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<h1>How to create frequency tables</h1>
<h4 class="author">Matthijs S. Berends</h4>
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<h4 class="date">10 July 2019</h4>
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<div class="hidden name"><code>freq.Rmd</code></div>
</div>
<div id="introduction" class="section level2">
<h2 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h2>
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<p>Frequency tables (or frequency distributions) are summaries of the distribution of values in a sample. With the <code><a href="../reference/freq.html">freq()</a></code> function, you can create univariate frequency tables. Multiple variables will be pasted into one variable, so it forces a univariate distribution. We take the <code>septic_patients</code> dataset (included in this AMR package) as example.</p>
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</div>
<div id="frequencies-of-one-variable" class="section level2">
<h2 class="hasAnchor">
<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>
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<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="co"># Any of these will work:</span></a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="co"># freq(septic_patients$gender)</span></a>
<a class="sourceLine" id="cb1-3" data-line-number="3"><span class="co"># freq(septic_patients[, "gender"])</span></a>
<a class="sourceLine" id="cb1-4" data-line-number="4"></a>
<a class="sourceLine" id="cb1-5" data-line-number="5"><span class="co"># Using tidyverse:</span></a>
<a class="sourceLine" id="cb1-6" data-line-number="6"><span class="co"># septic_patients$gender %&gt;% freq()</span></a>
<a class="sourceLine" id="cb1-7" data-line-number="7"><span class="co"># septic_patients[, "gender"] %&gt;% freq()</span></a>
<a class="sourceLine" id="cb1-8" data-line-number="8"><span class="co"># septic_patients %&gt;% freq("gender")</span></a>
<a class="sourceLine" id="cb1-9" data-line-number="9"></a>
<a class="sourceLine" id="cb1-10" data-line-number="10"><span class="co"># Probably the fastest and easiest:</span></a>
<a class="sourceLine" id="cb1-11" data-line-number="11">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>
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<p><strong>Frequency table of <code>gender</code> from <code>septic_patients</code> (2,000 x 49)</strong></p>
fixes for microorganisms.codes
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<p>Class: character<br>
mo codes for WHONET
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Length: 2,000 (of which NA: 0 = 0.00%)<br>
Unique: 2</p>
<p>Shortest: 1<br>
Longest: 1</p>
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<table class="table">
<thead><tr class="header">
<th align="left"></th>
<th align="left">Item</th>
<th align="right">Count</th>
<th align="right">Percent</th>
<th align="right">Cum. Count</th>
<th align="right">Cum. Percent</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">1,031</td>
<td align="right">51.6%</td>
<td align="right">1,031</td>
<td align="right">51.6%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">969</td>
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<td align="right">48.4%</td>
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<td align="right">2,000</td>
<td align="right">100.0%</td>
</tr>
</tbody>
</table>
<p>This immediately shows the class of the variable, its length and availability (i.e. the amount of <code>NA</code>), the amount of unique values and (most importantly) that among septic patients men are more prevalent than women.</p>
</div>
<div id="frequencies-of-more-than-one-variable" class="section level2">
<h2 class="hasAnchor">
<a href="#frequencies-of-more-than-one-variable" class="anchor"></a>Frequencies of more than one variable</h2>
<p>Multiple variables will be pasted into one variable to review individual cases, keeping a univariate frequency table.</p>
<p>For illustration, we could add some more variables to the <code>septic_patients</code> dataset to learn about bacterial properties:</p>
(v0.7.1.90012) mo_shortname fix
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<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">my_patients &lt;-<span class="st"> </span>septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/join.html">left_join_microorganisms</a></span>()</a>
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="co"># Joining, by = "mo"</span></a></code></pre></div>
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<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>
(v0.7.1.90012) mo_shortname fix
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<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="kw"><a href="https://www.rdocumentation.org/packages/base/topics/colnames">colnames</a></span>(microorganisms)</a>
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="co"># [1] "mo" "col_id" "fullname" "kingdom" "phylum" </span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co"># [6] "class" "order" "family" "genus" "species" </span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># [11] "subspecies" "rank" "ref" "species_id" "source" </span></a>
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co"># [16] "prevalence"</span></a></code></pre></div>
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<p>If we compare the dimensions between the old and new dataset, we can see that these 15 variables were added:</p>
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<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="kw"><a href="https://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(septic_patients)</a>
<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="co"># [1] 2000 49</span></a>
<a class="sourceLine" id="cb4-3" data-line-number="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" data-line-number="4"><span class="co"># [1] 2000 64</span></a></code></pre></div>
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<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>
(v0.7.1.90012) mo_shortname fix
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<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>
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<p><strong>Frequency table of <code>genus</code> and <code>species</code> from <code>my_patients</code> (2,000 x 64)</strong></p>
benchmarks plots
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<p>Columns: 2<br>
mo codes for WHONET
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Length: 2,000 (of which NA: 0 = 0.00%)<br>
Catalogue of Life, replaces ITIS
2019-02-18 02:33:37 +01:00
Unique: 95</p>
<p>Shortest: 8<br>
mo codes for WHONET
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Longest: 34</p>
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<table class="table">
<thead><tr class="header">
<th align="left"></th>
<th align="left">Item</th>
<th align="right">Count</th>
<th align="right">Percent</th>
<th align="right">Cum. Count</th>
<th align="right">Cum. Percent</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">467</td>
<td align="right">23.4%</td>
<td align="right">467</td>
<td align="right">23.4%</td>
</tr>
<tr class="even">
<td align="left">2</td>
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<td align="left">Staphylococcus coagulase-negative</td>
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<td align="right">313</td>
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<td align="right">15.6%</td>
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<td align="right">780</td>
<td align="right">39.0%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">235</td>
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<td align="right">11.7%</td>
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<td align="right">1,015</td>
<td align="right">50.7%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Staphylococcus epidermidis</td>
<td align="right">174</td>
<td align="right">8.7%</td>
<td align="right">1,189</td>
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<td align="right">59.4%</td>
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</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">117</td>
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<td align="right">5.8%</td>
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<td align="right">1,306</td>
<td align="right">65.3%</td>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="left">Staphylococcus hominis</td>
<td align="right">81</td>
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<td align="right">4.0%</td>
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<td align="right">1,387</td>
<td align="right">69.4%</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">58</td>
<td align="right">2.9%</td>
<td align="right">1,445</td>
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<td align="right">72.2%</td>
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</tr>
<tr class="even">
<td align="left">8</td>
<td align="left">Enterococcus faecalis</td>
<td align="right">39</td>
<td align="right">2.0%</td>
<td align="right">1,484</td>
<td align="right">74.2%</td>
</tr>
<tr class="odd">
<td align="left">9</td>
<td align="left">Proteus mirabilis</td>
<td align="right">36</td>
<td align="right">1.8%</td>
<td align="right">1,520</td>
<td align="right">76.0%</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="left">Pseudomonas aeruginosa</td>
<td align="right">30</td>
<td align="right">1.5%</td>
<td align="right">1,550</td>
<td align="right">77.5%</td>
</tr>
<tr class="odd">
<td align="left">11</td>
<td align="left">Serratia marcescens</td>
<td align="right">25</td>
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<td align="right">1.2%</td>
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<td align="right">1,575</td>
<td align="right">78.8%</td>
</tr>
<tr class="even">
<td align="left">12</td>
<td align="left">Enterobacter cloacae</td>
<td align="right">23</td>
<td align="right">1.2%</td>
<td align="right">1,598</td>
<td align="right">79.9%</td>
</tr>
<tr class="odd">
<td align="left">13</td>
<td align="left">Enterococcus faecium</td>
<td align="right">21</td>
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<td align="right">1.0%</td>
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<td align="right">1,619</td>
<td align="right">81.0%</td>
</tr>
<tr class="even">
<td align="left">14</td>
<td align="left">Staphylococcus capitis</td>
<td align="right">21</td>
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<td align="right">1.0%</td>
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<td align="right">1,640</td>
<td align="right">82.0%</td>
</tr>
<tr class="odd">
<td align="left">15</td>
<td align="left">Bacteroides fragilis</td>
<td align="right">20</td>
<td align="right">1.0%</td>
<td align="right">1,660</td>
<td align="right">83.0%</td>
</tr>
</tbody>
</table>
Catalogue of Life, replaces ITIS
2019-02-18 02:33:37 +01:00
<p>(omitted 80 entries, n = 340 [17.0%])</p>
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</div>
<div id="frequencies-of-numeric-values" class="section level2">
<h2 class="hasAnchor">
<a href="#frequencies-of-numeric-values" class="anchor"></a>Frequencies of numeric values</h2>
<p>Frequency tables can be created of any input.</p>
<p>In case of numeric values (like integers, doubles, etc.) additional descriptive statistics will be calculated and shown into the header:</p>
(v0.7.1.90012) mo_shortname fix
2019-07-10 21:36:51 +02:00
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="co"># # get age distribution of unique patients</span></a>
<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>
benchmarks plots
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<p><strong>Frequency table of <code>age</code> from a <code>data.frame</code> (981 x 49)</strong></p>
fixes for microorganisms.codes
2019-05-28 16:50:40 +02:00
<p>Class: numeric<br>
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Length: 981 (of which NA: 0 = 0.00%)<br>
Unique: 73</p>
<p>Mean: 71.08<br>
SD: 14.05 (CV: 0.20, MAD: 13.34)<br>
Five-Num: 14 | 63 | 74 | 82 | 97 (IQR: 19, CQV: 0.13)<br>
Outliers: 15 (unique count: 12)</p>
<table class="table">
<thead><tr class="header">
<th align="left"></th>
<th align="right">Item</th>
<th align="right">Count</th>
<th align="right">Percent</th>
<th align="right">Cum. Count</th>
<th align="right">Cum. Percent</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="right">83</td>
<td align="right">44</td>
<td align="right">4.5%</td>
<td align="right">44</td>
<td align="right">4.5%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="right">76</td>
<td align="right">43</td>
<td align="right">4.4%</td>
<td align="right">87</td>
<td align="right">8.9%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="right">75</td>
<td align="right">37</td>
<td align="right">3.8%</td>
<td align="right">124</td>
<td align="right">12.6%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="right">82</td>
<td align="right">33</td>
<td align="right">3.4%</td>
<td align="right">157</td>
<td align="right">16.0%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="right">78</td>
<td align="right">32</td>
<td align="right">3.3%</td>
<td align="right">189</td>
<td align="right">19.3%</td>
</tr>
</tbody>
</table>
<p>(omitted 68 entries, n = 792 [80.7%])</p>
<p>So the following properties are determined, where <code>NA</code> values are always ignored:</p>
<ul>
<li><p><strong>Mean</strong></p></li>
<li><p><strong>Standard deviation</strong></p></li>
<li><p><strong>Coefficient of variation</strong> (CV), the standard deviation divided by the mean</p></li>
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<li><p><strong>Mean absolute deviation</strong> (MAD), the median of the absolute deviations from the median - a more robust statistic than the standard deviation</p></li>
<li><p><strong>Five numbers of Tukey</strong>, namely: the minimum, Q1, median, Q3 and maximum</p></li>
<li><p><strong>Interquartile range</strong> (IQR), the distance between Q1 and Q3</p></li>
<li><p><strong>Coefficient of quartile variation</strong> (CQV, sometimes called <em>coefficient of dispersion</em>), calculated as (Q3 - Q1) / (Q3 + Q1) using <code><a href="https://www.rdocumentation.org/packages/stats/topics/quantile">quantile()</a></code> with <code>type = 6</code> as quantile algorithm to comply with SPSS standards</p></li>
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<li><p><strong>Outliers</strong> (total count and unique count)</p></li>
</ul>
<p>So for example, the above frequency table quickly shows the median age of patients being 74.</p>
</div>
<div id="frequencies-of-factors" class="section level2">
<h2 class="hasAnchor">
<a href="#frequencies-of-factors" class="anchor"></a>Frequencies of factors</h2>
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<p>To sort frequencies of factors on their levels instead of item count, use the <code>sort.count</code> parameter.</p>
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<p><code>sort.count</code> is <code>TRUE</code> by default. Compare this default behaviour…</p>
(v0.7.1.90012) mo_shortname fix
2019-07-10 21:36:51 +02:00
<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>
(v0.7.0.9001) new pathovars, small fixes
2019-06-07 22:47:37 +02:00
<p><strong>Frequency table of <code>hospital_id</code> from <code>septic_patients</code> (2,000 x 49)</strong></p>
fixes for microorganisms.codes
2019-05-28 16:50:40 +02:00
<p>Class: factor (numeric)<br>
mo codes for WHONET
2019-02-08 16:06:54 +01:00
Length: 2,000 (of which NA: 0 = 0.00%)<br>
fixes for microorganisms.codes
2019-05-28 16:50:40 +02:00
Levels: 4: A, B, C, D<br>
mo codes for WHONET
2019-02-08 16:06:54 +01:00
Unique: 4</p>
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<table class="table">
<thead><tr class="header">
<th align="left"></th>
<th align="left">Item</th>
<th align="right">Count</th>
<th align="right">Percent</th>
<th align="right">Cum. Count</th>
<th align="right">Cum. Percent</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="left">D</td>
<td align="right">762</td>
<td align="right">38.1%</td>
<td align="right">762</td>
<td align="right">38.1%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">B</td>
<td align="right">663</td>
<td align="right">33.2%</td>
<td align="right">1,425</td>
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<td align="right">71.2%</td>
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</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">A</td>
<td align="right">321</td>
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<td align="right">16.0%</td>
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<td align="right">1,746</td>
<td align="right">87.3%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">C</td>
<td align="right">254</td>
<td align="right">12.7%</td>
<td align="right">2,000</td>
<td align="right">100.0%</td>
</tr>
</tbody>
</table>
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2019-05-29 00:36:48 +02:00
<p>… to this, where items are now sorted on factor levels:</p>
(v0.7.1.90012) mo_shortname fix
2019-07-10 21:36:51 +02:00
<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>
(v0.7.0.9001) new pathovars, small fixes
2019-06-07 22:47:37 +02:00
<p><strong>Frequency table of <code>hospital_id</code> from <code>septic_patients</code> (2,000 x 49)</strong></p>
fixes for microorganisms.codes
2019-05-28 16:50:40 +02:00
<p>Class: factor (numeric)<br>
mo codes for WHONET
2019-02-08 16:06:54 +01:00
Length: 2,000 (of which NA: 0 = 0.00%)<br>
fixes for microorganisms.codes
2019-05-28 16:50:40 +02:00
Levels: 4: A, B, C, D<br>
mo codes for WHONET
2019-02-08 16:06:54 +01:00
Unique: 4</p>
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<table class="table">
<thead><tr class="header">
<th align="left"></th>
<th align="left">Item</th>
<th align="right">Count</th>
<th align="right">Percent</th>
<th align="right">Cum. Count</th>
<th align="right">Cum. Percent</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="left">A</td>
<td align="right">321</td>
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<td align="right">16.0%</td>
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<td align="right">321</td>
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<td align="right">16.0%</td>
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</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">B</td>
<td align="right">663</td>
<td align="right">33.2%</td>
<td align="right">984</td>
<td align="right">49.2%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">C</td>
<td align="right">254</td>
<td align="right">12.7%</td>
<td align="right">1,238</td>
<td align="right">61.9%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">D</td>
<td align="right">762</td>
<td align="right">38.1%</td>
<td align="right">2,000</td>
<td align="right">100.0%</td>
</tr>
</tbody>
</table>
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<p>All classes will be printed into the header. 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>
(v0.7.1.90012) mo_shortname fix
2019-07-10 21:36:51 +02:00
<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>(AMX, <span class="dt">header =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
(v0.7.0.9001) new pathovars, small fixes
2019-06-07 22:47:37 +02:00
<p><strong>Frequency table of <code>AMX</code> from <code>septic_patients</code> (2,000 x 49)</strong></p>
fixes for microorganisms.codes
2019-05-28 16:50:40 +02:00
<p>Class: factor &gt; ordered &gt; rsi (numeric)<br>
as.rsi warning, site update
2019-02-09 22:16:24 +01:00
Length: 2,000 (of which NA: 771 = 38.55%)<br>
fixes for microorganisms.codes
2019-05-28 16:50:40 +02:00
Levels: 3: S &lt; I &lt; R<br>
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Unique: 3</p>
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<p>Drug: Amoxicillin (AMX, J01CA04)<br>
Group: Beta-lactams/penicillins<br>
%SI: 44.43%</p>
big website update, licence txt update
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<table class="table">
<thead><tr class="header">
<th align="left"></th>
<th align="left">Item</th>
<th align="right">Count</th>
<th align="right">Percent</th>
<th align="right">Cum. Count</th>
<th align="right">Cum. Percent</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="left">R</td>
<td align="right">683</td>
as.rsi warning, site update
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<td align="right">55.6%</td>
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<td align="right">683</td>
as.rsi warning, site update
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<td align="right">55.6%</td>
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</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">S</td>
as.rsi warning, site update
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<td align="right">543</td>
<td align="right">44.2%</td>
<td align="right">1,226</td>
<td align="right">99.8%</td>
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</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">I</td>
<td align="right">3</td>
as.rsi warning, site update
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<td align="right">0.2%</td>
<td align="right">1,229</td>
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<td align="right">100.0%</td>
</tr>
</tbody>
</table>
</div>
<div id="frequencies-of-dates" class="section level2">
<h2 class="hasAnchor">
<a href="#frequencies-of-dates" class="anchor"></a>Frequencies of dates</h2>
<p>Frequencies of dates will show the oldest and newest date in the data, and the amount of days between them:</p>
(v0.7.1.90012) mo_shortname fix
2019-07-10 21:36:51 +02:00
<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>
(v0.7.0.9001) new pathovars, small fixes
2019-06-07 22:47:37 +02:00
<p><strong>Frequency table of <code>date</code> from <code>septic_patients</code> (2,000 x 49)</strong></p>
fixes for microorganisms.codes
2019-05-28 16:50:40 +02:00
<p>Class: Date (numeric)<br>
big website update, licence txt update
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Length: 2,000 (of which NA: 0 = 0.00%)<br>
Unique: 1,140</p>
<p>Oldest: 2 January 2002<br>
Newest: 28 December 2017 (+5,839)<br>
Median: 31 July 2009 (47.39%)</p>
<table class="table">
<thead><tr class="header">
<th align="left"></th>
<th align="left">Item</th>
<th align="right">Count</th>
<th align="right">Percent</th>
<th align="right">Cum. Count</th>
<th align="right">Cum. Percent</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="left">2016-05-21</td>
<td align="right">10</td>
<td align="right">0.5%</td>
<td align="right">10</td>
<td align="right">0.5%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">2004-11-15</td>
<td align="right">8</td>
<td align="right">0.4%</td>
<td align="right">18</td>
<td align="right">0.9%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">2013-07-29</td>
<td align="right">8</td>
<td align="right">0.4%</td>
<td align="right">26</td>
<td align="right">1.3%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">2017-06-12</td>
<td align="right">8</td>
<td align="right">0.4%</td>
<td align="right">34</td>
<td align="right">1.7%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">2015-11-19</td>
<td align="right">7</td>
<td align="right">0.4%</td>
<td align="right">41</td>
website update
2019-05-12 07:22:03 +02:00
<td align="right">2.0%</td>
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</tr>
</tbody>
</table>
<p>(omitted 1,135 entries, n = 1,959 [98.0%])</p>
</div>
<div id="assigning-a-frequency-table-to-an-object" class="section level2">
<h2 class="hasAnchor">
<a href="#assigning-a-frequency-table-to-an-object" class="anchor"></a>Assigning a frequency table to an object</h2>
added mdr_tb()
2019-05-23 16:58:59 +02:00
<p>A frequency table is actually a regular <code>data.frame</code>, with the exception that it contains an additional class.</p>
(v0.7.1.90012) mo_shortname fix
2019-07-10 21:36:51 +02:00
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1">my_df &lt;-<span class="st"> </span>septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age)</a>
<a class="sourceLine" id="cb11-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/class">class</a></span>(my_df)</a></code></pre></div>
added boxplot for (grouped) freq()
2019-05-29 19:56:17 +02:00
<p>[1] “freq” “data.frame”</p>
big website update, licence txt update
2019-01-02 23:24:07 +01:00
<p>Because of this additional class, a frequency table prints like the examples above. But the object itself contains the complete table without a row limitation:</p>
(v0.7.1.90012) mo_shortname fix
2019-07-10 21:36:51 +02:00
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(my_df)</a></code></pre></div>
big website update, licence txt update
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<p>[1] 74 5</p>
</div>
<div id="additional-parameters" class="section level2">
<h2 class="hasAnchor">
<a href="#additional-parameters" class="anchor"></a>Additional parameters</h2>
<div id="parameter-na-rm" class="section level3">
<h3 class="hasAnchor">
<a href="#parameter-na-rm" class="anchor"></a>Parameter <code>na.rm</code>
</h3>
added mdr_tb()
2019-05-23 16:58:59 +02:00
<p>With the <code>na.rm</code> parameter you can remove <code>NA</code> values from the frequency table (defaults to <code>TRUE</code>, but the number of <code>NA</code> values will always be shown into the header):</p>
(v0.7.1.90012) mo_shortname fix
2019-07-10 21:36:51 +02:00
<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>(AMX, <span class="dt">na.rm =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
(v0.7.0.9001) new pathovars, small fixes
2019-06-07 22:47:37 +02:00
<p><strong>Frequency table of <code>AMX</code> from <code>septic_patients</code> (2,000 x 49)</strong></p>
fixes for microorganisms.codes
2019-05-28 16:50:40 +02:00
<p>Class: factor &gt; ordered &gt; rsi (numeric)<br>
benchmarks plots
2019-02-14 10:23:51 +01:00
Length: 2,000 (of which NA: 771 = 38.55%)<br>
fixes for microorganisms.codes
2019-05-28 16:50:40 +02:00
Levels: 3: S &lt; I &lt; R<br>
mo codes for WHONET
2019-02-08 16:06:54 +01:00
Unique: 4</p>
website update
2019-05-12 07:22:03 +02:00
<p>Drug: Amoxicillin (AMX, J01CA04)<br>
Group: Beta-lactams/penicillins<br>
%SI: 44.43%</p>
big website update, licence txt update
2019-01-02 23:24:07 +01:00
<table class="table">
<thead><tr class="header">
<th align="left"></th>
<th align="left">Item</th>
<th align="right">Count</th>
<th align="right">Percent</th>
<th align="right">Cum. Count</th>
<th align="right">Cum. Percent</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="left">(NA)</td>
as.rsi warning, site update
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<td align="right">771</td>
<td align="right">38.6%</td>
<td align="right">771</td>
<td align="right">38.6%</td>
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</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">R</td>
<td align="right">683</td>
<td align="right">34.2%</td>
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<td align="right">1,454</td>
<td align="right">72.7%</td>
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</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">S</td>
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<td align="right">543</td>
<td align="right">27.2%</td>
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<td align="right">1,997</td>
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<td align="right">99.8%</td>
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</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">I</td>
<td align="right">3</td>
<td align="right">0.2%</td>
<td align="right">2,000</td>
<td align="right">100.0%</td>
</tr>
</tbody>
</table>
</div>
<div id="parameter-row-names" class="section level3">
<h3 class="hasAnchor">
<a href="#parameter-row-names" class="anchor"></a>Parameter <code>row.names</code>
</h3>
added mdr_tb()
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<p>A frequency table shows row indices. To remove them, use <code>row.names = FALSE</code>:</p>
(v0.7.1.90012) mo_shortname fix
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<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>
(v0.7.0.9001) new pathovars, small fixes
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<p><strong>Frequency table of <code>hospital_id</code> from <code>septic_patients</code> (2,000 x 49)</strong></p>
fixes for microorganisms.codes
2019-05-28 16:50:40 +02:00
<p>Class: factor (numeric)<br>
mo codes for WHONET
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Length: 2,000 (of which NA: 0 = 0.00%)<br>
fixes for microorganisms.codes
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Levels: 4: A, B, C, D<br>
mo codes for WHONET
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Unique: 4</p>
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<table class="table">
<thead><tr class="header">
<th align="left">Item</th>
<th align="right">Count</th>
<th align="right">Percent</th>
<th align="right">Cum. Count</th>
<th align="right">Cum. Percent</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">D</td>
<td align="right">762</td>
<td align="right">38.1%</td>
<td align="right">762</td>
<td align="right">38.1%</td>
</tr>
<tr class="even">
<td align="left">B</td>
<td align="right">663</td>
<td align="right">33.2%</td>
<td align="right">1,425</td>
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<td align="right">71.2%</td>
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</tr>
<tr class="odd">
<td align="left">A</td>
<td align="right">321</td>
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<td align="right">16.0%</td>
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<td align="right">1,746</td>
<td align="right">87.3%</td>
</tr>
<tr class="even">
<td align="left">C</td>
<td align="right">254</td>
<td align="right">12.7%</td>
<td align="right">2,000</td>
<td align="right">100.0%</td>
</tr>
</tbody>
</table>
</div>
<div id="parameter-markdown" class="section level3">
<h3 class="hasAnchor">
<a href="#parameter-markdown" class="anchor"></a>Parameter <code>markdown</code>
</h3>
website update
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<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. Without markdown (like in regular R), a frequency table would print like:</p>
(v0.7.1.90012) mo_shortname fix
2019-07-10 21:36:51 +02:00
<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">FALSE</span>)</a>
<a class="sourceLine" id="cb15-3" data-line-number="3"><span class="co"># Frequency table of `hospital_id` from `septic_patients` (2,000 x 49) </span></a>
<a class="sourceLine" id="cb15-4" data-line-number="4"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-5" data-line-number="5"><span class="co"># Class: factor (numeric)</span></a>
<a class="sourceLine" id="cb15-6" data-line-number="6"><span class="co"># Length: 2,000 (of which NA: 0 = 0.00%)</span></a>
<a class="sourceLine" id="cb15-7" data-line-number="7"><span class="co"># Levels: 4: A, B, C, D</span></a>
<a class="sourceLine" id="cb15-8" data-line-number="8"><span class="co"># Unique: 4</span></a>
<a class="sourceLine" id="cb15-9" data-line-number="9"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-10" data-line-number="10"><span class="co"># Item Count Percent Cum. Count Cum. Percent</span></a>
<a class="sourceLine" id="cb15-11" data-line-number="11"><span class="co"># --- ----- ------ -------- ----------- -------------</span></a>
<a class="sourceLine" id="cb15-12" data-line-number="12"><span class="co"># 1 D 762 38.1% 762 38.1%</span></a>
<a class="sourceLine" id="cb15-13" data-line-number="13"><span class="co"># 2 B 663 33.2% 1,425 71.2%</span></a>
<a class="sourceLine" id="cb15-14" data-line-number="14"><span class="co"># 3 A 321 16.0% 1,746 87.3%</span></a>
<a class="sourceLine" id="cb15-15" data-line-number="15"><span class="co"># 4 C 254 12.7% 2,000 100.0%</span></a></code></pre></div>
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</div>
</div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<div id="tocnav">
<h2 class="hasAnchor">
<a href="#tocnav" class="anchor"></a>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#introduction">Introduction</a></li>
<li><a href="#frequencies-of-one-variable">Frequencies of one variable</a></li>
<li><a href="#frequencies-of-more-than-one-variable">Frequencies of more than one variable</a></li>
<li><a href="#frequencies-of-numeric-values">Frequencies of numeric values</a></li>
<li><a href="#frequencies-of-factors">Frequencies of factors</a></li>
<li><a href="#frequencies-of-dates">Frequencies of dates</a></li>
<li><a href="#assigning-a-frequency-table-to-an-object">Assigning a frequency table to an object</a></li>
<li><a href="#additional-parameters">Additional parameters</a></li>
</ul>
</div>
</div>
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<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>.</p>
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