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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">0.5.0.9016</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
</span>
</div>
@ -185,7 +185,7 @@
<h1>How to work with WHONET data</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">08 February 2019</h4>
<h4 class="date">09 February 2019</h4>
<div class="hidden name"><code>WHONET.Rmd</code></div>
@ -227,10 +227,10 @@
<p><strong>Frequency table of <code>mo</code> from a <code>data.frame</code> (500 x 54)</strong><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>
Genera: 23<br>
Species: 51</p>
Unique: 39</p>
<p>Families: 9<br>
Genera: 16<br>
Species: 36</p>
<table class="table">
<thead><tr class="header">
<th align="left"></th>
@ -244,86 +244,86 @@ Species: 51</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">B_ESCHR_COL</td>
<td align="right">127</td>
<td align="right">25.4%</td>
<td align="right">127</td>
<td align="right">25.4%</td>
<td align="right">245</td>
<td align="right">49.0%</td>
<td align="right">245</td>
<td align="right">49.0%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">B_STPHY_CNS</td>
<td align="right">80</td>
<td align="right">16.0%</td>
<td align="right">207</td>
<td align="right">41.4%</td>
<td align="right">74</td>
<td align="right">14.8%</td>
<td align="right">319</td>
<td align="right">63.8%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">B_STPHY_AUR</td>
<td align="right">50</td>
<td align="right">10.0%</td>
<td align="right">257</td>
<td align="right">51.4%</td>
<td align="left">B_STPHY_EPI</td>
<td align="right">38</td>
<td align="right">7.6%</td>
<td align="right">357</td>
<td align="right">71.4%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">B_STPHY_EPI</td>
<td align="right">37</td>
<td align="right">7.4%</td>
<td align="right">294</td>
<td align="right">58.8%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">B_STRPTC_PNE</td>
<td align="right">31</td>
<td align="right">6.2%</td>
<td align="right">325</td>
<td align="right">65.0%</td>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="left">B_STPHY_HOM</td>
<td align="right">23</td>
<td align="right">4.6%</td>
<td align="right">348</td>
<td align="right">69.6%</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="left">B_PROTS_MIR</td>
<td align="right">13</td>
<td align="right">2.6%</td>
<td align="right">361</td>
<td align="right">72.2%</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="left">B_KLBSL_PNE</td>
<td align="right">11</td>
<td align="right">2.2%</td>
<td align="right">372</td>
<td align="right">74.4%</td>
</tr>
<tr class="odd">
<td align="left">9</td>
<td align="left">B_PDMNS_AER</td>
<td align="right">8</td>
<td align="right">1.6%</td>
<td align="right">380</td>
<td align="right">76.0%</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="left">B_STPHY_CAP</td>
<td align="right">8</td>
<td align="right">1.6%</td>
<td align="right">388</td>
<td align="right">77.6%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">B_STPHY_HOM</td>
<td align="right">21</td>
<td align="right">4.2%</td>
<td align="right">409</td>
<td align="right">81.8%</td>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="left">B_PROTS_MIR</td>
<td align="right">9</td>
<td align="right">1.8%</td>
<td align="right">418</td>
<td align="right">83.6%</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="left">B_ENTRC_IUM</td>
<td align="right">8</td>
<td align="right">1.6%</td>
<td align="right">426</td>
<td align="right">85.2%</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="left">B_STPHY_CAP</td>
<td align="right">8</td>
<td align="right">1.6%</td>
<td align="right">434</td>
<td align="right">86.8%</td>
</tr>
<tr class="odd">
<td align="left">9</td>
<td align="left">B_ENTRB_CLO</td>
<td align="right">5</td>
<td align="right">1.0%</td>
<td align="right">439</td>
<td align="right">87.8%</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="left">B_ENTRC</td>
<td align="right">4</td>
<td align="right">0.8%</td>
<td align="right">443</td>
<td align="right">88.6%</td>
</tr>
</tbody>
</table>
<p>(omitted 46 entries, n = 112 [22.4%])</p>
<p>(omitted 29 entries, n = 57 [11.4%])</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"></a>
<a class="sourceLine" id="cb5-2" data-line-number="2"><span class="co"># our transformed antibiotic columns</span></a>
<a class="sourceLine" id="cb5-3" data-line-number="3"><span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span></a>
@ -331,9 +331,9 @@ Species: 51</p>
<p><strong>Frequency table of <code>AMC_ND2</code> from a <code>data.frame</code> (500 x 54)</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: 500 (of which NA: 41 = 8.20%)<br>
Length: 500 (of which NA: 19 = 3.80%)<br>
Unique: 3</p>
<p>%IR: 28.98% (ratio S : IR = 1.0 : 0.4)</p>
<p>%IR: 25.99% (ratio S : IR = 1.0 : 0.4)</p>
<table class="table">
<thead><tr class="header">
<th align="left"></th>
@ -347,25 +347,25 @@ Unique: 3</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">S</td>
<td align="right">326</td>
<td align="right">71.0%</td>
<td align="right">326</td>
<td align="right">71.0%</td>
<td align="right">356</td>
<td align="right">74.0%</td>
<td align="right">356</td>
<td align="right">74.0%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">R</td>
<td align="right">111</td>
<td align="right">24.2%</td>
<td align="right">437</td>
<td align="right">95.2%</td>
<td align="right">103</td>
<td align="right">21.4%</td>
<td align="right">459</td>
<td align="right">95.4%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">I</td>
<td align="right">22</td>
<td align="right">4.8%</td>
<td align="right">459</td>
<td align="right">4.6%</td>
<td align="right">481</td>
<td align="right">100.0%</td>
</tr>
</tbody>