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WHO update, antibiotics update

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dr. M.S. (Matthijs) Berends
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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">0.5.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9012</span>
</span>
</div>
@ -178,7 +178,7 @@
<h1>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">12 January 2019</h4>
<h4 class="date">25 January 2019</h4>
<div class="hidden name"><code>EUCAST.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">0.5.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9012</span>
</span>
</div>
@ -178,7 +178,7 @@
<h1>How to use the <em>G</em>-test</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">12 January 2019</h4>
<h4 class="date">25 January 2019</h4>
<div class="hidden name"><code>G_test.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">0.5.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9012</span>
</span>
</div>
@ -178,7 +178,7 @@
<h1>How to predict antimicrobial resistance</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">12 January 2019</h4>
<h4 class="date">25 January 2019</h4>
<div class="hidden name"><code>Predict.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">0.5.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9012</span>
</span>
</div>
@ -178,7 +178,7 @@
<h1>How to get properties of an antibiotic</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">11 January 2019</h4>
<h4 class="date">25 January 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">0.5.0.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9012</span>
</span>
</div>
@ -178,7 +178,7 @@
<h1>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">21 January 2019</h4>
<h4 class="date">25 January 2019</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -240,15 +240,15 @@
<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/library">library</a></span>(dplyr)</a>
<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="co"># take 500,000 random MO codes from the septic_patients data set</span></a>
<a class="sourceLine" id="cb4-3" data-line-number="3">x =<span class="st"> </span>septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample_n</a></span>(<span class="dv">500000</span>, <span class="dt">replace =</span> <span class="ot">TRUE</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb4-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/pull.html">pull</a></span>(mo)</a>
<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/dplyr/topics/sample">sample_n</a></span>(<span class="dv">500000</span>, <span class="dt">replace =</span> <span class="ot">TRUE</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb4-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/dplyr/topics/pull">pull</a></span>(mo)</a>
<a class="sourceLine" id="cb4-6" data-line-number="6"> </a>
<a class="sourceLine" id="cb4-7" data-line-number="7"><span class="co"># got the right length?</span></a>
<a class="sourceLine" id="cb4-8" data-line-number="8"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/length">length</a></span>(x)</a>
<a class="sourceLine" id="cb4-9" data-line-number="9"><span class="co"># [1] 500000</span></a>
<a class="sourceLine" id="cb4-10" data-line-number="10"></a>
<a class="sourceLine" id="cb4-11" data-line-number="11"><span class="co"># and how many unique values do we have?</span></a>
<a class="sourceLine" id="cb4-12" data-line-number="12"><span class="kw"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(x)</a>
<a class="sourceLine" id="cb4-12" data-line-number="12"><span class="kw"><a href="https://www.rdocumentation.org/packages/dplyr/topics/n_distinct">n_distinct</a></span>(x)</a>
<a class="sourceLine" id="cb4-13" data-line-number="13"><span class="co"># [1] 96</span></a>
<a class="sourceLine" id="cb4-14" data-line-number="14"></a>
<a class="sourceLine" id="cb4-15" data-line-number="15"><span class="co"># only 96, but distributed in 500,000 results. now let's see:</span></a>

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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">0.5.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9012</span>
</span>
</div>
@ -178,7 +178,7 @@
<h1>How to create frequency tables</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">12 January 2019</h4>
<h4 class="date">25 January 2019</h4>
<div class="hidden name"><code>freq.Rmd</code></div>
@ -196,7 +196,7 @@
<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>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">septic_patients %&gt;%<span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</code></pre></div>
<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 of <code>gender</code></strong></p>
<table class="table">
<thead><tr class="header">
@ -233,21 +233,21 @@
<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>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">my_patients &lt;-<span class="st"> </span>septic_patients %&gt;%<span class="st"> </span><span class="kw"><a href="../reference/join.html">left_join_microorganisms</a></span>()
<span class="co"># Joining, by = "mo"</span></code></pre></div>
<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>
<p>Now all variables of the <code>microorganisms</code> dataset have been joined to the <code>septic_patients</code> dataset. The <code>microorganisms</code> dataset consists of the following variables:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/colnames">colnames</a></span>(microorganisms)
<span class="co"># [1] "mo" "tsn" "genus" "species" "subspecies"</span>
<span class="co"># [6] "fullname" "family" "order" "class" "phylum" </span>
<span class="co"># [11] "subkingdom" "kingdom" "gramstain" "prevalence" "ref"</span></code></pre></div>
<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" "tsn" "genus" "species" "subspecies"</span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co"># [6] "fullname" "family" "order" "class" "phylum" </span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># [11] "subkingdom" "kingdom" "gramstain" "prevalence" "ref"</span></a></code></pre></div>
<p>If we compare the dimensions between the old and new dataset, we can see that these 14 variables were added:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(septic_patients)
<span class="co"># [1] 2000 49</span>
<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(my_patients)
<span class="co"># [1] 2000 63</span></code></pre></div>
<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 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"><pre class="sourceCode r"><code class="sourceCode r">my_patients %&gt;%
<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>)</code></pre></div>
<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 of <code>genus</code> and <code>species</code></strong></p>
<table class="table">
<thead><tr class="header">
@ -388,10 +388,10 @@
<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>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># # get age distribution of unique patients</span>
septic_patients %&gt;%<span class="st"> </span>
<span class="st"> </span><span class="kw">distinct</span>(patient_id, <span class="dt">.keep_all =</span> <span class="ot">TRUE</span>) %&gt;%<span class="st"> </span>
<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>)</code></pre></div>
<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>
<p><strong>Frequency table of <code>age</code></strong><br>
Class: numeric<br>
Length: 981 (of which NA: 0 = 0.00%)<br>
@ -469,8 +469,8 @@ Outliers: 15 (unique count: 12)</p>
<a href="#frequencies-of-factors" class="anchor"></a>Frequencies of factors</h2>
<p>To sort frequencies of factors on factor level instead of item count, use the <code>sort.count</code> parameter.</p>
<p><code>sort.count</code> is <code>TRUE</code> by default. Compare this default behaviour…</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">septic_patients %&gt;%
<span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id)</code></pre></div>
<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 of <code>hospital_id</code></strong></p>
<table class="table">
<thead><tr class="header">
@ -517,8 +517,8 @@ Outliers: 15 (unique count: 12)</p>
</tbody>
</table>
<p>… with this, where items are now sorted on count:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">septic_patients %&gt;%
<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>)</code></pre></div>
<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 of <code>hospital_id</code></strong></p>
<table class="table">
<thead><tr class="header">
@ -565,8 +565,8 @@ Outliers: 15 (unique count: 12)</p>
</tbody>
</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"><pre class="sourceCode r"><code class="sourceCode r">septic_patients %&gt;%
<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>)</code></pre></div>
<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 of <code>amox</code></strong><br>
Class: factor &gt; ordered &gt; rsi (numeric)<br>
Levels: S &lt; I &lt; R<br>
@ -614,8 +614,8 @@ Unique: 3</p>
<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>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">septic_patients %&gt;%
<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>)</code></pre></div>
<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 of <code>date</code></strong><br>
Class: Date (numeric)<br>
Length: 2,000 (of which NA: 0 = 0.00%)<br>
@ -681,11 +681,11 @@ Median: 31 July 2009 (47.39%)</p>
<h2 class="hasAnchor">
<a href="#assigning-a-frequency-table-to-an-object" class="anchor"></a>Assigning a frequency table to an object</h2>
<p>A frequency table is actaually a regular <code>data.frame</code>, with the exception that it contains an additional class.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">my_df &lt;-<span class="st"> </span>septic_patients %&gt;%<span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age)
<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/class">class</a></span>(my_df)</code></pre></div>
<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>
<p>[1] “frequency_tbl” “data.frame”</p>
<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>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(my_df)</code></pre></div>
<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>
<p>[1] 74 5</p>
</div>
<div id="additional-parameters" class="section level2">
@ -696,8 +696,8 @@ Median: 31 July 2009 (47.39%)</p>
<a href="#parameter-na-rm" class="anchor"></a>Parameter <code>na.rm</code>
</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"><pre class="sourceCode r"><code class="sourceCode r">septic_patients %&gt;%
<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>)</code></pre></div>
<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 of <code>amox</code></strong></p>
<table class="table">
<thead><tr class="header">
@ -749,8 +749,8 @@ Median: 31 July 2009 (47.39%)</p>
<a href="#parameter-row-names" class="anchor"></a>Parameter <code>row.names</code>
</h3>
<p>The default frequency tables shows row indices. To remove them, use <code>row.names = FALSE</code>:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">septic_patients %&gt;%
<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>)</code></pre></div>
<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 of <code>hospital_id</code></strong></p>
<table class="table">
<thead><tr class="header">
@ -797,8 +797,8 @@ Median: 31 July 2009 (47.39%)</p>
<a href="#parameter-markdown" class="anchor"></a>Parameter <code>markdown</code>
</h3>
<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"><pre class="sourceCode r"><code class="sourceCode r">septic_patients %&gt;%
<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>)</code></pre></div>
<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 of <code>hospital_id</code></strong></p>
<table class="table">
<thead><tr class="header">

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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">0.5.0.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9012</span>
</span>
</div>

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@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9012</span>
</span>
</div>
@ -178,7 +178,7 @@
<h1>How to get properties of a microorganism</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">12 January 2019</h4>
<h4 class="date">25 January 2019</h4>
<div class="hidden name"><code>mo_property.Rmd</code></div>