
<a class="sourceLine" id="cb25-2" title="2"><span class="co">#&gt; [1] 0.4771275</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">0.4658398</td>
<td align="center">0.4661749</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4821041</td>
<td align="center">0.4820906</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4874459</td>
<td align="center">0.4847862</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4803681</td>
<td align="center">0.4790875</td>
</tr>
</tbody>
</table>
@ -1014,23 +1014,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4658398</td>
<td align="center">4757</td>
<td align="center">0.4661749</td>
<td align="center">4745</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4821041</td>
<td align="center">5532</td>
<td align="center">0.4820906</td>
<td align="center">5472</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4874459</td>
<td align="center">2310</td>
<td align="center">0.4847862</td>
<td align="center">2432</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4803681</td>
<td align="center">3260</td>
<td align="center">0.4790875</td>
<td align="center">3156</td>
</tr>
</tbody>
</table>
@ -1050,27 +1050,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7305798</td>
<td align="center">0.8974359</td>
<td align="center">0.9760010</td>
<td align="center">0.7332054</td>
<td align="center">0.9033909</td>
<td align="center">0.9754319</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.7370441</td>
<td align="center">0.9040307</td>
<td align="center">0.9776072</td>
<td align="center">0.7142857</td>
<td align="center">0.9095675</td>
<td align="center">0.9737877</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7303256</td>
<td align="center">0.9200205</td>
<td align="center">0.9771853</td>
<td align="center">0.7179037</td>
<td align="center">0.9162487</td>
<td align="center">0.9779338</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.7332526</td>
<td align="center">0.7289984</td>
<td align="center">0.0000000</td>
<td align="center">0.7332526</td>
<td align="center">0.7289984</td>
</tr>
</tbody>
</table>

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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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">14 February 2019</h4>
<h4 class="date">18 February 2019</h4>
<div class="hidden name"><code>EUCAST.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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</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">14 February 2019</h4>
<h4 class="date">18 February 2019</h4>
<div class="hidden name"><code>G_test.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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
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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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</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">14 February 2019</h4>
<h4 class="date">18 February 2019</h4>
<div class="hidden name"><code>WHONET.Rmd</code></div>
@ -274,7 +274,7 @@ Species: 36</p>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">B_STRPTC_PNE</td>
<td align="left">B_STRPT_PNE</td>
<td align="right">31</td>
<td align="right">6.2%</td>
<td align="right">388</td>

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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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</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">14 February 2019</h4>
<h4 class="date">18 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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to create frequency tables</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">14 February 2019</h4>
<h4 class="date">18 February 2019</h4>
<div class="hidden name"><code>freq.Rmd</code></div>
@ -256,22 +256,22 @@ Longest: 1</p>
<a class="sourceLine" id="cb2-2" title="2"><span class="co"># Joining, by = "mo"</span></a></code></pre></div>
<p>Now all variables of the <code>microorganisms</code> dataset have been joined to the <code>septic_patients</code> dataset. The <code>microorganisms</code> dataset consists of the following variables:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/colnames">colnames</a></span>(microorganisms)</a>
<a class="sourceLine" id="cb3-2" title="2"><span class="co"># [1] "mo" "tsn" "genus" "species" "subspecies"</span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># [6] "fullname" "family" "order" "class" "phylum" </span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># [11] "subkingdom" "kingdom" "gramstain" "prevalence" "ref"</span></a></code></pre></div>
<p>If we compare the dimensions between the old and new dataset, we can see that these 14 variables were added:</p>
<a class="sourceLine" id="cb3-2" title="2"><span class="co"># [1] "mo" "col_id" "fullname" "kingdom" "phylum" </span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># [6] "class" "order" "family" "genus" "species" </span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># [11] "subspecies" "rank" "ref"</span></a></code></pre></div>
<p>If we compare the dimensions between the old and new dataset, we can see that these 12 variables were added:</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/base/topics/dim">dim</a></span>(septic_patients)</a>
<a class="sourceLine" id="cb4-2" title="2"><span class="co"># [1] 2000 49</span></a>
<a class="sourceLine" id="cb4-3" title="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(my_patients)</a>
<a class="sourceLine" id="cb4-4" title="4"><span class="co"># [1] 2000 63</span></a></code></pre></div>
<a class="sourceLine" id="cb4-4" title="4"><span class="co"># [1] 2000 61</span></a></code></pre></div>
<p>So now the <code>genus</code> and <code>species</code> variables are available. A frequency table of these combined variables can be created like this:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1">my_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus, species, <span class="dt">nmax =</span> <span class="dv">15</span>)</a></code></pre></div>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (2,000 x 63)</strong></p>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (2,000 x 61)</strong></p>
<p>Columns: 2<br>
Length: 2,000 (of which NA: 0 = 0.00%)<br>
Unique: 96</p>
<p>Shortest: 12<br>
Unique: 95</p>
<p>Shortest: 8<br>
Longest: 34</p>
<table class="table">
<thead><tr class="header">
@ -405,7 +405,7 @@ Longest: 34</p>
</tr>
</tbody>
</table>
<p>(omitted 81 entries, n = 340 [17.0%])</p>
<p>(omitted 80 entries, n = 340 [17.0%])</p>
</div>
<div id="frequencies-of-numeric-values" class="section level2">
<h2 class="hasAnchor">

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</button>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
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</button>
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</span>
</div>
@ -192,7 +192,7 @@
<h1>How to get properties of a microorganism</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">14 February 2019</h4>
<h4 class="date">18 February 2019</h4>
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</span>
</div>
@ -192,7 +192,7 @@
<h1>How to predict antimicrobial resistance</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">14 February 2019</h4>
<h4 class="date">18 February 2019</h4>
<div class="hidden name"><code>resistance_predict.Rmd</code></div>

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</button>
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</span>
</div>
@ -237,12 +237,27 @@
<a href="#amr-05090xx" class="anchor"></a>AMR 0.5.0.90xx<small> Unreleased </small>
</h1>
<p><strong>Note: this is the development version, which will eventually be released as AMR 0.6.0.</strong></p>
<p><strong>New website!</strong></p>
<p>We’ve got a new website: <a href="https://msberends.gitlab.io/AMR/">https://msberends.gitlab.io/AMR</a> (built with the great <a href="https://pkgdown.r-lib.org/"><code>pkgdown</code></a>)</p>
<ul>
<li>Contains the complete manual of this package and all of its functions with an explanation of their parameters</li>
<li>Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis, import data from WHONET or SPSS and many more.</li>
</ul>
<div id="new" class="section level4">
<h4 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h4>
<ul>
<li>
<strong>BREAKING</strong>: removed deprecated functions, parameters and references to ‘bactid’. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> to identify an MO code.</li>
<li>Catalogue of Life (CoL) inclusion for data about microorganisms, which also contains all ITIS data we used previously. The <code>microorganisms</code> data set now contains:
<ul>
<li>Almost 60,000 species from six different kingdoms</li>
<li>Almost 15,000 previously accepted names which are now taxonomic ‘synonyms’</li>
<li>All (sub)species from the kingdoms Archaea, Bacteria, Chromista, Protozoa and Viruses</li>
<li>All (sub)species from the orders Eurotiales, Saccharomycetales and Onygenales of the kingdom Fungi. The complete taxonomy of this kingdom has more than 130,000 species. The orders we included contains at least all memebers of the families <em>Candida</em>, <em>Aspergillus</em> and <em>Trichophyton</em>.</li>
<li>Due to this change, the ID of <em>Streptococcus</em> was changed from <code>B_STRPTC</code> to <code>B_STRPT</code>.</li>
</ul>
</li>
<li>Support for data from <a href="https://whonet.org/">WHONET</a> and <a href="https://ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/ears-net">EARS-Net</a> (European Antimicrobial Resistance Surveillance Network):
<ul>
<li>Exported files from WHONET can be read and used in this package. For functions like <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, all parameters will be filled in automatically.</li>
@ -260,12 +275,6 @@
<a class="sourceLine" id="cb1-6" title="6">ab_umcg -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_umcg</a></span>()</a>
<a class="sourceLine" id="cb1-7" title="7">ab_tradenames -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_tradenames</a></span>()</a></code></pre></div>
These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code> internally. The old <code>atc_property</code> has been renamed <code><a href="../reference/atc_online.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><a href="../reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</li>
<li>New website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a> (built with the great <a href="https://pkgdown.r-lib.org/"><code>pkgdown</code></a>)
<ul>
<li>Contains the complete manual of this package and all of its functions with an explanation of their parameters</li>
<li>Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis</li>
</ul>
</li>
<li>New functions <code><a href="../reference/mo_source.html">set_mo_source()</a></code> and <code><a href="../reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as input for <code><a href="../reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions</li>
<li>Support for the upcoming <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li>
<li>New function <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code> to find an antibiotic column in a table</li>
@ -308,7 +317,7 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<li>New info is returned when running this function, stating exactly what has been changed or added. Use <code><a href="../reference/eucast_rules.html">eucast_rules(..., verbose = TRUE)</a></code> to get a data set with all changed per bug and drug combination.</li>
</ul>
</li>
<li>Added 605 <em>Aspergillus</em> species and 23 <em>Trichophyton</em> species to the <code>microorganisms</code> data set</li>
<li>Removed data sets <code>microorganisms.oldDT</code>, <code>microorganisms.prevDT</code>, <code>microorganisms.unprevDT</code> and <code>microorganismsDT</code> since they were no longer needed and only contained info already available in the <code>microorganisms</code> data set</li>
<li>Added 65 antibiotics to the <code>antibiotics</code> data set, from the <a href="http://ec.europa.eu/health/documents/community-register/html/atc.htm">Pharmaceuticals Community Register</a> of the European Commission</li>
<li>Removed columns <code>atc_group1_nl</code> and <code>atc_group2_nl</code> from the <code>antibiotics</code> data set</li>
<li>Functions <code><a href="../reference/AMR-deprecated.html">atc_ddd()</a></code> and <code><a href="../reference/AMR-deprecated.html">atc_groups()</a></code> have been renamed <code><a href="../reference/atc_online.html">atc_online_ddd()</a></code> and <code><a href="../reference/atc_online.html">atc_online_groups()</a></code>. The old functions are deprecated and will be removed in a future version.</li>

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@ -296,7 +296,8 @@
| | | ----&gt; subspecies, a 3-4 letter acronym
| | ----&gt; species, a 3-4 letter acronym
| ----&gt; genus, a 5-7 letter acronym, mostly without vowels
----&gt; taxonomic kingdom, either B (Bacteria), F (Fungi) or P (Protozoa)
----&gt; taxonomic kingdom: A (Archaea), B (Bacteria), C (Chromista),
F (Fungi), P (Protozoa) or V (Viruses)
</pre>
<p>Use the <code><a href='mo_property.html'>mo_property</a></code> functions to get properties based on the returned code, see Examples.</p>
<p>This function uses Artificial Intelligence (AI) to help getting fast and logical results. It tries to find matches in this order:</p><ul>
@ -320,7 +321,7 @@ When using <code>allow_uncertain = TRUE</code> (which is the default setting), i
<li><p>It tries to look for some manual changes which are not yet published to the ITIS database (like <em>Propionibacterium</em> not yet being <em>Cutibacterium</em>)</p></li>
</ul>
<p>Examples:</p><ul>
<li><p><code>"Streptococcus group B (known as S. agalactiae)"</code>. The text between brackets will be removed and a warning will be thrown that the result <em>Streptococcus group B</em> (<code>B_STRPTC_GRB</code>) needs review.</p></li>
<li><p><code>"Streptococcus group B (known as S. agalactiae)"</code>. The text between brackets will be removed and a warning will be thrown that the result <em>Streptococcus group B</em> (<code>B_STRPT_GRB</code>) needs review.</p></li>
<li><p><code>"S. aureus - please mind: MRSA"</code>. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result <em>Staphylococcus aureus</em> (<code>B_STPHY_AUR</code>) needs review.</p></li>
<li><p><code>"D. spartina"</code>. This is the abbreviation of an old taxonomic name: <em>Didymosphaeria spartinae</em> (the last "e" was missing from the input). This fungus was renamed to <em>Leptosphaeria obiones</em>, so a warning will be thrown that this result (<code>F_LPTSP_OBI</code>) needs review.</p></li>
<li><p><code>"Fluoroquinolone-resistant Neisseria gonorrhoeae"</code>. The first word will be stripped, after which the function will try to find a match. A warning will be thrown that the result <em>Neisseria gonorrhoeae</em> (<code>B_NESSR_GON</code>) needs review.</p></li>
@ -369,8 +370,6 @@ The <code><a href='mo_property.html'>mo_property</a></code> functions (like <cod
<span class='fu'>as.mo</span>(<span class='st'>"MRSA"</span>) <span class='co'># Methicillin Resistant S. aureus</span>
<span class='fu'>as.mo</span>(<span class='st'>"VISA"</span>) <span class='co'># Vancomycin Intermediate S. aureus</span>
<span class='fu'>as.mo</span>(<span class='st'>"VRSA"</span>) <span class='co'># Vancomycin Resistant S. aureus</span>
<span class='fu'>as.mo</span>(<span class='fl'>369</span>) <span class='co'># Search on TSN (Taxonomic Serial Number), a unique identifier</span>
<span class='co'># for the Integrated Taxonomic Information System (ITIS)</span>
<span class='fu'>as.mo</span>(<span class='st'>"Streptococcus group A"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"GAS"</span>) <span class='co'># Group A Streptococci</span>
@ -379,8 +378,8 @@ The <code><a href='mo_property.html'>mo_property</a></code> functions (like <cod
<span class='fu'>as.mo</span>(<span class='st'>"S. epidermidis"</span>) <span class='co'># will remain species: B_STPHY_EPI</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. epidermidis"</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STPHY_CNS</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>) <span class='co'># will remain species: B_STRPTC_PYO</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STRPTC_GRA</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>) <span class='co'># will remain species: B_STRPT_PYO</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STRPT_GRA</span>
<span class='co'># Use mo_* functions to get a specific property based on `mo`</span>
<span class='no'>Ecoli</span> <span class='kw'>&lt;-</span> <span class='fu'>as.mo</span>(<span class='st'>"E. coli"</span>) <span class='co'># returns `B_ESCHR_COL`</span>

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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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@ -80,7 +80,7 @@
</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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

2
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@ -80,7 +80,7 @@
</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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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@ -80,7 +80,7 @@
</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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

2
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@ -80,7 +80,7 @@
</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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

2
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@ -80,7 +80,7 @@
</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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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@ -81,7 +81,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
</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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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@ -80,7 +80,7 @@
</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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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@ -80,7 +80,7 @@
</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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

2
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@ -80,7 +80,7 @@
</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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

2
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@ -80,7 +80,7 @@
</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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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@ -78,7 +78,7 @@
</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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>
@ -349,7 +349,7 @@
</tr><tr>
<td>
<p><code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_subkingdom()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_TSN()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
<p><code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_subkingdom()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
</td>
<td><p>Property of a microorganism</p></td>
</tr><tr>
@ -481,7 +481,7 @@
<td>
<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
</td>
<td><p>Data set with ~20,000 microorganisms</p></td>
<td><p>Data set with ~60,000 microorganisms</p></td>
</tr><tr>
<td>
@ -506,12 +506,6 @@
<p><code><a href="microorganisms.old.html">microorganisms.old</a></code> </p>
</td>
<td><p>Data set with previously accepted taxonomic names</p></td>
</tr><tr>
<td>
<p><code><a href="supplementary_data.html">microorganismsDT</a></code> <code><a href="supplementary_data.html">microorganisms.prevDT</a></code> <code><a href="supplementary_data.html">microorganisms.unprevDT</a></code> <code><a href="supplementary_data.html">microorganisms.oldDT</a></code> </p>
</td>
<td><p>Supplementary Data</p></td>
</tr>
</tbody><tbody>
<tr>

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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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

2
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@ -80,7 +80,7 @@
</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">0.5.0.9017</span>
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2
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@ -80,7 +80,7 @@
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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">0.5.0.9017</span>
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</span>
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2
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@ -80,7 +80,7 @@
</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">0.5.0.9017</span>
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</span>
</div>

2
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@ -80,7 +80,7 @@
</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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

2
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@ -80,7 +80,7 @@
</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">0.5.0.9017</span>
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</span>
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@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Data set with ~20,000 microorganisms — microorganisms • AMR (for R)</title>
<title>Data set with ~60,000 microorganisms — microorganisms • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -45,9 +45,9 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Data set with ~20,000 microorganisms — microorganisms" />
<meta property="og:title" content="Data set with ~60,000 microorganisms — microorganisms" />
<meta property="og:description" content="A data set containing the complete microbial taxonomy of the kingdoms Bacteria, Fungi and Protozoa from ITIS. MO codes can be looked up using as.mo." />
<meta property="og:description" content="A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using as.mo." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
@ -80,7 +80,7 @@
</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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>
@ -230,14 +230,14 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data set with ~20,000 microorganisms</h1>
<h1>Data set with ~60,000 microorganisms</h1>
<div class="hidden name"><code>microorganisms.Rd</code></div>
</div>
<div class="ref-description">
<p>A data set containing the complete microbial taxonomy of the kingdoms Bacteria, Fungi and Protozoa from ITIS. MO codes can be looked up using <code><a href='as.mo.html'>as.mo</a></code>.</p>
<p>A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using <code><a href='as.mo.html'>as.mo</a></code>.</p>
</div>
@ -245,9 +245,9 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 19,456 observations and 15 variables:</p><dl class='dl-horizontal'>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 56,659 observations and 15 variables:</p><dl class='dl-horizontal'>
<dt><code>mo</code></dt><dd><p>ID of microorganism</p></dd>
<dt><code>tsn</code></dt><dd><p>Taxonomic Serial Number (TSN), as defined by ITIS</p></dd>
<dt><code>col_id</code></dt><dd><p>Catalogue of Life ID</p></dd>
<dt><code>genus</code></dt><dd><p>Taxonomic genus of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>species</code></dt><dd><p>Taxonomic species of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>subspecies</code></dt><dd><p>Taxonomic subspecies of the microorganism as found in ITIS, see Source</p></dd>
@ -270,14 +270,10 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Manually added were:</p><ul>
<li><p>605 species of Aspergillus (as Aspergillus misses from ITIS, list from https://en.wikipedia.org/wiki/List_of_Aspergillus_species on 2019-02-05)</p></li>
<li><p>23 species of Trichophyton (as Trichophyton misses from ITIS, list from https://en.wikipedia.org/wiki/Trichophyton on 2019-02-05)</p></li>
<li><p>9 species of Streptococcus (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)</p></li>
<li><p>2 species of Straphylococcus (coagulase-negative [CoNS] and coagulase-positive [CoPS])</p></li>
<li><p>1 species of Candida (C. glabrata)</p></li>
<li><p>9 species of <em>Streptococcus</em> (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)</p></li>
<li><p>2 species of <em>Staphylococcus</em> (coagulase-negative [CoNS] and coagulase-positive [CoPS])</p></li>
<li><p>2 other undefined (unknown Gram negatives and unknown Gram positives)</p></li>
</ul>
<p>These manual entries have no Taxonomic Serial Number (TSN), so can be looked up with <code>filter(microorganisms, is.na(tsn)</code>.</p>
<h2 class="hasAnchor" id="itis"><a class="anchor" href="#itis"></a>ITIS</h2>

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@ -80,7 +80,7 @@
</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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>
@ -245,11 +245,11 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 2,383 observations and 4 variables:</p><dl class='dl-horizontal'>
<dt><code>tsn</code></dt><dd><p>Old Taxonomic Serial Number (TSN), as defined by ITIS</p></dd>
<dt><code>name</code></dt><dd><p>Old taxonomic name of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>tsn_new</code></dt><dd><p>New Taxonomic Serial Number (TSN), as defined by ITIS</p></dd>
<dt><code>ref</code></dt><dd><p>Author(s) and year of concerning publication as found in ITIS, see Source</p></dd>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 14,506 observations and 4 variables:</p><dl class='dl-horizontal'>
<dt><code>col_id</code></dt><dd><p>Catalogue of Life ID</p></dd>
<dt><code>tsn_new</code></dt><dd><p>New Catalogue of Life ID</p></dd>
<dt><code>fullname</code></dt><dd><p>Old taxonomic name of the microorganism as found in the CoL, see Source</p></dd>
<dt><code>ref</code></dt><dd><p>Author(s) and year of concerning publication as found in the CoL, see Source</p></dd>
</dl>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>

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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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>
@ -267,8 +267,6 @@
<span class='fu'>mo_gramstain</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_TSN</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_ref</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_authors</span>(<span class='no'>x</span>, <span class='no'>...</span>)
@ -304,7 +302,7 @@
<ul>
<li><p>An <code>integer</code> in case of <code>mo_TSN</code> and <code>mo_year</code></p></li>
<li><p>An <code>integer</code> in case of <code>mo_year</code></p></li>
<li><p>A <code>list</code> in case of <code>mo_taxonomy</code></p></li>
<li><p>A <code>character</code> in all other cases</p></li>
</ul>
@ -362,7 +360,6 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='fu'>mo_genus</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia"</span>
<span class='fu'>mo_species</span>(<span class='st'>"E. coli"</span>) <span class='co'># "coli"</span>
<span class='fu'>mo_subspecies</span>(<span class='st'>"E. coli"</span>) <span class='co'># NA</span>
<span class='fu'>mo_TSN</span>(<span class='st'>"E. coli"</span>) <span class='co'># 285 (Taxonomic Serial Number)</span>
<span class='co'>## colloquial properties</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia coli"</span>

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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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
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@ -80,7 +80,7 @@
</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">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
</button>
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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">0.5.0.9017</span>
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2
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@ -80,7 +80,7 @@
</button>
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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">0.5.0.9017</span>
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2
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@ -80,7 +80,7 @@
</button>
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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">0.5.0.9017</span>
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@ -80,7 +80,7 @@
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docs/reference/septic_patients.html
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@ -80,7 +80,7 @@
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2
docs/reference/skewness.html
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@ -81,7 +81,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
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3
docs/sitemap.xml
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@ -126,9 +126,6 @@
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