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fixes for microorganisms.codes

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dr. M.S. (Matthijs) Berends
2019-05-28 16:50:40 +02:00
parent 7e0e171512
commit 27380fa021
73 changed files with 679 additions and 412 deletions
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docs/articles/WHONET.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">0.6.1.9035</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9037</span>
</span>
</div>
@ -199,7 +199,7 @@
<h1>How to work with WHONET data</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">23 May 2019</h4>
<h4 class="date">28 May 2019</h4>
<div class="hidden name"><code>WHONET.Rmd</code></div>
@ -239,7 +239,7 @@
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="co"># our newly created `mo` variable</span></a>
<a class="sourceLine" id="cb4-2" title="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></p>
<p>Class: <code>mo</code> (<code>character</code>)<br>
<p>Class: mo (character)<br>
Length: 500 (of which NA: 0 = 0.00%)<br>
Unique: 39</p>
<p>Families: 10<br>
@ -343,9 +343,9 @@ Species: 38</p>
<a class="sourceLine" id="cb5-3" title="3"><span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span></a>
<a class="sourceLine" id="cb5-4" title="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></p>
<p>Class: <code>factor</code> &gt; <code>ordered</code> &gt; <code>rsi</code> (<code>numeric</code>)<br>
<p>Class: factor &gt; ordered &gt; rsi (numeric)<br>
Length: 500 (of which NA: 19 = 3.80%)<br>
Levels: 3: <code>S</code> &lt; <code>I</code> &lt; <code>R</code><br>
Levels: 3: S &lt; I &lt; R<br>
Unique: 3</p>
<p>Drug: Amoxicillin/clavulanic acid (AMC, J01CR02)<br>
Group: Beta-lactams/penicillins<br>