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dr. M.S. (Matthijs) Berends
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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">0.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
</span>
</div>
@ -105,7 +105,7 @@
</a>
</li>
<li>
<a href="../reference/atc_property.html">
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
@ -192,7 +192,7 @@
<h1>How to create frequency tables</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">27 March 2019</h4>
<h4 class="date">12 May 2019</h4>
<div class="hidden name"><code>freq.Rmd</code></div>
@ -239,7 +239,7 @@ Longest: 1</p>
<td align="left">2</td>
<td align="left">F</td>
<td align="right">969</td>
<td align="right">48.5%</td>
<td align="right">48.4%</td>
<td align="right">2,000</td>
<td align="right">100.0%</td>
</tr>
@ -258,17 +258,16 @@ Longest: 1</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/colnames">colnames</a></span>(microorganisms)</a>
<a class="sourceLine" id="cb3-2" title="2"><span class="co"># [1] "mo" "col_id" "fullname" "kingdom" "phylum" </span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># [6] "class" "order" "family" "genus" "species" </span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># [11] "subspecies" "rank" "ref" "species_id" "source" </span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="co"># [16] "prevalence"</span></a></code></pre></div>
<p>If we compare the dimensions between the old and new dataset, we can see that these 15 variables were added:</p>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># [11] "subspecies" "rank" "ref" "species_id" "source"</span></a></code></pre></div>
<p>If we compare the dimensions between the old and new dataset, we can see that these 14 variables were added:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(septic_patients)</a>
<a class="sourceLine" id="cb4-2" title="2"><span class="co"># [1] 2000 49</span></a>
<a class="sourceLine" id="cb4-3" title="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(my_patients)</a>
<a class="sourceLine" id="cb4-4" title="4"><span class="co"># [1] 2000 64</span></a></code></pre></div>
<a class="sourceLine" id="cb4-4" title="4"><span class="co"># [1] 2000 63</span></a></code></pre></div>
<p>So now the <code>genus</code> and <code>species</code> variables are available. A frequency table of these combined variables can be created like this:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1">my_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus, species, <span class="dt">nmax =</span> <span class="dv">15</span>)</a></code></pre></div>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (2,000 x 64)</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></p>
<p>Columns: 2<br>
Length: 2,000 (of which NA: 0 = 0.00%)<br>
Unique: 95</p>
@ -296,7 +295,7 @@ Longest: 34</p>
<td align="left">2</td>
<td align="left">Staphylococcus coagulase-negative</td>
<td align="right">313</td>
<td align="right">15.7%</td>
<td align="right">15.6%</td>
<td align="right">780</td>
<td align="right">39.0%</td>
</tr>
@ -304,7 +303,7 @@ Longest: 34</p>
<td align="left">3</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">235</td>
<td align="right">11.8%</td>
<td align="right">11.7%</td>
<td align="right">1,015</td>
<td align="right">50.7%</td>
</tr>
@ -314,13 +313,13 @@ Longest: 34</p>
<td align="right">174</td>
<td align="right">8.7%</td>
<td align="right">1,189</td>
<td align="right">59.5%</td>
<td align="right">59.4%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">117</td>
<td align="right">5.9%</td>
<td align="right">5.8%</td>
<td align="right">1,306</td>
<td align="right">65.3%</td>
</tr>
@ -328,7 +327,7 @@ Longest: 34</p>
<td align="left">6</td>
<td align="left">Staphylococcus hominis</td>
<td align="right">81</td>
<td align="right">4.1%</td>
<td align="right">4.0%</td>
<td align="right">1,387</td>
<td align="right">69.4%</td>
</tr>
@ -338,7 +337,7 @@ Longest: 34</p>
<td align="right">58</td>
<td align="right">2.9%</td>
<td align="right">1,445</td>
<td align="right">72.3%</td>
<td align="right">72.2%</td>
</tr>
<tr class="even">
<td align="left">8</td>
@ -368,7 +367,7 @@ Longest: 34</p>
<td align="left">11</td>
<td align="left">Serratia marcescens</td>
<td align="right">25</td>
<td align="right">1.3%</td>
<td align="right">1.2%</td>
<td align="right">1,575</td>
<td align="right">78.8%</td>
</tr>
@ -384,7 +383,7 @@ Longest: 34</p>
<td align="left">13</td>
<td align="left">Enterococcus faecium</td>
<td align="right">21</td>
<td align="right">1.1%</td>
<td align="right">1.0%</td>
<td align="right">1,619</td>
<td align="right">81.0%</td>
</tr>
@ -392,7 +391,7 @@ Longest: 34</p>
<td align="left">14</td>
<td align="left">Staphylococcus capitis</td>
<td align="right">21</td>
<td align="right">1.1%</td>
<td align="right">1.0%</td>
<td align="right">1,640</td>
<td align="right">82.0%</td>
</tr>
@ -525,13 +524,13 @@ Unique: 4</p>
<td align="right">663</td>
<td align="right">33.2%</td>
<td align="right">1,425</td>
<td align="right">71.3%</td>
<td align="right">71.2%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">A</td>
<td align="right">321</td>
<td align="right">16.1%</td>
<td align="right">16.0%</td>
<td align="right">1,746</td>
<td align="right">87.3%</td>
</tr>
@ -567,9 +566,9 @@ Unique: 4</p>
<td align="left">1</td>
<td align="left">A</td>
<td align="right">321</td>
<td align="right">16.1%</td>
<td align="right">16.0%</td>
<td align="right">321</td>
<td align="right">16.1%</td>
<td align="right">16.0%</td>
</tr>
<tr class="even">
<td align="left">2</td>
@ -599,14 +598,15 @@ Unique: 4</p>
</table>
<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" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb9-2" title="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 of <code>amox</code> from a <code>data.frame</code> (2,000 x 49)</strong></p>
<a class="sourceLine" id="cb9-2" title="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>
<p><strong>Frequency table of <code>AMX</code> from a <code>data.frame</code> (2,000 x 49)</strong></p>
<p>Class: <code>factor</code> &gt; <code>ordered</code> &gt; <code>rsi</code> (<code>numeric</code>)<br>
Length: 2,000 (of which NA: 771 = 38.55%)<br>
Levels: 3: <code>S</code> &lt; <code>I</code> &lt; <code>R</code><br>
Unique: 3</p>
<p>Drug: Amoxicillin<br>
%IR: 55.82%</p>
<p>Drug: Amoxicillin (AMX, J01CA04)<br>
Group: Beta-lactams/penicillins<br>
%SI: 44.43%</p>
<table class="table">
<thead><tr class="header">
<th align="left"></th>
@ -705,7 +705,7 @@ Median: 31 July 2009 (47.39%)</p>
<td align="right">7</td>
<td align="right">0.4%</td>
<td align="right">41</td>
<td align="right">2.1%</td>
<td align="right">2.0%</td>
</tr>
</tbody>
</table>
@ -731,14 +731,15 @@ Median: 31 July 2009 (47.39%)</p>
</h3>
<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" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb13-2" title="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 of <code>amox</code> from a <code>data.frame</code> (2,000 x 49)</strong></p>
<a class="sourceLine" id="cb13-2" title="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>
<p><strong>Frequency table of <code>AMX</code> from a <code>data.frame</code> (2,000 x 49)</strong></p>
<p>Class: <code>factor</code> &gt; <code>ordered</code> &gt; <code>rsi</code> (<code>numeric</code>)<br>
Length: 2,000 (of which NA: 771 = 38.55%)<br>
Levels: 3: <code>S</code> &lt; <code>I</code> &lt; <code>R</code><br>
Unique: 4</p>
<p>Drug: Amoxicillin<br>
%IR: 55.82%</p>
<p>Drug: Amoxicillin (AMX, J01CA04)<br>
Group: Beta-lactams/penicillins<br>
%SI: 44.43%</p>
<table class="table">
<thead><tr class="header">
<th align="left"></th>
@ -771,7 +772,7 @@ Unique: 4</p>
<td align="right">543</td>
<td align="right">27.2%</td>
<td align="right">1,997</td>
<td align="right">99.9%</td>
<td align="right">99.8%</td>
</tr>
<tr class="even">
<td align="left">4</td>
@ -817,12 +818,12 @@ Unique: 4</p>
<td align="right">663</td>
<td align="right">33.2%</td>
<td align="right">1,425</td>
<td align="right">71.3%</td>
<td align="right">71.2%</td>
</tr>
<tr class="odd">
<td align="left">A</td>
<td align="right">321</td>
<td align="right">16.1%</td>
<td align="right">16.0%</td>
<td align="right">1,746</td>
<td align="right">87.3%</td>
</tr>
@ -872,13 +873,13 @@ Unique: 4</p>
<td align="right">663</td>
<td align="right">33.2%</td>
<td align="right">1,425</td>
<td align="right">71.3%</td>
<td align="right">71.2%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">A</td>
<td align="right">321</td>
<td align="right">16.1%</td>
<td align="right">16.0%</td>
<td align="right">1,746</td>
<td align="right">87.3%</td>
</tr>