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<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">04 February 2019</h4>
<h4 class="date">08 February 2019</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -194,7 +194,7 @@
<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 04 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 08 February 2019.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -210,21 +210,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2019-02-04</td>
<td align="center">2019-02-08</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">2019-02-04</td>
<td align="center">2019-02-08</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">2019-02-04</td>
<td align="center">2019-02-08</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -313,41 +313,52 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-05-26</td>
<td align="center">E8</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">2010-10-06</td>
<td align="center">F7</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</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">2016-11-27</td>
<td align="center">D6</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2015-03-24</td>
<td align="center">J2</td>
<tr class="even">
<td align="center">2015-07-29</td>
<td align="center">T1</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2017-10-20</td>
<td align="center">P2</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-09-12</td>
<td align="center">Y4</td>
<td align="center">2010-02-07</td>
<td align="center">Z6</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2012-06-26</td>
<td align="center">V4</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
@ -356,22 +367,11 @@
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-05-27</td>
<td align="center">M8</td>
<tr class="even">
<td align="center">2016-02-08</td>
<td align="center">S2</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-10-14</td>
<td align="center">R8</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -388,7 +388,7 @@
<a href="#cleaning-the-data" class="anchor"></a>Cleaning the data</h1>
<p>Use the frequency table function <code><a href="../reference/freq.html">freq()</a></code> to look specifically for unique values in any variable. For example, for the <code>gender</code> variable:</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1">data <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender) <span class="co"># this would be the same: freq(data$gender)</span></a></code></pre></div>
<pre><code># Frequency table of `gender` from a `data.frame` (5,000 x 9)
<pre><code># Frequency table of `gender` from a data.frame (5,000 x 9)
# Class: factor (numeric)
# Levels: F, M
# Length: 5,000 (of which NA: 0 = 0.00%)
@ -396,8 +396,8 @@
#
# Item Count Percent Cum. Count Cum. Percent
# --- ----- ------ -------- ----------- -------------
# 1 M 2,560 51.2% 2,560 51.2%
# 2 F 2,440 48.8% 5,000 100.0%</code></pre>
# 1 M 2,551 51.0% 2,551 51.0%
# 2 F 2,449 49.0% 5,000 100.0%</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" data-line-number="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span></a>
@ -428,10 +428,10 @@
<a class="sourceLine" id="cb14-19" data-line-number="19"><span class="co"># Kingella kingae (no changes)</span></a>
<a class="sourceLine" id="cb14-20" data-line-number="20"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-21" data-line-number="21"><span class="co"># EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
<a class="sourceLine" id="cb14-22" data-line-number="22"><span class="co"># Table 1: Intrinsic resistance in Enterobacteriaceae (348 changes)</span></a>
<a class="sourceLine" id="cb14-22" data-line-number="22"><span class="co"># Table 1: Intrinsic resistance in Enterobacteriaceae (345 changes)</span></a>
<a class="sourceLine" id="cb14-23" data-line-number="23"><span class="co"># Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb14-24" data-line-number="24"><span class="co"># Table 3: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb14-25" data-line-number="25"><span class="co"># Table 4: Intrinsic resistance in Gram-positive bacteria (702 changes)</span></a>
<a class="sourceLine" id="cb14-25" data-line-number="25"><span class="co"># Table 4: Intrinsic resistance in Gram-positive bacteria (673 changes)</span></a>
<a class="sourceLine" id="cb14-26" data-line-number="26"><span class="co"># Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></a>
<a class="sourceLine" id="cb14-27" data-line-number="27"><span class="co"># Table 9: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></a>
<a class="sourceLine" id="cb14-28" data-line-number="28"><span class="co"># Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria (no changes)</span></a>
@ -447,7 +447,9 @@
<a class="sourceLine" id="cb14-38" data-line-number="38"><span class="co"># Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)</span></a>
<a class="sourceLine" id="cb14-39" data-line-number="39"><span class="co"># Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)</span></a>
<a class="sourceLine" id="cb14-40" data-line-number="40"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-41" data-line-number="41"><span class="co"># =&gt; EUCAST rules affected 1,820 out of 5,000 rows -&gt; changed 1,050 test results.</span></a></code></pre></div>
<a class="sourceLine" id="cb14-41" data-line-number="41"><span class="co"># =&gt; EUCAST rules affected 1,814 out of 5,000 rows</span></a>
<a class="sourceLine" id="cb14-42" data-line-number="42"><span class="co"># -&gt; added 0 test results</span></a>
<a class="sourceLine" id="cb14-43" data-line-number="43"><span class="co"># -&gt; changed 1,018 test results (0 to S; 0 to I; 1,018 to R)</span></a></code></pre></div>
</div>
<div id="adding-new-variables" class="section level1">
<h1 class="hasAnchor">
@ -472,8 +474,8 @@
<a class="sourceLine" id="cb16-3" data-line-number="3"><span class="co"># </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" data-line-number="4"><span class="co"># </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" data-line-number="5"><span class="co"># </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" data-line-number="6"><span class="co"># =&gt; Found 2,951 first isolates (59.0% of total)</span></a></code></pre></div>
<p>So only 59% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<a class="sourceLine" id="cb16-6" data-line-number="6"><span class="co"># =&gt; Found 2,939 first isolates (58.8% of total)</span></a></code></pre></div>
<p>So only 58.8% 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" data-line-number="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" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(first <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>)</a></code></pre></div>
<p>For future use, the above two syntaxes can be shortened with the <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> function:</p>
@ -499,30 +501,30 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-03-08</td>
<td align="center">G3</td>
<td align="center">2010-04-03</td>
<td align="center">C3</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">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-05-08</td>
<td align="center">G3</td>
<td align="center">2010-10-31</td>
<td align="center">C3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-06-21</td>
<td align="center">G3</td>
<td align="center">2010-11-12</td>
<td align="center">C3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -532,21 +534,21 @@
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-12-01</td>
<td align="center">G3</td>
<td align="center">2010-11-21</td>
<td align="center">C3</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">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2011-01-05</td>
<td align="center">G3</td>
<td align="center">2010-12-01</td>
<td align="center">C3</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>
@ -554,52 +556,41 @@
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2012-01-16</td>
<td align="center">G3</td>
<td align="center">2011-10-22</td>
<td align="center">C3</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">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2012-04-11</td>
<td align="center">G3</td>
<td align="center">2012-03-22</td>
<td align="center">C3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2012-10-23</td>
<td align="center">G3</td>
<td align="center">2012-05-14</td>
<td align="center">C3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2012-11-24</td>
<td align="center">G3</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>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2014-01-26</td>
<td align="center">G3</td>
<td align="center">2012-10-26</td>
<td align="center">C3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -607,6 +598,17 @@
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2013-06-13</td>
<td align="center">C3</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">FALSE</td>
</tr>
</tbody>
</table>
<p>Only 3 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>
@ -620,7 +622,7 @@
<a class="sourceLine" id="cb19-7" data-line-number="7"><span class="co"># </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" data-line-number="8"><span class="co"># </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" data-line-number="9"><span class="co"># [Criterion] Inclusion based on key antibiotics, ignoring I.</span></a>
<a class="sourceLine" id="cb19-10" data-line-number="10"><span class="co"># =&gt; Found 4,424 first weighted isolates (88.5% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb19-10" data-line-number="10"><span class="co"># =&gt; Found 4,387 first weighted isolates (87.7% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -637,11 +639,11 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-03-08</td>
<td align="center">G3</td>
<td align="center">2010-04-03</td>
<td align="center">C3</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">TRUE</td>
@ -649,20 +651,20 @@
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-05-08</td>
<td align="center">G3</td>
<td align="center">2010-10-31</td>
<td align="center">C3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-06-21</td>
<td align="center">G3</td>
<td align="center">2010-11-12</td>
<td align="center">C3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -673,22 +675,22 @@
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-12-01</td>
<td align="center">G3</td>
<td align="center">2010-11-21</td>
<td align="center">C3</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">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2011-01-05</td>
<td align="center">G3</td>
<td align="center">2010-12-01</td>
<td align="center">C3</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>
@ -697,11 +699,11 @@
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2012-01-16</td>
<td align="center">G3</td>
<td align="center">2011-10-22</td>
<td align="center">C3</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">TRUE</td>
@ -709,23 +711,23 @@
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2012-04-11</td>
<td align="center">G3</td>
<td align="center">2012-03-22</td>
<td align="center">C3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2012-10-23</td>
<td align="center">G3</td>
<td align="center">2012-05-14</td>
<td align="center">C3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
@ -733,20 +735,8 @@
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2012-11-24</td>
<td align="center">G3</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>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2014-01-26</td>
<td align="center">G3</td>
<td align="center">2012-10-26</td>
<td align="center">C3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -755,13 +745,25 @@
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2013-06-13</td>
<td align="center">C3</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">FALSE</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Instead of 3, now 9 isolates are flagged. In total, 88.5% of all isolates are marked ‘first weighted’ - 29.5% 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 3, now 9 isolates are flagged. In total, 87.7% of all isolates are marked ‘first weighted’ - 29% 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" data-line-number="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" data-line-number="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 4,424 isolates for analysis.</p>
<p>So we end up with 4,387 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" data-line-number="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" data-line-number="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>
@ -769,6 +771,7 @@
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="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>
@ -785,58 +788,46 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-05-26</td>
<td align="center">E8</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COL</td>
<td>1</td>
<td align="center">2010-10-06</td>
<td align="center">F7</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNE</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">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 align="center">2016-11-27</td>
<td align="center">D6</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPTC_PNE</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram positive</td>
<td align="center">Streptococcus</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-03-24</td>
<td align="center">J2</td>
<tr class="even">
<td>2</td>
<td align="center">2015-07-29</td>
<td align="center">T1</td>
<td align="center">Hospital A</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">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">2014-09-12</td>
<td align="center">Y4</td>
<td align="center">Hospital A</td>
<tr class="odd">
<td>3</td>
<td align="center">2017-10-20</td>
<td align="center">P2</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram positive</td>
@ -844,31 +835,49 @@
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-05-27</td>
<td align="center">M8</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COL</td>
<tr class="even">
<td>4</td>
<td align="center">2010-02-07</td>
<td align="center">Z6</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNE</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>6</td>
<td align="center">2016-02-08</td>
<td align="center">S2</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-10-14</td>
<td align="center">R8</td>
<td>9</td>
<td align="center">2016-10-31</td>
<td align="center">H3</td>
<td align="center">Hospital C</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">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>
@ -891,9 +900,9 @@
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" data-line-number="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" data-line-number="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> (4,424 x 13)</strong><br>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (4,387 x 13)</strong><br>
Columns: 2<br>
Length: 4,424 (of which NA: 0 = 0.00%)<br>
Length: 4,387 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -910,33 +919,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">2,141</td>
<td align="right">48.4%</td>
<td align="right">2,141</td>
<td align="right">48.4%</td>
<td align="right">2,129</td>
<td align="right">48.5%</td>
<td align="right">2,129</td>
<td align="right">48.5%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">1,126</td>
<td align="right">25.5%</td>
<td align="right">3,267</td>
<td align="right">73.8%</td>
<td align="right">1,098</td>
<td align="right">25.0%</td>
<td align="right">3,227</td>
<td align="right">73.6%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">699</td>
<td align="right">15.8%</td>
<td align="right">3,966</td>
<td align="right">89.6%</td>
<td align="right">688</td>
<td align="right">15.7%</td>
<td align="right">3,915</td>
<td align="right">89.2%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">458</td>
<td align="right">10.4%</td>
<td align="right">4,424</td>
<td align="right">472</td>
<td align="right">10.8%</td>
<td align="right">4,387</td>
<td align="right">100.0%</td>
</tr>
</tbody>
@ -947,7 +956,7 @@ 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" data-line-number="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" data-line-number="2"><span class="co"># [1] 0.4622514</span></a></code></pre></div>
<a class="sourceLine" id="cb25-2" data-line-number="2"><span class="co"># [1] 0.4700251</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" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb26-2" data-line-number="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>
@ -960,19 +969,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4566642</td>
<td align="center">0.4544765</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4615894</td>
<td align="center">0.4920107</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4807122</td>
<td align="center">0.4686567</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4579008</td>
<td align="center">0.4570792</td>
</tr>
</tbody>
</table>
@ -990,23 +999,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4566642</td>
<td align="center">1373</td>
<td align="center">0.4544765</td>
<td align="center">1318</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4615894</td>
<td align="center">1510</td>
<td align="center">0.4920107</td>
<td align="center">1502</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4807122</td>
<td align="center">674</td>
<td align="center">0.4686567</td>
<td align="center">670</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4579008</td>
<td align="center">867</td>
<td align="center">0.4570792</td>
<td align="center">897</td>
</tr>
</tbody>
</table>
@ -1026,27 +1035,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7356376</td>
<td align="center">0.9033162</td>
<td align="center">0.9729099</td>
<td align="center">0.7491780</td>
<td align="center">0.9074683</td>
<td align="center">0.9798027</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.7445415</td>
<td align="center">0.8930131</td>
<td align="center">0.9694323</td>
<td align="center">0.7521186</td>
<td align="center">0.9067797</td>
<td align="center">0.9745763</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7566607</td>
<td align="center">0.9174067</td>
<td align="center">0.9760213</td>
<td align="center">0.7349727</td>
<td align="center">0.9171220</td>
<td align="center">0.9708561</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.7668097</td>
<td align="center">0.7398256</td>
<td align="center">0.0000000</td>
<td align="center">0.7668097</td>
<td align="center">0.7398256</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">0.5.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9016</span>
</span>
</div>
@ -185,7 +185,7 @@
<h1>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">29 January 2019</h4>
<h4 class="date">08 February 2019</h4>
<div class="hidden name"><code>EUCAST.Rmd</code></div>

4
docs/articles/G_test.html
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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">0.5.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9016</span>
</span>
</div>
@ -185,7 +185,7 @@
<h1>How to use the <em>G</em>-test</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">29 January 2019</h4>
<h4 class="date">08 February 2019</h4>
<div class="hidden name"><code>G_test.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">0.5.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9016</span>
</span>
</div>
@ -185,7 +185,7 @@
<h1>How to predict antimicrobial resistance</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">29 January 2019</h4>
<h4 class="date">08 February 2019</h4>
<div class="hidden name"><code>Predict.Rmd</code></div>

12
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@ -185,7 +185,7 @@
<h1>How to work with WHONET data</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">30 January 2019</h4>
<h4 class="date">08 February 2019</h4>
<div class="hidden name"><code>WHONET.Rmd</code></div>
@ -212,20 +212,20 @@
<a class="sourceLine" id="cb2-3" data-line-number="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(AMR) <span class="co"># this package</span></a></code></pre></div>
<p>We will have to transform some variables to simplify and automate the analysis:</p>
<ul>
<li>Microorganisms should be transformed to our own microorganism IDs (called an <code>mo</code>) using <a href="./reference/ITIS.html">the ITIS reference data set</a>, which contains all ~20,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with <code><a href="../reference/as.mo.html">as.mo()</a></code>.</li>
<li>Microorganisms should be transformed to our own microorganism IDs (called an <code>mo</code>) using <a href="./reference/ITIS.html">the ITIS reference data set</a>, which contains all ~20,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with <code><a href="../reference/as.mo.html">as.mo()</a></code>. This function also recognises almost all WHONET abbreviations of microorganisms.</li>
<li>Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values <code>"S"</code>, <code>"I"</code> or <code>"R"</code>. That is exactly where the <code><a href="../reference/as.rsi.html">as.rsi()</a></code> function is for.</li>
</ul>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="co"># transform variables</span></a>
<a class="sourceLine" id="cb3-2" data-line-number="2">data &lt;-<span class="st"> </span>WHONET <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="st"> </span><span class="co"># get microbial ID based on given organism</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/dplyr/topics/mutate">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="cb3-4" data-line-number="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" data-line-number="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" data-line-number="6"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/dplyr/topics/summarise_all">mutate_at</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/dplyr/topics/vars">vars</a></span>(AMP_ND10<span class="op">:</span>CIP_EE), as.rsi)</a></code></pre></div>
<a class="sourceLine" id="cb3-6" data-line-number="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>
<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" data-line-number="1"><span class="co"># our newly created `mo` variable</span></a>
<a class="sourceLine" id="cb4-2" data-line-number="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><br>
Class: mo (character)<br>
Class: <code>mo</code> (<code>character</code>)<br>
Length: 500 (of which NA: 0 = 0.00%)<br>
Unique: 56</p>
<p>Families: 14<br>
@ -329,7 +329,7 @@ Species: 51</p>
<a class="sourceLine" id="cb5-3" data-line-number="3"><span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span></a>
<a class="sourceLine" id="cb5-4" data-line-number="4">data <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(AMC_ND2)</a></code></pre></div>
<p><strong>Frequency table of <code>AMC_ND2</code> from a <code>data.frame</code> (500 x 54)</strong><br>
Class: factor &gt; ordered &gt; rsi (numeric)<br>
Class: <code>factor</code> &gt; <code>ordered</code> &gt; <code>rsi</code> (<code>numeric</code>)<br>
Levels: S &lt; I &lt; R<br>
Length: 500 (of which NA: 41 = 8.20%)<br>
Unique: 3</p>

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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">0.5.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9016</span>
</span>
</div>
@ -185,7 +185,7 @@
<h1>How to get properties of an antibiotic</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">29 January 2019</h4>
<h4 class="date">08 February 2019</h4>
<div class="hidden name"><code>ab_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">0.5.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9016</span>
</span>
</div>
@ -185,7 +185,7 @@
<h1>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">29 January 2019</h4>
<h4 class="date">08 February 2019</h4>
<div class="hidden name"><code>benchmarks.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">0.5.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9016</span>
</span>
</div>
@ -185,7 +185,7 @@
<h1>How to create frequency tables</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">29 January 2019</h4>
<h4 class="date">08 February 2019</h4>
<div class="hidden name"><code>freq.Rmd</code></div>
@ -204,7 +204,12 @@
<a href="#frequencies-of-one-variable" class="anchor"></a>Frequencies of one variable</h2>
<p>To only show and quickly review the content of one variable, you can just select this variable in various ways. Let’s say we want to get the frequencies of the <code>gender</code> variable of the <code>septic_patients</code> dataset:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
<p><strong>Frequency table</strong></p>
<p><strong>Frequency table of <code>gender</code> from a <code>data.frame</code> (2,000 x 49)</strong><br>
Class: <code>character</code> (<code>character</code>)<br>
Length: 2,000 (of which NA: 0 = 0.00%)<br>
Unique: 2</p>
<p>Shortest: 1<br>
Longest: 1</p>
<table class="table">
<thead><tr class="header">
<th align="left"></th>
@ -255,7 +260,12 @@
<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" data-line-number="1">my_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-2" data-line-number="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</strong></p>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (2,000 x 63)</strong><br>
Columns: 2<br>
Length: 2,000 (of which NA: 0 = 0.00%)<br>
Unique: 96</p>
<p>Shortest: 12<br>
Longest: 34</p>
<table class="table">
<thead><tr class="header">
<th align="left"></th>
@ -399,8 +409,8 @@
<a class="sourceLine" id="cb6-2" data-line-number="2">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb6-3" data-line-number="3"><span class="st"> </span><span class="kw">distinct</span>(patient_id, <span class="dt">.keep_all =</span> <span class="ot">TRUE</span>) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb6-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age, <span class="dt">nmax =</span> <span class="dv">5</span>, <span class="dt">header =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
<p><strong>Frequency table</strong><br>
Class: numeric<br>
<p><strong>Frequency table of <code>age</code> from a <code>data.frame</code> (981 x 49)</strong><br>
Class: <code>numeric</code> (<code>numeric</code>)<br>
Length: 981 (of which NA: 0 = 0.00%)<br>
Unique: 73</p>
<p>Mean: 71.08<br>
@ -478,7 +488,11 @@ Outliers: 15 (unique count: 12)</p>
<p><code>sort.count</code> is <code>TRUE</code> by default. Compare this default behaviour…</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb7-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id)</a></code></pre></div>
<p><strong>Frequency table</strong></p>
<p><strong>Frequency table of <code>hospital_id</code> from a <code>data.frame</code> (2,000 x 49)</strong><br>
Class: <code>factor</code> (<code>numeric</code>)<br>
Levels: A, B, C, D<br>
Length: 2,000 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<table class="table">
<thead><tr class="header">
<th align="left"></th>
@ -526,7 +540,11 @@ Outliers: 15 (unique count: 12)</p>
<p>… with this, where items are now sorted on count:</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb8-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id, <span class="dt">sort.count =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<p><strong>Frequency table</strong></p>
<p><strong>Frequency table of <code>hospital_id</code> from a <code>data.frame</code> (2,000 x 49)</strong><br>
Class: <code>factor</code> (<code>numeric</code>)<br>
Levels: A, B, C, D<br>
Length: 2,000 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<table class="table">
<thead><tr class="header">
<th align="left"></th>
@ -574,8 +592,8 @@ Outliers: 15 (unique count: 12)</p>
<p>All classes will be printed into the header (default is <code>FALSE</code> when using markdown like this document). Variables with the new <code>rsi</code> class of this AMR package are actually ordered factors and have three classes (look at <code>Class</code> in the header):</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb9-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(amox, <span class="dt">header =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
<p><strong>Frequency table</strong><br>
Class: factor &gt; ordered &gt; rsi (numeric)<br>
<p><strong>Frequency table of <code>amox</code> from a <code>data.frame</code> (2,000 x 49)</strong><br>
Class: <code>factor</code> &gt; <code>ordered</code> &gt; <code>rsi</code> (<code>numeric</code>)<br>
Levels: S &lt; I &lt; R<br>
Length: 2,000 (of which NA: 828 = 41.40%)<br>
Unique: 3</p>
@ -623,8 +641,8 @@ Unique: 3</p>
<p>Frequencies of dates will show the oldest and newest date in the data, and the amount of days between them:</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb10-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(date, <span class="dt">nmax =</span> <span class="dv">5</span>, <span class="dt">header =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
<p><strong>Frequency table</strong><br>
Class: Date (numeric)<br>
<p><strong>Frequency table of <code>date</code> from a <code>data.frame</code> (2,000 x 49)</strong><br>
Class: <code>Date</code> (<code>numeric</code>)<br>
Length: 2,000 (of which NA: 0 = 0.00%)<br>
Unique: 1,140</p>
<p>Oldest: 2 January 2002<br>
@ -705,7 +723,12 @@ Median: 31 July 2009 (47.39%)</p>
<p>With the <code>na.rm</code> parameter (defaults to <code>TRUE</code>, but they will always be shown into the header), you can include <code>NA</code> values in the frequency table:</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb13-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(amox, <span class="dt">na.rm =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<p><strong>Frequency table</strong></p>
<p><strong>Frequency table of <code>amox</code> from a <code>data.frame</code> (2,000 x 49)</strong><br>
Class: <code>factor</code> &gt; <code>ordered</code> &gt; <code>rsi</code> (<code>numeric</code>)<br>
Levels: S &lt; I &lt; R<br>
Length: 2,828 (of which NA: 828 = 29.28%)<br>
Unique: 4</p>
<p>%IR: 34.30% (ratio S : IR = 1.0 : 1.4)</p>
<table class="table">
<thead><tr class="header">
<th align="left"></th>
@ -758,7 +781,11 @@ Median: 31 July 2009 (47.39%)</p>
<p>The default frequency tables shows row indices. To remove them, use <code>row.names = FALSE</code>:</p>
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb14-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id, <span class="dt">row.names =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<p><strong>Frequency table</strong></p>
<p><strong>Frequency table of <code>hospital_id</code> from a <code>data.frame</code> (2,000 x 49)</strong><br>
Class: <code>factor</code> (<code>numeric</code>)<br>
Levels: A, B, C, D<br>
Length: 2,000 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<table class="table">
<thead><tr class="header">
<th align="left">Item</th>
@ -806,7 +833,11 @@ Median: 31 July 2009 (47.39%)</p>
<p>The <code>markdown</code> parameter is <code>TRUE</code> at default in non-interactive sessions, like in reports created with R Markdown. This will always print all rows, unless <code>nmax</code> is set.</p>
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb15-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id, <span class="dt">markdown =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
<p><strong>Frequency table</strong></p>
<p><strong>Frequency table of <code>hospital_id</code> from a <code>data.frame</code> (2,000 x 49)</strong><br>
Class: <code>factor</code> (<code>numeric</code>)<br>
Levels: A, B, C, D<br>
Length: 2,000 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<table class="table">
<thead><tr class="header">
<th align="left"></th>

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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">0.5.0.9016</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</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">0.5.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9016</span>
</span>
</div>
@ -185,7 +185,7 @@
<h1>How to get properties of a microorganism</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">29 January 2019</h4>
<h4 class="date">08 February 2019</h4>
<div class="hidden name"><code>mo_property.Rmd</code></div>