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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="Latest development version">0.7.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9012</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">01 July 2019</h4>
<h4 class="date">10 July 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="Latest development version">0.7.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9012</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">01 July 2019</h4>
<h4 class="date">10 July 2019</h4>
<div class="hidden name"><code>MDR.Rmd</code></div>
@ -208,57 +208,57 @@
<li>“WIP-Richtlijn Bijzonder Resistente Micro-organismen (BRMO)”, by RIVM (Rijksinstituut voor de Volksgezondheid, the Netherlands National Institute for Public Health and the Environment)</li>
</ul>
<p>As an example, I will make a data set to determine multi-drug resistant TB:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="co"># a helper function to get a random vector with values S, I and R</span></a>
<a class="sourceLine" id="cb1-2" title="2"><span class="co"># with the probabilities 50%-10%-40%</span></a>
<a class="sourceLine" id="cb1-3" title="3">sample_rsi &lt;-<span class="st"> </span><span class="cf">function</span>() {</a>
<a class="sourceLine" id="cb1-4" title="4"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/sample">sample</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>),</a>
<a class="sourceLine" id="cb1-5" title="5"> <span class="dt">size =</span> <span class="dv">5000</span>,</a>
<a class="sourceLine" id="cb1-6" title="6"> <span class="dt">prob =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.1</span>, <span class="fl">0.4</span>),</a>
<a class="sourceLine" id="cb1-7" title="7"> <span class="dt">replace =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb1-8" title="8">}</a>
<a class="sourceLine" id="cb1-9" title="9"></a>
<a class="sourceLine" id="cb1-10" title="10">my_TB_data &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(<span class="dt">rifampicin =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-11" title="11"> <span class="dt">isoniazid =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-12" title="12"> <span class="dt">gatifloxacin =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-13" title="13"> <span class="dt">ethambutol =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-14" title="14"> <span class="dt">pyrazinamide =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-15" title="15"> <span class="dt">moxifloxacin =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-16" title="16"> <span class="dt">kanamycin =</span> <span class="kw">sample_rsi</span>())</a></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"><span class="co"># a helper function to get a random vector with values S, I and R</span></a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="co"># with the probabilities 50%-10%-40%</span></a>
<a class="sourceLine" id="cb1-3" data-line-number="3">sample_rsi &lt;-<span class="st"> </span><span class="cf">function</span>() {</a>
<a class="sourceLine" id="cb1-4" data-line-number="4"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/sample">sample</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>),</a>
<a class="sourceLine" id="cb1-5" data-line-number="5"> <span class="dt">size =</span> <span class="dv">5000</span>,</a>
<a class="sourceLine" id="cb1-6" data-line-number="6"> <span class="dt">prob =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.1</span>, <span class="fl">0.4</span>),</a>
<a class="sourceLine" id="cb1-7" data-line-number="7"> <span class="dt">replace =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb1-8" data-line-number="8">}</a>
<a class="sourceLine" id="cb1-9" data-line-number="9"></a>
<a class="sourceLine" id="cb1-10" data-line-number="10">my_TB_data &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(<span class="dt">rifampicin =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-11" data-line-number="11"> <span class="dt">isoniazid =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-12" data-line-number="12"> <span class="dt">gatifloxacin =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-13" data-line-number="13"> <span class="dt">ethambutol =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-14" data-line-number="14"> <span class="dt">pyrazinamide =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-15" data-line-number="15"> <span class="dt">moxifloxacin =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-16" data-line-number="16"> <span class="dt">kanamycin =</span> <span class="kw">sample_rsi</span>())</a></code></pre></div>
<p>Because all column names are automatically verified for valid drug names or codes, this would have worked exactly the same:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1">my_TB_data &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(<span class="dt">RIF =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb2-2" title="2"> <span class="dt">INH =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb2-3" title="3"> <span class="dt">GAT =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb2-4" title="4"> <span class="dt">ETH =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb2-5" title="5"> <span class="dt">PZA =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb2-6" title="6"> <span class="dt">MFX =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb2-7" title="7"> <span class="dt">KAN =</span> <span class="kw">sample_rsi</span>())</a></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_TB_data &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(<span class="dt">RIF =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb2-2" data-line-number="2"> <span class="dt">INH =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb2-3" data-line-number="3"> <span class="dt">GAT =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb2-4" data-line-number="4"> <span class="dt">ETH =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb2-5" data-line-number="5"> <span class="dt">PZA =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb2-6" data-line-number="6"> <span class="dt">MFX =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb2-7" data-line-number="7"> <span class="dt">KAN =</span> <span class="kw">sample_rsi</span>())</a></code></pre></div>
<p>The data set looks like this now:</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/utils/topics/head">head</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb3-2" title="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># 1 R R S S R I</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># 2 R R S R S R</span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="co"># 3 R S S R R R</span></a>
<a class="sourceLine" id="cb3-6" title="6"><span class="co"># 4 R R S S S I</span></a>
<a class="sourceLine" id="cb3-7" title="7"><span class="co"># 5 R R S S R I</span></a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># 6 R S R R S S</span></a>
<a class="sourceLine" id="cb3-9" title="9"><span class="co"># kanamycin</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co"># 1 S</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># 2 S</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># 3 S</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># 4 R</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># 5 R</span></a>
<a class="sourceLine" id="cb3-15" title="15"><span class="co"># 6 S</span></a></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/utils/topics/head">head</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co"># 1 R S S R S R</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># 2 R S R S S S</span></a>
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co"># 3 R R R R S R</span></a>
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co"># 4 S S R S R S</span></a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co"># 5 R R S I S S</span></a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># 6 S S R R R S</span></a>
<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co"># kanamycin</span></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># 1 S</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># 2 S</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># 3 S</span></a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># 4 R</span></a>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># 5 R</span></a>
<a class="sourceLine" id="cb3-15" data-line-number="15"><span class="co"># 6 S</span></a></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">my_TB_data<span class="op">$</span>mdr &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mdro.html">mdr_tb</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb4-2" title="2"><span class="co"># </span><span class="al">NOTE</span><span class="co">: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span></a>
<a class="sourceLine" id="cb4-3" title="3"><span class="co"># Determining multidrug-resistant organisms (MDRO), according to:</span></a>
<a class="sourceLine" id="cb4-4" title="4"><span class="co"># Guideline: Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis</span></a>
<a class="sourceLine" id="cb4-5" title="5"><span class="co"># Version: WHO/HTM/TB/2014.11</span></a>
<a class="sourceLine" id="cb4-6" title="6"><span class="co"># Author: WHO (World Health Organization)</span></a>
<a class="sourceLine" id="cb4-7" title="7"><span class="co"># Source: https://www.who.int/tb/publications/pmdt_companionhandbook/en/</span></a>
<a class="sourceLine" id="cb4-8" title="8"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Reliability might be improved if these antimicrobial results would be available too: CAP (capreomycin), RIB (rifabutin), RFP (rifapentine)</span></a></code></pre></div>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">my_TB_data<span class="op">$</span>mdr &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mdro.html">mdr_tb</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="co"># </span><span class="al">NOTE</span><span class="co">: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span></a>
<a class="sourceLine" id="cb4-3" data-line-number="3"><span class="co"># Determining multidrug-resistant organisms (MDRO), according to:</span></a>
<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="co"># Guideline: Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis</span></a>
<a class="sourceLine" id="cb4-5" data-line-number="5"><span class="co"># Version: WHO/HTM/TB/2014.11</span></a>
<a class="sourceLine" id="cb4-6" data-line-number="6"><span class="co"># Author: WHO (World Health Organization)</span></a>
<a class="sourceLine" id="cb4-7" data-line-number="7"><span class="co"># Source: https://www.who.int/tb/publications/pmdt_companionhandbook/en/</span></a>
<a class="sourceLine" id="cb4-8" data-line-number="8"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Reliability might be improved if these antimicrobial results would be available too: CAP (capreomycin), RIB (rifabutin), RFP (rifapentine)</span></a></code></pre></div>
<p>And review the result with a frequency table:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_TB_data<span class="op">$</span>mdr)</a></code></pre></div>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_TB_data<span class="op">$</span>mdr)</a></code></pre></div>
<p><strong>Frequency table of <code>mdr</code> from <code>my_TB_data</code> (5,000 x 8)</strong></p>
<p>Class: factor &gt; ordered (numeric)<br>
Length: 5,000 (of which NA: 0 = 0.00%)<br>
@ -277,40 +277,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistance</td>
<td align="right">3,222</td>
<td align="right">64.4%</td>
<td align="right">3,222</td>
<td align="right">64.4%</td>
<td align="right">3,273</td>
<td align="right">65.5%</td>
<td align="right">3,273</td>
<td align="right">65.5%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">659</td>
<td align="right">13.2%</td>
<td align="right">3,881</td>
<td align="right">77.6%</td>
<td align="right">687</td>
<td align="right">13.7%</td>
<td align="right">3,960</td>
<td align="right">79.2%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multidrug resistance</td>
<td align="right">589</td>
<td align="right">11.8%</td>
<td align="right">4,470</td>
<td align="right">89.4%</td>
<td align="right">569</td>
<td align="right">11.4%</td>
<td align="right">4,529</td>
<td align="right">90.6%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistance</td>
<td align="right">313</td>
<td align="right">6.3%</td>
<td align="right">4,783</td>
<td align="right">95.7%</td>
<td align="right">277</td>
<td align="right">5.5%</td>
<td align="right">4,806</td>
<td align="right">96.1%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensive drug resistance</td>
<td align="right">217</td>
<td align="right">4.3%</td>
<td align="right">194</td>
<td align="right">3.9%</td>
<td align="right">5,000</td>
<td align="right">100.0%</td>
</tr>

204
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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="Latest development version">0.7.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9012</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">01 July 2019</h4>
<h4 class="date">10 July 2019</h4>
<div class="hidden name"><code>SPSS.Rmd</code></div>
@ -242,39 +242,39 @@
</ul>
<p>If you sometimes write syntaxes in SPSS to run a complete analysis or to ‘automate’ some of your work, you should perhaps do this in R. You will notice that writing syntaxes in R is a lot more nifty and clever than in SPSS. Still, as working with any statistical package, you will have to have knowledge about what you are doing (statistically) and what you are willing to accomplish.</p>
<p>To demonstrate the first point:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="co"># not all values are valid MIC values:</span></a>
<a class="sourceLine" id="cb1-2" title="2"><span class="kw"><a href="../reference/as.mic.html">as.mic</a></span>(<span class="fl">0.125</span>)</a>
<a class="sourceLine" id="cb1-3" title="3"><span class="co"># Class 'mic'</span></a>
<a class="sourceLine" id="cb1-4" title="4"><span class="co"># [1] 0.125</span></a>
<a class="sourceLine" id="cb1-5" title="5"><span class="kw"><a href="../reference/as.mic.html">as.mic</a></span>(<span class="st">"testvalue"</span>)</a>
<a class="sourceLine" id="cb1-6" title="6"><span class="co"># Class 'mic'</span></a>
<a class="sourceLine" id="cb1-7" title="7"><span class="co"># [1] &lt;NA&gt;</span></a>
<a class="sourceLine" id="cb1-8" title="8"></a>
<a class="sourceLine" id="cb1-9" title="9"><span class="co"># the Gram stain is avaiable for all bacteria:</span></a>
<a class="sourceLine" id="cb1-10" title="10"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a>
<a class="sourceLine" id="cb1-11" title="11"><span class="co"># [1] "Gram-negative"</span></a>
<a class="sourceLine" id="cb1-12" title="12"></a>
<a class="sourceLine" id="cb1-13" title="13"><span class="co"># Klebsiella is intrinsic resistant to amoxicllin, according to EUCAST:</span></a>
<a class="sourceLine" id="cb1-14" title="14">klebsiella_test &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(<span class="dt">mo =</span> <span class="st">"klebsiella"</span>, </a>
<a class="sourceLine" id="cb1-15" title="15"> <span class="dt">amox =</span> <span class="st">"S"</span>,</a>
<a class="sourceLine" id="cb1-16" title="16"> <span class="dt">stringsAsFactors =</span> <span class="ot">FALSE</span>)</a>
<a class="sourceLine" id="cb1-17" title="17">klebsiella_test</a>
<a class="sourceLine" id="cb1-18" title="18"><span class="co"># mo amox</span></a>
<a class="sourceLine" id="cb1-19" title="19"><span class="co"># 1 klebsiella S</span></a>
<a class="sourceLine" id="cb1-20" title="20"><span class="kw"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(klebsiella_test, <span class="dt">info =</span> <span class="ot">FALSE</span>)</a>
<a class="sourceLine" id="cb1-21" title="21"><span class="co"># mo amox</span></a>
<a class="sourceLine" id="cb1-22" title="22"><span class="co"># 1 klebsiella R</span></a>
<a class="sourceLine" id="cb1-23" title="23"></a>
<a class="sourceLine" id="cb1-24" title="24"><span class="co"># hundreds of trade names can be translated to a name, trade name or an ATC code:</span></a>
<a class="sourceLine" id="cb1-25" title="25"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="st">"floxapen"</span>)</a>
<a class="sourceLine" id="cb1-26" title="26"><span class="co"># [1] "Flucloxacillin"</span></a>
<a class="sourceLine" id="cb1-27" title="27"><span class="kw"><a href="../reference/ab_property.html">ab_tradenames</a></span>(<span class="st">"floxapen"</span>)</a>
<a class="sourceLine" id="cb1-28" title="28"><span class="co"># [1] "Floxacillin" "FLOXACILLIN" "Floxapen" </span></a>
<a class="sourceLine" id="cb1-29" title="29"><span class="co"># [4] "Floxapen sodium salt" "Fluclox" "Flucloxacilina" </span></a>
<a class="sourceLine" id="cb1-30" title="30"><span class="co"># [7] "Flucloxacillin" "Flucloxacilline" "Flucloxacillinum" </span></a>
<a class="sourceLine" id="cb1-31" title="31"><span class="co"># [10] "Fluorochloroxacillin"</span></a>
<a class="sourceLine" id="cb1-32" title="32"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="st">"floxapen"</span>)</a>
<a class="sourceLine" id="cb1-33" title="33"><span class="co"># [1] "J01CF05"</span></a></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"><span class="co"># not all values are valid MIC values:</span></a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="kw"><a href="../reference/as.mic.html">as.mic</a></span>(<span class="fl">0.125</span>)</a>
<a class="sourceLine" id="cb1-3" data-line-number="3"><span class="co"># Class 'mic'</span></a>
<a class="sourceLine" id="cb1-4" data-line-number="4"><span class="co"># [1] 0.125</span></a>
<a class="sourceLine" id="cb1-5" data-line-number="5"><span class="kw"><a href="../reference/as.mic.html">as.mic</a></span>(<span class="st">"testvalue"</span>)</a>
<a class="sourceLine" id="cb1-6" data-line-number="6"><span class="co"># Class 'mic'</span></a>
<a class="sourceLine" id="cb1-7" data-line-number="7"><span class="co"># [1] &lt;NA&gt;</span></a>
<a class="sourceLine" id="cb1-8" data-line-number="8"></a>
<a class="sourceLine" id="cb1-9" data-line-number="9"><span class="co"># the Gram stain is avaiable for all bacteria:</span></a>
<a class="sourceLine" id="cb1-10" data-line-number="10"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a>
<a class="sourceLine" id="cb1-11" data-line-number="11"><span class="co"># [1] "Gram-negative"</span></a>
<a class="sourceLine" id="cb1-12" data-line-number="12"></a>
<a class="sourceLine" id="cb1-13" data-line-number="13"><span class="co"># Klebsiella is intrinsic resistant to amoxicllin, according to EUCAST:</span></a>
<a class="sourceLine" id="cb1-14" data-line-number="14">klebsiella_test &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(<span class="dt">mo =</span> <span class="st">"klebsiella"</span>, </a>
<a class="sourceLine" id="cb1-15" data-line-number="15"> <span class="dt">amox =</span> <span class="st">"S"</span>,</a>
<a class="sourceLine" id="cb1-16" data-line-number="16"> <span class="dt">stringsAsFactors =</span> <span class="ot">FALSE</span>)</a>
<a class="sourceLine" id="cb1-17" data-line-number="17">klebsiella_test</a>
<a class="sourceLine" id="cb1-18" data-line-number="18"><span class="co"># mo amox</span></a>
<a class="sourceLine" id="cb1-19" data-line-number="19"><span class="co"># 1 klebsiella S</span></a>
<a class="sourceLine" id="cb1-20" data-line-number="20"><span class="kw"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(klebsiella_test, <span class="dt">info =</span> <span class="ot">FALSE</span>)</a>
<a class="sourceLine" id="cb1-21" data-line-number="21"><span class="co"># mo amox</span></a>
<a class="sourceLine" id="cb1-22" data-line-number="22"><span class="co"># 1 klebsiella R</span></a>
<a class="sourceLine" id="cb1-23" data-line-number="23"></a>
<a class="sourceLine" id="cb1-24" data-line-number="24"><span class="co"># hundreds of trade names can be translated to a name, trade name or an ATC code:</span></a>
<a class="sourceLine" id="cb1-25" data-line-number="25"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="st">"floxapen"</span>)</a>
<a class="sourceLine" id="cb1-26" data-line-number="26"><span class="co"># [1] "Flucloxacillin"</span></a>
<a class="sourceLine" id="cb1-27" data-line-number="27"><span class="kw"><a href="../reference/ab_property.html">ab_tradenames</a></span>(<span class="st">"floxapen"</span>)</a>
<a class="sourceLine" id="cb1-28" data-line-number="28"><span class="co"># [1] "Floxacillin" "FLOXACILLIN" "Floxapen" </span></a>
<a class="sourceLine" id="cb1-29" data-line-number="29"><span class="co"># [4] "Floxapen sodium salt" "Fluclox" "Flucloxacilina" </span></a>
<a class="sourceLine" id="cb1-30" data-line-number="30"><span class="co"># [7] "Flucloxacillin" "Flucloxacilline" "Flucloxacillinum" </span></a>
<a class="sourceLine" id="cb1-31" data-line-number="31"><span class="co"># [10] "Fluorochloroxacillin"</span></a>
<a class="sourceLine" id="cb1-32" data-line-number="32"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="st">"floxapen"</span>)</a>
<a class="sourceLine" id="cb1-33" data-line-number="33"><span class="co"># [1] "J01CF05"</span></a></code></pre></div>
</div>
<div id="import-data-from-spsssasstata" class="section level2">
<h2 class="hasAnchor">
@ -290,97 +290,97 @@
<p><img src="https://gitlab.com/msberends/AMR/raw/master/docs/import2.png"></p>
<p>If you want named variables to be imported as factors so it resembles SPSS more, use <code><a href="https://haven.tidyverse.org/reference/as_factor.html">as_factor()</a></code>.</p>
<p>The difference is this:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1">SPSS_data</a>
<a class="sourceLine" id="cb2-2" title="2"><span class="co"># # A tibble: 4,203 x 4</span></a>
<a class="sourceLine" id="cb2-3" title="3"><span class="co"># v001 sex status statusage</span></a>
<a class="sourceLine" id="cb2-4" title="4"><span class="co"># &lt;dbl&gt; &lt;dbl+lbl&gt; &lt;dbl+lbl&gt; &lt;dbl&gt;</span></a>
<a class="sourceLine" id="cb2-5" title="5"><span class="co"># 1 10002 1 1 76.6</span></a>
<a class="sourceLine" id="cb2-6" title="6"><span class="co"># 2 10004 0 1 59.1</span></a>
<a class="sourceLine" id="cb2-7" title="7"><span class="co"># 3 10005 1 1 54.5</span></a>
<a class="sourceLine" id="cb2-8" title="8"><span class="co"># 4 10006 1 1 54.1</span></a>
<a class="sourceLine" id="cb2-9" title="9"><span class="co"># 5 10007 1 1 57.7</span></a>
<a class="sourceLine" id="cb2-10" title="10"><span class="co"># 6 10008 1 1 62.8</span></a>
<a class="sourceLine" id="cb2-11" title="11"><span class="co"># 7 10010 0 1 63.7</span></a>
<a class="sourceLine" id="cb2-12" title="12"><span class="co"># 8 10011 1 1 73.1</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co"># 9 10017 1 1 56.7</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co"># 10 10018 0 1 66.6</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co"># # … with 4,193 more rows</span></a>
<a class="sourceLine" id="cb2-16" title="16"></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="kw">as_factor</span>(SPSS_data)</a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co"># # A tibble: 4,203 x 4</span></a>
<a class="sourceLine" id="cb2-19" title="19"><span class="co"># v001 sex status statusage</span></a>
<a class="sourceLine" id="cb2-20" title="20"><span class="co"># &lt;dbl&gt; &lt;fct&gt; &lt;fct&gt; &lt;dbl&gt;</span></a>
<a class="sourceLine" id="cb2-21" title="21"><span class="co"># 1 10002 Male alive 76.6</span></a>
<a class="sourceLine" id="cb2-22" title="22"><span class="co"># 2 10004 Female alive 59.1</span></a>
<a class="sourceLine" id="cb2-23" title="23"><span class="co"># 3 10005 Male alive 54.5</span></a>
<a class="sourceLine" id="cb2-24" title="24"><span class="co"># 4 10006 Male alive 54.1</span></a>
<a class="sourceLine" id="cb2-25" title="25"><span class="co"># 5 10007 Male alive 57.7</span></a>
<a class="sourceLine" id="cb2-26" title="26"><span class="co"># 6 10008 Male alive 62.8</span></a>
<a class="sourceLine" id="cb2-27" title="27"><span class="co"># 7 10010 Female alive 63.7</span></a>
<a class="sourceLine" id="cb2-28" title="28"><span class="co"># 8 10011 Male alive 73.1</span></a>
<a class="sourceLine" id="cb2-29" title="29"><span class="co"># 9 10017 Male alive 56.7</span></a>
<a class="sourceLine" id="cb2-30" title="30"><span class="co"># 10 10018 Female alive 66.6</span></a>
<a class="sourceLine" id="cb2-31" title="31"><span class="co"># # … with 4,193 more rows</span></a></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">SPSS_data</a>
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="co"># # A tibble: 4,203 x 4</span></a>
<a class="sourceLine" id="cb2-3" data-line-number="3"><span class="co"># v001 sex status statusage</span></a>
<a class="sourceLine" id="cb2-4" data-line-number="4"><span class="co"># &lt;dbl&gt; &lt;dbl+lbl&gt; &lt;dbl+lbl&gt; &lt;dbl&gt;</span></a>
<a class="sourceLine" id="cb2-5" data-line-number="5"><span class="co"># 1 10002 1 1 76.6</span></a>
<a class="sourceLine" id="cb2-6" data-line-number="6"><span class="co"># 2 10004 0 1 59.1</span></a>
<a class="sourceLine" id="cb2-7" data-line-number="7"><span class="co"># 3 10005 1 1 54.5</span></a>
<a class="sourceLine" id="cb2-8" data-line-number="8"><span class="co"># 4 10006 1 1 54.1</span></a>
<a class="sourceLine" id="cb2-9" data-line-number="9"><span class="co"># 5 10007 1 1 57.7</span></a>
<a class="sourceLine" id="cb2-10" data-line-number="10"><span class="co"># 6 10008 1 1 62.8</span></a>
<a class="sourceLine" id="cb2-11" data-line-number="11"><span class="co"># 7 10010 0 1 63.7</span></a>
<a class="sourceLine" id="cb2-12" data-line-number="12"><span class="co"># 8 10011 1 1 73.1</span></a>
<a class="sourceLine" id="cb2-13" data-line-number="13"><span class="co"># 9 10017 1 1 56.7</span></a>
<a class="sourceLine" id="cb2-14" data-line-number="14"><span class="co"># 10 10018 0 1 66.6</span></a>
<a class="sourceLine" id="cb2-15" data-line-number="15"><span class="co"># # … with 4,193 more rows</span></a>
<a class="sourceLine" id="cb2-16" data-line-number="16"></a>
<a class="sourceLine" id="cb2-17" data-line-number="17"><span class="kw">as_factor</span>(SPSS_data)</a>
<a class="sourceLine" id="cb2-18" data-line-number="18"><span class="co"># # A tibble: 4,203 x 4</span></a>
<a class="sourceLine" id="cb2-19" data-line-number="19"><span class="co"># v001 sex status statusage</span></a>
<a class="sourceLine" id="cb2-20" data-line-number="20"><span class="co"># &lt;dbl&gt; &lt;fct&gt; &lt;fct&gt; &lt;dbl&gt;</span></a>
<a class="sourceLine" id="cb2-21" data-line-number="21"><span class="co"># 1 10002 Male alive 76.6</span></a>
<a class="sourceLine" id="cb2-22" data-line-number="22"><span class="co"># 2 10004 Female alive 59.1</span></a>
<a class="sourceLine" id="cb2-23" data-line-number="23"><span class="co"># 3 10005 Male alive 54.5</span></a>
<a class="sourceLine" id="cb2-24" data-line-number="24"><span class="co"># 4 10006 Male alive 54.1</span></a>
<a class="sourceLine" id="cb2-25" data-line-number="25"><span class="co"># 5 10007 Male alive 57.7</span></a>
<a class="sourceLine" id="cb2-26" data-line-number="26"><span class="co"># 6 10008 Male alive 62.8</span></a>
<a class="sourceLine" id="cb2-27" data-line-number="27"><span class="co"># 7 10010 Female alive 63.7</span></a>
<a class="sourceLine" id="cb2-28" data-line-number="28"><span class="co"># 8 10011 Male alive 73.1</span></a>
<a class="sourceLine" id="cb2-29" data-line-number="29"><span class="co"># 9 10017 Male alive 56.7</span></a>
<a class="sourceLine" id="cb2-30" data-line-number="30"><span class="co"># 10 10018 Female alive 66.6</span></a>
<a class="sourceLine" id="cb2-31" data-line-number="31"><span class="co"># # … with 4,193 more rows</span></a></code></pre></div>
</div>
<div id="base-r" class="section level3">
<h3 class="hasAnchor">
<a href="#base-r" class="anchor"></a>Base R</h3>
<p>To import data from SPSS, SAS or Stata, you can use the <a href="https://haven.tidyverse.org/">great <code>haven</code> package</a> yourself:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="co"># download and install the latest version:</span></a>
<a class="sourceLine" id="cb3-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"haven"</span>)</a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># load the package you just installed:</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(haven) </a></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="co"># download and install the latest version:</span></a>
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"haven"</span>)</a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co"># load the package you just installed:</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(haven) </a></code></pre></div>
<p>You can now import files as follows:</p>
<div id="spss" class="section level4">
<h4 class="hasAnchor">
<a href="#spss" class="anchor"></a>SPSS</h4>
<p>To read files from SPSS into R:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="co"># read any SPSS file based on file extension (best way):</span></a>
<a class="sourceLine" id="cb4-2" title="2"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_spss</a></span>(<span class="dt">file =</span> <span class="st">"path/to/file"</span>)</a>
<a class="sourceLine" id="cb4-3" title="3"></a>
<a class="sourceLine" id="cb4-4" title="4"><span class="co"># read .sav or .zsav file:</span></a>
<a class="sourceLine" id="cb4-5" title="5"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_sav</a></span>(<span class="dt">file =</span> <span class="st">"path/to/file"</span>)</a>
<a class="sourceLine" id="cb4-6" title="6"></a>
<a class="sourceLine" id="cb4-7" title="7"><span class="co"># read .por file:</span></a>
<a class="sourceLine" id="cb4-8" title="8"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_por</a></span>(<span class="dt">file =</span> <span class="st">"path/to/file"</span>)</a></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="co"># read any SPSS file based on file extension (best way):</span></a>
<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_spss</a></span>(<span class="dt">file =</span> <span class="st">"path/to/file"</span>)</a>
<a class="sourceLine" id="cb4-3" data-line-number="3"></a>
<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="co"># read .sav or .zsav file:</span></a>
<a class="sourceLine" id="cb4-5" data-line-number="5"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_sav</a></span>(<span class="dt">file =</span> <span class="st">"path/to/file"</span>)</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"># read .por file:</span></a>
<a class="sourceLine" id="cb4-8" data-line-number="8"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_por</a></span>(<span class="dt">file =</span> <span class="st">"path/to/file"</span>)</a></code></pre></div>
<p>Do not forget about <code><a href="https://haven.tidyverse.org/reference/as_factor.html">as_factor()</a></code>, as mentioned above.</p>
<p>To export your R objects to the SPSS file format:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="co"># save as .sav file:</span></a>
<a class="sourceLine" id="cb5-2" title="2"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span>(<span class="dt">data =</span> yourdata, <span class="dt">path =</span> <span class="st">"path/to/file"</span>)</a>
<a class="sourceLine" id="cb5-3" title="3"></a>
<a class="sourceLine" id="cb5-4" title="4"><span class="co"># save as compressed .zsav file:</span></a>
<a class="sourceLine" id="cb5-5" title="5"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span>(<span class="dt">data =</span> yourdata, <span class="dt">path =</span> <span class="st">"path/to/file"</span>, <span class="dt">compress =</span> <span class="ot">TRUE</span>)</a></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"><span class="co"># save as .sav file:</span></a>
<a class="sourceLine" id="cb5-2" data-line-number="2"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span>(<span class="dt">data =</span> yourdata, <span class="dt">path =</span> <span class="st">"path/to/file"</span>)</a>
<a class="sourceLine" id="cb5-3" data-line-number="3"></a>
<a class="sourceLine" id="cb5-4" data-line-number="4"><span class="co"># save as compressed .zsav file:</span></a>
<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span>(<span class="dt">data =</span> yourdata, <span class="dt">path =</span> <span class="st">"path/to/file"</span>, <span class="dt">compress =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
</div>
<div id="sas" class="section level4">
<h4 class="hasAnchor">
<a href="#sas" class="anchor"></a>SAS</h4>
<p>To read files from SAS into R:</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1"><span class="co"># read .sas7bdat + .sas7bcat files:</span></a>
<a class="sourceLine" id="cb6-2" title="2"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_sas.html">read_sas</a></span>(<span class="dt">data_file =</span> <span class="st">"path/to/file"</span>, <span class="dt">catalog_file =</span> <span class="ot">NULL</span>)</a>
<a class="sourceLine" id="cb6-3" title="3"></a>
<a class="sourceLine" id="cb6-4" title="4"><span class="co"># read SAS transport files (version 5 and version 8):</span></a>
<a class="sourceLine" id="cb6-5" title="5"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_xpt.html">read_xpt</a></span>(<span class="dt">file =</span> <span class="st">"path/to/file"</span>)</a></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"># read .sas7bdat + .sas7bcat files:</span></a>
<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_sas.html">read_sas</a></span>(<span class="dt">data_file =</span> <span class="st">"path/to/file"</span>, <span class="dt">catalog_file =</span> <span class="ot">NULL</span>)</a>
<a class="sourceLine" id="cb6-3" data-line-number="3"></a>
<a class="sourceLine" id="cb6-4" data-line-number="4"><span class="co"># read SAS transport files (version 5 and version 8):</span></a>
<a class="sourceLine" id="cb6-5" data-line-number="5"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_xpt.html">read_xpt</a></span>(<span class="dt">file =</span> <span class="st">"path/to/file"</span>)</a></code></pre></div>
<p>To export your R objects to the SAS file format:</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1"><span class="co"># save as regular SAS file:</span></a>
<a class="sourceLine" id="cb7-2" title="2"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_sas.html">write_sas</a></span>(<span class="dt">data =</span> yourdata, <span class="dt">path =</span> <span class="st">"path/to/file"</span>)</a>
<a class="sourceLine" id="cb7-3" title="3"></a>
<a class="sourceLine" id="cb7-4" title="4"><span class="co"># the SAS transport format is an open format </span></a>
<a class="sourceLine" id="cb7-5" title="5"><span class="co"># (required for submission of the data to the FDA)</span></a>
<a class="sourceLine" id="cb7-6" title="6"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_xpt.html">write_xpt</a></span>(<span class="dt">data =</span> yourdata, <span class="dt">path =</span> <span class="st">"path/to/file"</span>, <span class="dt">version =</span> <span class="dv">8</span>)</a></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"><span class="co"># save as regular SAS file:</span></a>
<a class="sourceLine" id="cb7-2" data-line-number="2"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_sas.html">write_sas</a></span>(<span class="dt">data =</span> yourdata, <span class="dt">path =</span> <span class="st">"path/to/file"</span>)</a>
<a class="sourceLine" id="cb7-3" data-line-number="3"></a>
<a class="sourceLine" id="cb7-4" data-line-number="4"><span class="co"># the SAS transport format is an open format </span></a>
<a class="sourceLine" id="cb7-5" data-line-number="5"><span class="co"># (required for submission of the data to the FDA)</span></a>
<a class="sourceLine" id="cb7-6" data-line-number="6"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_xpt.html">write_xpt</a></span>(<span class="dt">data =</span> yourdata, <span class="dt">path =</span> <span class="st">"path/to/file"</span>, <span class="dt">version =</span> <span class="dv">8</span>)</a></code></pre></div>
</div>
<div id="stata" class="section level4">
<h4 class="hasAnchor">
<a href="#stata" class="anchor"></a>Stata</h4>
<p>To read files from Stata into R:</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1"><span class="co"># read .dta file:</span></a>
<a class="sourceLine" id="cb8-2" title="2"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_stata</a></span>(<span class="dt">file =</span> <span class="st">"/path/to/file"</span>)</a>
<a class="sourceLine" id="cb8-3" title="3"></a>
<a class="sourceLine" id="cb8-4" title="4"><span class="co"># works exactly the same:</span></a>
<a class="sourceLine" id="cb8-5" title="5"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_dta</a></span>(<span class="dt">file =</span> <span class="st">"/path/to/file"</span>)</a></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"><span class="co"># read .dta file:</span></a>
<a class="sourceLine" id="cb8-2" data-line-number="2"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_stata</a></span>(<span class="dt">file =</span> <span class="st">"/path/to/file"</span>)</a>
<a class="sourceLine" id="cb8-3" data-line-number="3"></a>
<a class="sourceLine" id="cb8-4" data-line-number="4"><span class="co"># works exactly the same:</span></a>
<a class="sourceLine" id="cb8-5" data-line-number="5"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_dta</a></span>(<span class="dt">file =</span> <span class="st">"/path/to/file"</span>)</a></code></pre></div>
<p>To export your R objects to the Stata file format:</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="co"># save as .dta file, Stata version 14:</span></a>
<a class="sourceLine" id="cb9-2" title="2"><span class="co"># (supports Stata v8 until v15 at the time of writing)</span></a>
<a class="sourceLine" id="cb9-3" title="3"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_dta.html">write_dta</a></span>(<span class="dt">data =</span> yourdata, <span class="dt">path =</span> <span class="st">"/path/to/file"</span>, <span class="dt">version =</span> <span class="dv">14</span>)</a></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"><span class="co"># save as .dta file, Stata version 14:</span></a>
<a class="sourceLine" id="cb9-2" data-line-number="2"><span class="co"># (supports Stata v8 until v15 at the time of writing)</span></a>
<a class="sourceLine" id="cb9-3" data-line-number="3"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_dta.html">write_dta</a></span>(<span class="dt">data =</span> yourdata, <span class="dt">path =</span> <span class="st">"/path/to/file"</span>, <span class="dt">version =</span> <span class="dv">14</span>)</a></code></pre></div>
</div>
</div>
</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="Latest development version">0.7.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9012</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to work with WHONET data</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">01 July 2019</h4>
<h4 class="date">10 July 2019</h4>
<div class="hidden name"><code>WHONET.Rmd</code></div>
@ -206,31 +206,31 @@
<a href="#import-of-data" class="anchor"></a>Import of data</h1>
<p>This tutorial assumes you already imported the WHONET data with e.g. the <a href="https://readxl.tidyverse.org/"><code>readxl</code> package</a>. In RStudio, this can be done using the menu button ‘Import Dataset’ in the tab ‘Environment’. Choose the option ‘From Excel’ and select your exported file. Make sure date fields are imported correctly.</p>
<p>An example syntax could look like this:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(readxl)</a>
<a class="sourceLine" id="cb1-2" title="2">data &lt;-<span class="st"> </span><span class="kw"><a href="https://readxl.tidyverse.org/reference/read_excel.html">read_excel</a></span>(<span class="dt">path =</span> <span class="st">"path/to/your/file.xlsx"</span>)</a></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"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(readxl)</a>
<a class="sourceLine" id="cb1-2" data-line-number="2">data &lt;-<span class="st"> </span><span class="kw"><a href="https://readxl.tidyverse.org/reference/read_excel.html">read_excel</a></span>(<span class="dt">path =</span> <span class="st">"path/to/your/file.xlsx"</span>)</a></code></pre></div>
<p>This package comes with an <a href="https://msberends.gitlab.io/AMR/reference/WHONET.html">example data set <code>WHONET</code></a>. We will use it for this analysis.</p>
</div>
<div id="preparation" class="section level1">
<h1 class="hasAnchor">
<a href="#preparation" class="anchor"></a>Preparation</h1>
<p>First, load the relevant packages if you did not yet did this. I use the tidyverse for all of my analyses. All of them. If you don’t know it yet, I suggest you read about it on their website: <a href="https://www.tidyverse.org/" class="uri">https://www.tidyverse.org/</a>.</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(dplyr) <span class="co"># part of tidyverse</span></a>
<a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(ggplot2) <span class="co"># part of tidyverse</span></a>
<a class="sourceLine" id="cb2-3" title="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(AMR) <span class="co"># this package</span></a></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"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(dplyr) <span class="co"># part of tidyverse</span></a>
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(ggplot2) <span class="co"># part of tidyverse</span></a>
<a class="sourceLine" id="cb2-3" data-line-number="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(AMR) <span class="co"># this package</span></a></code></pre></div>
<p>We will have to transform some variables to simplify and automate the analysis:</p>
<ul>
<li>Microorganisms should be transformed to our own microorganism IDs (called an <code>mo</code>) using <a href="https://msberends.gitlab.io/AMR/reference/ITIS.html">the ITIS reference data set</a>, which contains all ~20,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with <code><a href="../reference/as.mo.html">as.mo()</a></code>. This function also recognises almost all WHONET abbreviations of microorganisms.</li>
<li>Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values <code>"S"</code>, <code>"I"</code> or <code>"R"</code>. That is exactly where the <code><a href="../reference/as.rsi.html">as.rsi()</a></code> function is for.</li>
</ul>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="co"># transform variables</span></a>
<a class="sourceLine" id="cb3-2" title="2">data &lt;-<span class="st"> </span>WHONET <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="st"> </span><span class="co"># get microbial ID based on given organism</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">mo =</span> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(Organism)) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="st"> </span><span class="co"># transform everything from "AMP_ND10" to "CIP_EE" to the new `rsi` class</span></a>
<a class="sourceLine" id="cb3-6" title="6"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(AMP_ND10<span class="op">:</span>CIP_EE), as.rsi)</a></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="co"># transform variables</span></a>
<a class="sourceLine" id="cb3-2" data-line-number="2">data &lt;-<span class="st"> </span>WHONET <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="st"> </span><span class="co"># get microbial ID based on given organism</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">mo =</span> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(Organism)) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="st"> </span><span class="co"># transform everything from "AMP_ND10" to "CIP_EE" to the new `rsi` class</span></a>
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(AMP_ND10<span class="op">:</span>CIP_EE), as.rsi)</a></code></pre></div>
<p>No errors or warnings, so all values are transformed succesfully. Let’s check it though, with a couple of frequency tables:</p>
<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>
<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="co"># our newly created `mo` variable</span></a>
<a class="sourceLine" id="cb4-2" data-line-number="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 <code>data</code> (500 x 54)</strong></p>
<p>Class: mo (character)<br>
Length: 500 (of which NA: 0 = 0.00%)<br>
@ -331,10 +331,10 @@ Species: 38</p>
</tbody>
</table>
<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" title="1"></a>
<a class="sourceLine" id="cb5-2" title="2"><span class="co"># our transformed antibiotic columns</span></a>
<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>
<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>
<a class="sourceLine" id="cb5-4" data-line-number="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 <code>data</code> (500 x 54)</strong></p>
<p>Class: factor &gt; ordered &gt; rsi (numeric)<br>
Length: 500 (of which NA: 19 = 3.80%)<br>

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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="Latest development version">0.7.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9012</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">01 July 2019</h4>
<h4 class="date">10 July 2019</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -203,161 +203,161 @@
<p>One of the most important features of this package is the complete microbial taxonomic database, supplied by the <a href="http://catalogueoflife.org">Catalogue of Life</a>. We created a function <code><a href="../reference/as.mo.html">as.mo()</a></code> that transforms any user input value to a valid microbial ID by using intelligent rules combined with the taxonomic tree of Catalogue of Life.</p>
<p>Using the <code>microbenchmark</code> package, we can review the calculation performance of this function. Its function <code><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark()</a></code> runs different input expressions independently of each other and measures their time-to-result.</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(microbenchmark)</a>
<a class="sourceLine" id="cb1-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(AMR)</a></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"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(microbenchmark)</a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(AMR)</a></code></pre></div>
<p>In the next test, we try to ‘coerce’ different input values for <em>Staphylococcus aureus</em>. The actual result is the same every time: it returns its MO code <code>B_STPHY_AUR</code> (<em>B</em> stands for <em>Bacteria</em>, the taxonomic kingdom).</p>
<p>But the calculation time differs a lot:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1">S.aureus &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"sau"</span>),</a>
<a class="sourceLine" id="cb2-2" title="2"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"stau"</span>),</a>
<a class="sourceLine" id="cb2-3" title="3"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"staaur"</span>),</a>
<a class="sourceLine" id="cb2-4" title="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"STAAUR"</span>),</a>
<a class="sourceLine" id="cb2-5" title="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. aureus"</span>),</a>
<a class="sourceLine" id="cb2-6" title="6"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. aureus"</span>),</a>
<a class="sourceLine" id="cb2-7" title="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
<a class="sourceLine" id="cb2-8" title="8"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb2-9" title="9"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb2-10" title="10"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb2-11" title="11"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb2-12" title="12"><span class="co"># as.mo("sau") 18.0 18.0 22 18.0 18.0 61 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co"># as.mo("stau") 65.0 65.0 70 66.0 66.0 110 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co"># as.mo("staaur") 18.0 18.0 33 18.0 62.0 81 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co"># as.mo("STAAUR") 18.0 18.0 18 18.0 18.0 19 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co"># as.mo("S. aureus") 52.0 52.0 61 52.0 53.0 97 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co"># as.mo("S. aureus") 52.0 52.0 71 53.0 97.0 150 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co"># as.mo("Staphylococcus aureus") 8.1 8.1 14 8.1 8.2 63 10</span></a></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">S.aureus &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"sau"</span>),</a>
<a class="sourceLine" id="cb2-2" data-line-number="2"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"stau"</span>),</a>
<a class="sourceLine" id="cb2-3" data-line-number="3"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"staaur"</span>),</a>
<a class="sourceLine" id="cb2-4" data-line-number="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"STAAUR"</span>),</a>
<a class="sourceLine" id="cb2-5" data-line-number="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. aureus"</span>),</a>
<a class="sourceLine" id="cb2-6" data-line-number="6"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. aureus"</span>),</a>
<a class="sourceLine" id="cb2-7" data-line-number="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
<a class="sourceLine" id="cb2-8" data-line-number="8"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb2-9" data-line-number="9"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb2-10" data-line-number="10"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb2-11" data-line-number="11"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb2-12" data-line-number="12"><span class="co"># as.mo("sau") 8.5 8.7 12.0 8.9 9.4 26 10</span></a>
<a class="sourceLine" id="cb2-13" data-line-number="13"><span class="co"># as.mo("stau") 31.0 32.0 42.0 33.0 34.0 120 10</span></a>
<a class="sourceLine" id="cb2-14" data-line-number="14"><span class="co"># as.mo("staaur") 8.6 8.7 11.0 9.1 9.2 26 10</span></a>
<a class="sourceLine" id="cb2-15" data-line-number="15"><span class="co"># as.mo("STAAUR") 8.7 9.1 9.3 9.2 9.4 11 10</span></a>
<a class="sourceLine" id="cb2-16" data-line-number="16"><span class="co"># as.mo("S. aureus") 23.0 23.0 30.0 24.0 40.0 46 10</span></a>
<a class="sourceLine" id="cb2-17" data-line-number="17"><span class="co"># as.mo("S. aureus") 22.0 23.0 27.0 24.0 25.0 41 10</span></a>
<a class="sourceLine" id="cb2-18" data-line-number="18"><span class="co"># as.mo("Staphylococcus aureus") 3.9 4.0 5.7 4.1 4.4 20 10</span></a></code></pre></div>
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.</p>
<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Thermus islandicus</em> (<code>B_THERMS_ISL</code>), a bug probably never found before in humans:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">T.islandicus &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"theisl"</span>),</a>
<a class="sourceLine" id="cb3-2" title="2"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"THEISL"</span>),</a>
<a class="sourceLine" id="cb3-3" title="3"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"T. islandicus"</span>),</a>
<a class="sourceLine" id="cb3-4" title="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"T. islandicus"</span>),</a>
<a class="sourceLine" id="cb3-5" title="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Thermus islandicus"</span>),</a>
<a class="sourceLine" id="cb3-6" title="6"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb3-7" title="7"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(T.islandicus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb3-9" title="9"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co"># as.mo("theisl") 390 390 420 440 440 440 10</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># as.mo("THEISL") 390 390 410 400 440 440 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># as.mo("T. islandicus") 210 210 230 220 250 270 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># as.mo("T. islandicus") 210 210 240 260 260 280 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># as.mo("Thermus islandicus") 72 72 92 73 120 130 10</span></a></code></pre></div>
<p>That takes 6.8 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1">T.islandicus &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"theisl"</span>),</a>
<a class="sourceLine" id="cb3-2" data-line-number="2"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"THEISL"</span>),</a>
<a class="sourceLine" id="cb3-3" data-line-number="3"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"T. islandicus"</span>),</a>
<a class="sourceLine" id="cb3-4" data-line-number="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"T. islandicus"</span>),</a>
<a class="sourceLine" id="cb3-5" data-line-number="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Thermus islandicus"</span>),</a>
<a class="sourceLine" id="cb3-6" data-line-number="6"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(T.islandicus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># as.mo("theisl") 290 310 320 320 320 350 10</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># as.mo("THEISL") 290 300 310 310 330 340 10</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># as.mo("T. islandicus") 140 140 150 150 160 170 10</span></a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># as.mo("T. islandicus") 140 140 150 150 170 180 10</span></a>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># as.mo("Thermus islandicus") 50 52 58 54 68 70 10</span></a></code></pre></div>
<p>That takes 10.2 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
<p>In the figure below, we compare <em>Escherichia coli</em> (which is very common) with <em>Prevotella brevis</em> (which is moderately common) and with <em>Thermus islandicus</em> (which is very uncommon):</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/graphics/topics/par">par</a></span>(<span class="dt">mar =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">5</span>, <span class="dv">16</span>, <span class="dv">4</span>, <span class="dv">2</span>)) <span class="co"># set more space for left margin text (16)</span></a>
<a class="sourceLine" id="cb4-2" title="2"></a>
<a class="sourceLine" id="cb4-3" title="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Thermus islandicus"</span>),</a>
<a class="sourceLine" id="cb4-4" title="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Prevotella brevis"</span>),</a>
<a class="sourceLine" id="cb4-5" title="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Escherichia coli"</span>),</a>
<a class="sourceLine" id="cb4-6" title="6"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"T. islandicus"</span>),</a>
<a class="sourceLine" id="cb4-7" title="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"P. brevis"</span>),</a>
<a class="sourceLine" id="cb4-8" title="8"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>),</a>
<a class="sourceLine" id="cb4-9" title="9"> <span class="dt">times =</span> <span class="dv">10</span>),</a>
<a class="sourceLine" id="cb4-10" title="10"> <span class="dt">horizontal =</span> <span class="ot">TRUE</span>, <span class="dt">las =</span> <span class="dv">1</span>, <span class="dt">unit =</span> <span class="st">"s"</span>, <span class="dt">log =</span> <span class="ot">FALSE</span>,</a>
<a class="sourceLine" id="cb4-11" title="11"> <span class="dt">xlab =</span> <span class="st">""</span>, <span class="dt">ylab =</span> <span class="st">"Time in seconds"</span>,</a>
<a class="sourceLine" id="cb4-12" title="12"> <span class="dt">main =</span> <span class="st">"Benchmarks per prevalence"</span>)</a></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/graphics/topics/par">par</a></span>(<span class="dt">mar =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">5</span>, <span class="dv">16</span>, <span class="dv">4</span>, <span class="dv">2</span>)) <span class="co"># set more space for left margin text (16)</span></a>
<a class="sourceLine" id="cb4-2" data-line-number="2"></a>
<a class="sourceLine" id="cb4-3" data-line-number="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Thermus islandicus"</span>),</a>
<a class="sourceLine" id="cb4-4" data-line-number="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Prevotella brevis"</span>),</a>
<a class="sourceLine" id="cb4-5" data-line-number="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Escherichia coli"</span>),</a>
<a class="sourceLine" id="cb4-6" data-line-number="6"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"T. islandicus"</span>),</a>
<a class="sourceLine" id="cb4-7" data-line-number="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"P. brevis"</span>),</a>
<a class="sourceLine" id="cb4-8" data-line-number="8"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>),</a>
<a class="sourceLine" id="cb4-9" data-line-number="9"> <span class="dt">times =</span> <span class="dv">10</span>),</a>
<a class="sourceLine" id="cb4-10" data-line-number="10"> <span class="dt">horizontal =</span> <span class="ot">TRUE</span>, <span class="dt">las =</span> <span class="dv">1</span>, <span class="dt">unit =</span> <span class="st">"s"</span>, <span class="dt">log =</span> <span class="ot">FALSE</span>,</a>
<a class="sourceLine" id="cb4-11" data-line-number="11"> <span class="dt">xlab =</span> <span class="st">""</span>, <span class="dt">ylab =</span> <span class="st">"Time in seconds"</span>,</a>
<a class="sourceLine" id="cb4-12" data-line-number="12"> <span class="dt">main =</span> <span class="st">"Benchmarks per prevalence"</span>)</a></code></pre></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-5-1.png" width="720"></p>
<p>Uncommon microorganisms take a lot more time than common microorganisms. To relieve this pitfall and further improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
<div id="repetitive-results" class="section level3">
<h3 class="hasAnchor">
<a href="#repetitive-results" class="anchor"></a>Repetitive results</h3>
<p>Repetitive results are unique values that are present more than once. Unique values will only be calculated once by <code><a href="../reference/as.mo.html">as.mo()</a></code>. We will use <code><a href="../reference/mo_property.html">mo_fullname()</a></code> for this test - a helper function that returns the full microbial name (genus, species and possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()</a></code> internally.</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(dplyr)</a>
<a class="sourceLine" id="cb5-2" title="2"><span class="co"># take all MO codes from the septic_patients data set</span></a>
<a class="sourceLine" id="cb5-3" title="3">x &lt;-<span class="st"> </span>septic_patients<span class="op">$</span>mo <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-4" title="4"><span class="st"> </span><span class="co"># keep only the unique ones</span></a>
<a class="sourceLine" id="cb5-5" title="5"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/unique">unique</a></span>() <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-6" title="6"><span class="st"> </span><span class="co"># pick 50 of them at random</span></a>
<a class="sourceLine" id="cb5-7" title="7"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="dv">50</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-8" title="8"><span class="st"> </span><span class="co"># paste that 10,000 times</span></a>
<a class="sourceLine" id="cb5-9" title="9"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="dv">10000</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-10" title="10"><span class="st"> </span><span class="co"># scramble it</span></a>
<a class="sourceLine" id="cb5-11" title="11"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>()</a>
<a class="sourceLine" id="cb5-12" title="12"> </a>
<a class="sourceLine" id="cb5-13" title="13"><span class="co"># got indeed 50 times 10,000 = half a million?</span></a>
<a class="sourceLine" id="cb5-14" title="14"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/length">length</a></span>(x)</a>
<a class="sourceLine" id="cb5-15" title="15"><span class="co"># [1] 500000</span></a>
<a class="sourceLine" id="cb5-16" title="16"></a>
<a class="sourceLine" id="cb5-17" title="17"><span class="co"># and how many unique values do we have?</span></a>
<a class="sourceLine" id="cb5-18" title="18"><span class="kw"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(x)</a>
<a class="sourceLine" id="cb5-19" title="19"><span class="co"># [1] 50</span></a>
<a class="sourceLine" id="cb5-20" title="20"></a>
<a class="sourceLine" id="cb5-21" title="21"><span class="co"># now let's see:</span></a>
<a class="sourceLine" id="cb5-22" title="22">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(x),</a>
<a class="sourceLine" id="cb5-23" title="23"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb5-24" title="24"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb5-25" title="25"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb5-26" title="26"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb5-27" title="27"><span class="co"># mo_fullname(x) 1050 1050 1100 1090 1120 1230 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.09 seconds (1092 ms). You only lose time on your unique input values.</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" 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="cb5-2" data-line-number="2"><span class="co"># take all MO codes from the septic_patients data set</span></a>
<a class="sourceLine" id="cb5-3" data-line-number="3">x &lt;-<span class="st"> </span>septic_patients<span class="op">$</span>mo <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-4" data-line-number="4"><span class="st"> </span><span class="co"># keep only the unique ones</span></a>
<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/unique">unique</a></span>() <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="st"> </span><span class="co"># pick 50 of them at random</span></a>
<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="dv">50</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="st"> </span><span class="co"># paste that 10,000 times</span></a>
<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="dv">10000</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="st"> </span><span class="co"># scramble it</span></a>
<a class="sourceLine" id="cb5-11" data-line-number="11"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>()</a>
<a class="sourceLine" id="cb5-12" data-line-number="12"> </a>
<a class="sourceLine" id="cb5-13" data-line-number="13"><span class="co"># got indeed 50 times 10,000 = half a million?</span></a>
<a class="sourceLine" id="cb5-14" data-line-number="14"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/length">length</a></span>(x)</a>
<a class="sourceLine" id="cb5-15" data-line-number="15"><span class="co"># [1] 500000</span></a>
<a class="sourceLine" id="cb5-16" data-line-number="16"></a>
<a class="sourceLine" id="cb5-17" data-line-number="17"><span class="co"># and how many unique values do we have?</span></a>
<a class="sourceLine" id="cb5-18" data-line-number="18"><span class="kw"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(x)</a>
<a class="sourceLine" id="cb5-19" data-line-number="19"><span class="co"># [1] 50</span></a>
<a class="sourceLine" id="cb5-20" data-line-number="20"></a>
<a class="sourceLine" id="cb5-21" data-line-number="21"><span class="co"># now let's see:</span></a>
<a class="sourceLine" id="cb5-22" data-line-number="22">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(x),</a>
<a class="sourceLine" id="cb5-23" data-line-number="23"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb5-24" data-line-number="24"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb5-25" data-line-number="25"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb5-26" data-line-number="26"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb5-27" data-line-number="27"><span class="co"># mo_fullname(x) 611 628 643 635 650 714 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.63 seconds (634 ms). You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
<a href="#precalculated-results" class="anchor"></a>Precalculated results</h3>
<p>What about precalculated results? If the input is an already precalculated result of a helper function like <code><a href="../reference/mo_property.html">mo_fullname()</a></code>, it almost doesn’t take any time at all (see ‘C’ below):</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"B_STPHY_AUR"</span>),</a>
<a class="sourceLine" id="cb6-2" title="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. aureus"</span>),</a>
<a class="sourceLine" id="cb6-3" title="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
<a class="sourceLine" id="cb6-4" title="4"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb6-5" title="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb6-6" title="6"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb6-7" title="7"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb6-8" title="8"><span class="co"># A 13.00 13.20 13.60 13.60 14.00 14.40 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co"># B 49.40 50.00 57.50 51.90 52.40 103.00 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co"># C 1.52 1.72 1.81 1.78 1.98 1.99 10</span></a></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0018 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
<a class="sourceLine" id="cb7-2" title="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
<a class="sourceLine" id="cb7-3" title="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
<a class="sourceLine" id="cb7-4" title="4"> <span class="dt">D =</span> <span class="kw"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="st">"Staphylococcaceae"</span>),</a>
<a class="sourceLine" id="cb7-5" title="5"> <span class="dt">E =</span> <span class="kw"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="st">"Bacillales"</span>),</a>
<a class="sourceLine" id="cb7-6" title="6"> <span class="dt">F =</span> <span class="kw"><a href="../reference/mo_property.html">mo_class</a></span>(<span class="st">"Bacilli"</span>),</a>
<a class="sourceLine" id="cb7-7" title="7"> <span class="dt">G =</span> <span class="kw"><a href="../reference/mo_property.html">mo_phylum</a></span>(<span class="st">"Firmicutes"</span>),</a>
<a class="sourceLine" id="cb7-8" title="8"> <span class="dt">H =</span> <span class="kw"><a href="../reference/mo_property.html">mo_kingdom</a></span>(<span class="st">"Bacteria"</span>),</a>
<a class="sourceLine" id="cb7-9" title="9"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb7-10" title="10"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb7-11" title="11"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb7-12" title="12"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb7-13" title="13"><span class="co"># A 0.612 0.623 0.685 0.653 0.789 0.814 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co"># B 0.556 0.575 0.680 0.671 0.689 0.958 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co"># C 1.520 1.710 1.800 1.820 1.950 1.970 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co"># D 0.547 0.665 0.723 0.688 0.811 0.997 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co"># E 0.490 0.541 0.633 0.629 0.748 0.756 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co"># F 0.482 0.569 0.612 0.590 0.663 0.756 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co"># G 0.551 0.558 0.601 0.586 0.632 0.735 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co"># H 0.494 0.564 0.595 0.575 0.608 0.757 10</span></a></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">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"B_STPHY_AUR"</span>),</a>
<a class="sourceLine" id="cb6-2" data-line-number="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. aureus"</span>),</a>
<a class="sourceLine" id="cb6-3" data-line-number="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
<a class="sourceLine" id="cb6-4" data-line-number="4"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb6-5" data-line-number="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb6-6" data-line-number="6"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb6-7" data-line-number="7"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb6-8" data-line-number="8"><span class="co"># A 6.730 7.030 8.030 7.750 8.72 9.73 10</span></a>
<a class="sourceLine" id="cb6-9" data-line-number="9"><span class="co"># B 22.400 23.000 27.100 23.600 27.10 46.00 10</span></a>
<a class="sourceLine" id="cb6-10" data-line-number="10"><span class="co"># C 0.835 0.877 0.978 0.925 1.12 1.18 10</span></a></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0009 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
<a class="sourceLine" id="cb7-2" data-line-number="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
<a class="sourceLine" id="cb7-3" data-line-number="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
<a class="sourceLine" id="cb7-4" data-line-number="4"> <span class="dt">D =</span> <span class="kw"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="st">"Staphylococcaceae"</span>),</a>
<a class="sourceLine" id="cb7-5" data-line-number="5"> <span class="dt">E =</span> <span class="kw"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="st">"Bacillales"</span>),</a>
<a class="sourceLine" id="cb7-6" data-line-number="6"> <span class="dt">F =</span> <span class="kw"><a href="../reference/mo_property.html">mo_class</a></span>(<span class="st">"Bacilli"</span>),</a>
<a class="sourceLine" id="cb7-7" data-line-number="7"> <span class="dt">G =</span> <span class="kw"><a href="../reference/mo_property.html">mo_phylum</a></span>(<span class="st">"Firmicutes"</span>),</a>
<a class="sourceLine" id="cb7-8" data-line-number="8"> <span class="dt">H =</span> <span class="kw"><a href="../reference/mo_property.html">mo_kingdom</a></span>(<span class="st">"Bacteria"</span>),</a>
<a class="sourceLine" id="cb7-9" data-line-number="9"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb7-10" data-line-number="10"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb7-11" data-line-number="11"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb7-12" data-line-number="12"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb7-13" data-line-number="13"><span class="co"># A 0.468 0.470 0.533 0.489 0.595 0.690 10</span></a>
<a class="sourceLine" id="cb7-14" data-line-number="14"><span class="co"># B 0.504 0.513 0.555 0.520 0.571 0.711 10</span></a>
<a class="sourceLine" id="cb7-15" data-line-number="15"><span class="co"># C 0.629 0.687 0.864 0.855 1.050 1.130 10</span></a>
<a class="sourceLine" id="cb7-16" data-line-number="16"><span class="co"># D 0.505 0.515 0.575 0.530 0.649 0.767 10</span></a>
<a class="sourceLine" id="cb7-17" data-line-number="17"><span class="co"># E 0.442 0.457 0.529 0.481 0.531 0.774 10</span></a>
<a class="sourceLine" id="cb7-18" data-line-number="18"><span class="co"># F 0.447 0.510 0.554 0.568 0.609 0.618 10</span></a>
<a class="sourceLine" id="cb7-19" data-line-number="19"><span class="co"># G 0.443 0.470 0.492 0.477 0.506 0.601 10</span></a>
<a class="sourceLine" id="cb7-20" data-line-number="20"><span class="co"># H 0.448 0.459 0.491 0.466 0.515 0.633 10</span></a></code></pre></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> too, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
</div>
<div id="results-in-other-languages" class="section level3">
<h3 class="hasAnchor">
<a href="#results-in-other-languages" class="anchor"></a>Results in other languages</h3>
<p>When the system language is non-English and supported by this <code>AMR</code> package, some functions will have a translated result. This almost does’t take extra time:</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>) <span class="co"># or just mo_fullname("CoNS") on an English system</span></a>
<a class="sourceLine" id="cb8-2" title="2"><span class="co"># [1] "Coagulase-negative Staphylococcus (CoNS)"</span></a>
<a class="sourceLine" id="cb8-3" title="3"></a>
<a class="sourceLine" id="cb8-4" title="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># or just mo_fullname("CoNS") on a Spanish system</span></a>
<a class="sourceLine" id="cb8-5" title="5"><span class="co"># [1] "Staphylococcus coagulasa negativo (SCN)"</span></a>
<a class="sourceLine" id="cb8-6" title="6"></a>
<a class="sourceLine" id="cb8-7" title="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"nl"</span>) <span class="co"># or just mo_fullname("CoNS") on a Dutch system</span></a>
<a class="sourceLine" id="cb8-8" title="8"><span class="co"># [1] "Coagulase-negatieve Staphylococcus (CNS)"</span></a>
<a class="sourceLine" id="cb8-9" title="9"></a>
<a class="sourceLine" id="cb8-10" title="10">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">en =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>),</a>
<a class="sourceLine" id="cb8-11" title="11"> <span class="dt">de =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"de"</span>),</a>
<a class="sourceLine" id="cb8-12" title="12"> <span class="dt">nl =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"nl"</span>),</a>
<a class="sourceLine" id="cb8-13" title="13"> <span class="dt">es =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"es"</span>),</a>
<a class="sourceLine" id="cb8-14" title="14"> <span class="dt">it =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"it"</span>),</a>
<a class="sourceLine" id="cb8-15" title="15"> <span class="dt">fr =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"fr"</span>),</a>
<a class="sourceLine" id="cb8-16" title="16"> <span class="dt">pt =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>),</a>
<a class="sourceLine" id="cb8-17" title="17"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb8-18" title="18"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
<a class="sourceLine" id="cb8-19" title="19"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb8-20" title="20"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb8-21" title="21"><span class="co"># en 43.00 43.12 45.51 44.82 44.89 56.61 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co"># de 46.47 46.99 52.11 47.57 48.11 93.77 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co"># nl 60.86 62.72 67.57 63.69 63.99 108.20 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co"># es 45.74 46.05 52.37 46.42 47.98 103.00 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co"># it 45.84 45.89 51.90 47.66 47.73 94.83 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co"># fr 45.97 46.92 47.44 47.76 47.86 48.49 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co"># pt 45.93 46.77 47.36 47.77 47.93 48.12 10</span></a></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"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>) <span class="co"># or just mo_fullname("CoNS") on an English system</span></a>
<a class="sourceLine" id="cb8-2" data-line-number="2"><span class="co"># [1] "Coagulase-negative Staphylococcus (CoNS)"</span></a>
<a class="sourceLine" id="cb8-3" data-line-number="3"></a>
<a class="sourceLine" id="cb8-4" data-line-number="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># or just mo_fullname("CoNS") on a Spanish system</span></a>
<a class="sourceLine" id="cb8-5" data-line-number="5"><span class="co"># [1] "Staphylococcus coagulasa negativo (SCN)"</span></a>
<a class="sourceLine" id="cb8-6" data-line-number="6"></a>
<a class="sourceLine" id="cb8-7" data-line-number="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"nl"</span>) <span class="co"># or just mo_fullname("CoNS") on a Dutch system</span></a>
<a class="sourceLine" id="cb8-8" data-line-number="8"><span class="co"># [1] "Coagulase-negatieve Staphylococcus (CNS)"</span></a>
<a class="sourceLine" id="cb8-9" data-line-number="9"></a>
<a class="sourceLine" id="cb8-10" data-line-number="10">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">en =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>),</a>
<a class="sourceLine" id="cb8-11" data-line-number="11"> <span class="dt">de =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"de"</span>),</a>
<a class="sourceLine" id="cb8-12" data-line-number="12"> <span class="dt">nl =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"nl"</span>),</a>
<a class="sourceLine" id="cb8-13" data-line-number="13"> <span class="dt">es =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"es"</span>),</a>
<a class="sourceLine" id="cb8-14" data-line-number="14"> <span class="dt">it =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"it"</span>),</a>
<a class="sourceLine" id="cb8-15" data-line-number="15"> <span class="dt">fr =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"fr"</span>),</a>
<a class="sourceLine" id="cb8-16" data-line-number="16"> <span class="dt">pt =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>),</a>
<a class="sourceLine" id="cb8-17" data-line-number="17"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb8-18" data-line-number="18"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
<a class="sourceLine" id="cb8-19" data-line-number="19"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb8-20" data-line-number="20"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb8-21" data-line-number="21"><span class="co"># en 19.29 20.39 22.42 20.64 21.26 38.98 10</span></a>
<a class="sourceLine" id="cb8-22" data-line-number="22"><span class="co"># de 22.03 22.40 23.78 23.08 23.60 31.74 10</span></a>
<a class="sourceLine" id="cb8-23" data-line-number="23"><span class="co"># nl 27.98 28.60 29.22 28.87 30.13 30.53 10</span></a>
<a class="sourceLine" id="cb8-24" data-line-number="24"><span class="co"># es 21.44 22.97 30.04 24.11 45.71 46.46 10</span></a>
<a class="sourceLine" id="cb8-25" data-line-number="25"><span class="co"># it 21.17 21.82 22.47 22.44 23.27 23.52 10</span></a>
<a class="sourceLine" id="cb8-26" data-line-number="26"><span class="co"># fr 20.75 21.58 24.10 22.04 22.41 42.96 10</span></a>
<a class="sourceLine" id="cb8-27" data-line-number="27"><span class="co"># pt 21.24 21.92 24.31 22.75 23.26 39.91 10</span></a></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</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="Latest development version">0.7.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9012</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to create frequency tables</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">01 July 2019</h4>
<h4 class="date">10 July 2019</h4>
<div class="hidden name"><code>freq.Rmd</code></div>
@ -210,17 +210,17 @@
<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" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="co"># Any of these will work:</span></a>
<a class="sourceLine" id="cb1-2" title="2"><span class="co"># freq(septic_patients$gender)</span></a>
<a class="sourceLine" id="cb1-3" title="3"><span class="co"># freq(septic_patients[, "gender"])</span></a>
<a class="sourceLine" id="cb1-4" title="4"></a>
<a class="sourceLine" id="cb1-5" title="5"><span class="co"># Using tidyverse:</span></a>
<a class="sourceLine" id="cb1-6" title="6"><span class="co"># septic_patients$gender %&gt;% freq()</span></a>
<a class="sourceLine" id="cb1-7" title="7"><span class="co"># septic_patients[, "gender"] %&gt;% freq()</span></a>
<a class="sourceLine" id="cb1-8" title="8"><span class="co"># septic_patients %&gt;% freq("gender")</span></a>
<a class="sourceLine" id="cb1-9" title="9"></a>
<a class="sourceLine" id="cb1-10" title="10"><span class="co"># Probably the fastest and easiest:</span></a>
<a class="sourceLine" id="cb1-11" title="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>
<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>
<p><strong>Frequency table of <code>gender</code> from <code>septic_patients</code> (2,000 x 49)</strong></p>
<p>Class: character<br>
Length: 2,000 (of which NA: 0 = 0.00%)<br>
@ -262,22 +262,22 @@ Longest: 1</p>
<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" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="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" title="2"><span class="co"># Joining, by = "mo"</span></a></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" 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>
<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>
<p>If we compare the dimensions between the old and new dataset, we can see that these 15 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>
<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>
<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>
<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> from <code>my_patients</code> (2,000 x 64)</strong></p>
<p>Columns: 2<br>
Length: 2,000 (of which NA: 0 = 0.00%)<br>
@ -423,10 +423,10 @@ Longest: 34</p>
<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" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1"><span class="co"># # get age distribution of unique patients</span></a>
<a class="sourceLine" id="cb6-2" title="2">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb6-3" title="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" title="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>
<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> from a <code>data.frame</code> (981 x 49)</strong></p>
<p>Class: numeric<br>
Length: 981 (of which NA: 0 = 0.00%)<br>
@ -506,8 +506,8 @@ 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 their levels 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" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb7-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id)</a></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> from <code>septic_patients</code> (2,000 x 49)</strong></p>
<p>Class: factor (numeric)<br>
Length: 2,000 (of which NA: 0 = 0.00%)<br>
@ -558,8 +558,8 @@ Unique: 4</p>
</tbody>
</table>
<p>… to this, where items are now sorted on factor levels:</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb8-2" title="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>
<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> from <code>septic_patients</code> (2,000 x 49)</strong></p>
<p>Class: factor (numeric)<br>
Length: 2,000 (of which NA: 0 = 0.00%)<br>
@ -610,8 +610,8 @@ Unique: 4</p>
</tbody>
</table>
<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>
<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>(AMX, <span class="dt">header =</span> <span class="ot">TRUE</span>)</a></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>(AMX, <span class="dt">header =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
<p><strong>Frequency table of <code>AMX</code> from <code>septic_patients</code> (2,000 x 49)</strong></p>
<p>Class: factor &gt; ordered &gt; rsi (numeric)<br>
Length: 2,000 (of which NA: 771 = 38.55%)<br>
@ -661,8 +661,8 @@ Group: Beta-lactams/penicillins<br>
<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" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb10-2" title="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>
<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> from <code>septic_patients</code> (2,000 x 49)</strong></p>
<p>Class: Date (numeric)<br>
Length: 2,000 (of which NA: 0 = 0.00%)<br>
@ -728,11 +728,11 @@ 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 actually a regular <code>data.frame</code>, with the exception that it contains an additional class.</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="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" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/class">class</a></span>(my_df)</a></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] “freq” “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" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(my_df)</a></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">
@ -743,8 +743,8 @@ 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 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>
<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>(AMX, <span class="dt">na.rm =</span> <span class="ot">FALSE</span>)</a></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>(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 <code>septic_patients</code> (2,000 x 49)</strong></p>
<p>Class: factor &gt; ordered &gt; rsi (numeric)<br>
Length: 2,000 (of which NA: 771 = 38.55%)<br>
@ -803,8 +803,8 @@ Group: Beta-lactams/penicillins<br>
<a href="#parameter-row-names" class="anchor"></a>Parameter <code>row.names</code>
</h3>
<p>A frequency table shows row indices. To remove them, use <code>row.names = FALSE</code>:</p>
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb14-2" title="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>
<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> from <code>septic_patients</code> (2,000 x 49)</strong></p>
<p>Class: factor (numeric)<br>
Length: 2,000 (of which NA: 0 = 0.00%)<br>
@ -855,21 +855,21 @@ Unique: 4</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. Without markdown (like in regular R), a frequency table would print like:</p>
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb15-2" title="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" title="3"><span class="co"># Frequency table of `hospital_id` from `septic_patients` (2,000 x 49) </span></a>
<a class="sourceLine" id="cb15-4" title="4"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-5" title="5"><span class="co"># Class: factor (numeric)</span></a>
<a class="sourceLine" id="cb15-6" title="6"><span class="co"># Length: 2,000 (of which NA: 0 = 0.00%)</span></a>
<a class="sourceLine" id="cb15-7" title="7"><span class="co"># Levels: 4: A, B, C, D</span></a>
<a class="sourceLine" id="cb15-8" title="8"><span class="co"># Unique: 4</span></a>
<a class="sourceLine" id="cb15-9" title="9"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-10" title="10"><span class="co"># Item Count Percent Cum. Count Cum. Percent</span></a>
<a class="sourceLine" id="cb15-11" title="11"><span class="co"># --- ----- ------ -------- ----------- -------------</span></a>
<a class="sourceLine" id="cb15-12" title="12"><span class="co"># 1 D 762 38.1% 762 38.1%</span></a>
<a class="sourceLine" id="cb15-13" title="13"><span class="co"># 2 B 663 33.2% 1,425 71.2%</span></a>
<a class="sourceLine" id="cb15-14" title="14"><span class="co"># 3 A 321 16.0% 1,746 87.3%</span></a>
<a class="sourceLine" id="cb15-15" title="15"><span class="co"># 4 C 254 12.7% 2,000 100.0%</span></a></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">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>
</div>
</div>
</div>

2
docs/articles/index.html
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@ -78,7 +78,7 @@
</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="Latest development version">0.7.1.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9012</span>
</span>
</div>

146
docs/articles/resistance_predict.html
View File

@ -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="Latest development version">0.7.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9012</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to predict antimicrobial resistance</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">01 July 2019</h4>
<h4 class="date">10 July 2019</h4>
<div class="hidden name"><code>resistance_predict.Rmd</code></div>
@ -206,28 +206,28 @@
<a href="#needed-r-packages" class="anchor"></a>Needed R packages</h2>
<p>As with many uses in R, we need some additional packages for AMR analysis. Our package works closely together with the <a href="https://www.tidyverse.org">tidyverse packages</a> <a href="https://dplyr.tidyverse.org/"><code>dplyr</code></a> and <a href="https://ggplot2.tidyverse.org"><code>ggplot2</code></a> by Dr Hadley Wickham. The tidyverse tremendously improves the way we conduct data science - it allows for a very natural way of writing syntaxes and creating beautiful plots in R.</p>
<p>Our <code>AMR</code> package depends on these packages and even extends their use and functions.</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(dplyr)</a>
<a class="sourceLine" id="cb1-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(ggplot2)</a>
<a class="sourceLine" id="cb1-3" title="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(AMR)</a>
<a class="sourceLine" id="cb1-4" title="4"></a>
<a class="sourceLine" id="cb1-5" title="5"><span class="co"># (if not yet installed, install with:)</span></a>
<a class="sourceLine" id="cb1-6" title="6"><span class="co"># install.packages(c("tidyverse", "AMR"))</span></a></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"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(dplyr)</a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(ggplot2)</a>
<a class="sourceLine" id="cb1-3" data-line-number="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(AMR)</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"># (if not yet installed, install with:)</span></a>
<a class="sourceLine" id="cb1-6" data-line-number="6"><span class="co"># install.packages(c("tidyverse", "AMR"))</span></a></code></pre></div>
</div>
<div id="prediction-analysis" class="section level2">
<h2 class="hasAnchor">
<a href="#prediction-analysis" class="anchor"></a>Prediction analysis</h2>
<p>Our package contains a function <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>, which takes the same input as functions for <a href="./AMR.html">other AMR analysis</a>. Based on a date column, it calculates cases per year and uses a regression model to predict antimicrobial resistance.</p>
<p>It is basically as easy as:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="co"># resistance prediction of piperacillin/tazobactam (TZP):</span></a>
<a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">tbl =</span> septic_patients, <span class="dt">col_date =</span> <span class="st">"date"</span>, <span class="dt">col_ab =</span> <span class="st">"TZP"</span>)</a>
<a class="sourceLine" id="cb2-3" title="3"></a>
<a class="sourceLine" id="cb2-4" title="4"><span class="co"># or:</span></a>
<a class="sourceLine" id="cb2-5" title="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb2-6" title="6"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>)</a>
<a class="sourceLine" id="cb2-7" title="7"></a>
<a class="sourceLine" id="cb2-8" title="8"><span class="co"># to bind it to object 'predict_TZP' for example:</span></a>
<a class="sourceLine" id="cb2-9" title="9">predict_TZP &lt;-<span class="st"> </span>septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb2-10" title="10"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>)</a></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"><span class="co"># resistance prediction of piperacillin/tazobactam (TZP):</span></a>
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">tbl =</span> septic_patients, <span class="dt">col_date =</span> <span class="st">"date"</span>, <span class="dt">col_ab =</span> <span class="st">"TZP"</span>)</a>
<a class="sourceLine" id="cb2-3" data-line-number="3"></a>
<a class="sourceLine" id="cb2-4" data-line-number="4"><span class="co"># or:</span></a>
<a class="sourceLine" id="cb2-5" data-line-number="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb2-6" data-line-number="6"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>)</a>
<a class="sourceLine" id="cb2-7" data-line-number="7"></a>
<a class="sourceLine" id="cb2-8" data-line-number="8"><span class="co"># to bind it to object 'predict_TZP' for example:</span></a>
<a class="sourceLine" id="cb2-9" data-line-number="9">predict_TZP &lt;-<span class="st"> </span>septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb2-10" data-line-number="10"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>)</a></code></pre></div>
<p>The function will look for a date column itself if <code>col_date</code> is not set.</p>
<p>When running any of these commands, a summary of the regression model will be printed unless using <code><a href="../reference/resistance_predict.html">resistance_predict(..., info = FALSE)</a></code>.</p>
<pre><code># NOTE: Using column `date` as input for `col_date`.
@ -257,55 +257,55 @@
#
# Number of Fisher Scoring iterations: 4</code></pre>
<p>This text is only a printed summary - the actual result (output) of the function is a <code>data.frame</code> containing for each year: the number of observations, the actual observed resistance, the estimated resistance and the standard error below and above the estimation:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">predict_TZP</a>
<a class="sourceLine" id="cb4-2" title="2"><span class="co"># year value se_min se_max observations observed estimated</span></a>
<a class="sourceLine" id="cb4-3" title="3"><span class="co"># 1 2003 0.06250000 NA NA 32 0.06250000 0.05486389</span></a>
<a class="sourceLine" id="cb4-4" title="4"><span class="co"># 2 2004 0.08536585 NA NA 82 0.08536585 0.06089002</span></a>
<a class="sourceLine" id="cb4-5" title="5"><span class="co"># 3 2005 0.05000000 NA NA 60 0.05000000 0.06753075</span></a>
<a class="sourceLine" id="cb4-6" title="6"><span class="co"># 4 2006 0.05084746 NA NA 59 0.05084746 0.07483801</span></a>
<a class="sourceLine" id="cb4-7" title="7"><span class="co"># 5 2007 0.12121212 NA NA 66 0.12121212 0.08286570</span></a>
<a class="sourceLine" id="cb4-8" title="8"><span class="co"># 6 2008 0.04166667 NA NA 72 0.04166667 0.09166918</span></a>
<a class="sourceLine" id="cb4-9" title="9"><span class="co"># 7 2009 0.01639344 NA NA 61 0.01639344 0.10130461</span></a>
<a class="sourceLine" id="cb4-10" title="10"><span class="co"># 8 2010 0.05660377 NA NA 53 0.05660377 0.11182814</span></a>
<a class="sourceLine" id="cb4-11" title="11"><span class="co"># 9 2011 0.18279570 NA NA 93 0.18279570 0.12329488</span></a>
<a class="sourceLine" id="cb4-12" title="12"><span class="co"># 10 2012 0.30769231 NA NA 65 0.30769231 0.13575768</span></a>
<a class="sourceLine" id="cb4-13" title="13"><span class="co"># 11 2013 0.06896552 NA NA 58 0.06896552 0.14926576</span></a>
<a class="sourceLine" id="cb4-14" title="14"><span class="co"># 12 2014 0.10000000 NA NA 60 0.10000000 0.16386307</span></a>
<a class="sourceLine" id="cb4-15" title="15"><span class="co"># 13 2015 0.23636364 NA NA 55 0.23636364 0.17958657</span></a>
<a class="sourceLine" id="cb4-16" title="16"><span class="co"># 14 2016 0.22619048 NA NA 84 0.22619048 0.19646431</span></a>
<a class="sourceLine" id="cb4-17" title="17"><span class="co"># 15 2017 0.16279070 NA NA 86 0.16279070 0.21451350</span></a>
<a class="sourceLine" id="cb4-18" title="18"><span class="co"># 16 2018 0.23373852 0.2021578 0.2653193 NA NA 0.23373852</span></a>
<a class="sourceLine" id="cb4-19" title="19"><span class="co"># 17 2019 0.25412909 0.2168525 0.2914057 NA NA 0.25412909</span></a>
<a class="sourceLine" id="cb4-20" title="20"><span class="co"># 18 2020 0.27565854 0.2321869 0.3191302 NA NA 0.27565854</span></a>
<a class="sourceLine" id="cb4-21" title="21"><span class="co"># 19 2021 0.29828252 0.2481942 0.3483709 NA NA 0.29828252</span></a>
<a class="sourceLine" id="cb4-22" title="22"><span class="co"># 20 2022 0.32193804 0.2649008 0.3789753 NA NA 0.32193804</span></a>
<a class="sourceLine" id="cb4-23" title="23"><span class="co"># 21 2023 0.34654311 0.2823269 0.4107593 NA NA 0.34654311</span></a>
<a class="sourceLine" id="cb4-24" title="24"><span class="co"># 22 2024 0.37199700 0.3004860 0.4435080 NA NA 0.37199700</span></a>
<a class="sourceLine" id="cb4-25" title="25"><span class="co"># 23 2025 0.39818127 0.3193839 0.4769787 NA NA 0.39818127</span></a>
<a class="sourceLine" id="cb4-26" title="26"><span class="co"># 24 2026 0.42496142 0.3390173 0.5109056 NA NA 0.42496142</span></a>
<a class="sourceLine" id="cb4-27" title="27"><span class="co"># 25 2027 0.45218939 0.3593720 0.5450068 NA NA 0.45218939</span></a>
<a class="sourceLine" id="cb4-28" title="28"><span class="co"># 26 2028 0.47970658 0.3804212 0.5789920 NA NA 0.47970658</span></a>
<a class="sourceLine" id="cb4-29" title="29"><span class="co"># 27 2029 0.50734745 0.4021241 0.6125708 NA NA 0.50734745</span></a></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">predict_TZP</a>
<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="co"># year value se_min se_max observations observed estimated</span></a>
<a class="sourceLine" id="cb4-3" data-line-number="3"><span class="co"># 1 2003 0.06250000 NA NA 32 0.06250000 0.05486389</span></a>
<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="co"># 2 2004 0.08536585 NA NA 82 0.08536585 0.06089002</span></a>
<a class="sourceLine" id="cb4-5" data-line-number="5"><span class="co"># 3 2005 0.05000000 NA NA 60 0.05000000 0.06753075</span></a>
<a class="sourceLine" id="cb4-6" data-line-number="6"><span class="co"># 4 2006 0.05084746 NA NA 59 0.05084746 0.07483801</span></a>
<a class="sourceLine" id="cb4-7" data-line-number="7"><span class="co"># 5 2007 0.12121212 NA NA 66 0.12121212 0.08286570</span></a>
<a class="sourceLine" id="cb4-8" data-line-number="8"><span class="co"># 6 2008 0.04166667 NA NA 72 0.04166667 0.09166918</span></a>
<a class="sourceLine" id="cb4-9" data-line-number="9"><span class="co"># 7 2009 0.01639344 NA NA 61 0.01639344 0.10130461</span></a>
<a class="sourceLine" id="cb4-10" data-line-number="10"><span class="co"># 8 2010 0.05660377 NA NA 53 0.05660377 0.11182814</span></a>
<a class="sourceLine" id="cb4-11" data-line-number="11"><span class="co"># 9 2011 0.18279570 NA NA 93 0.18279570 0.12329488</span></a>
<a class="sourceLine" id="cb4-12" data-line-number="12"><span class="co"># 10 2012 0.30769231 NA NA 65 0.30769231 0.13575768</span></a>
<a class="sourceLine" id="cb4-13" data-line-number="13"><span class="co"># 11 2013 0.06896552 NA NA 58 0.06896552 0.14926576</span></a>
<a class="sourceLine" id="cb4-14" data-line-number="14"><span class="co"># 12 2014 0.10000000 NA NA 60 0.10000000 0.16386307</span></a>
<a class="sourceLine" id="cb4-15" data-line-number="15"><span class="co"># 13 2015 0.23636364 NA NA 55 0.23636364 0.17958657</span></a>
<a class="sourceLine" id="cb4-16" data-line-number="16"><span class="co"># 14 2016 0.22619048 NA NA 84 0.22619048 0.19646431</span></a>
<a class="sourceLine" id="cb4-17" data-line-number="17"><span class="co"># 15 2017 0.16279070 NA NA 86 0.16279070 0.21451350</span></a>
<a class="sourceLine" id="cb4-18" data-line-number="18"><span class="co"># 16 2018 0.23373852 0.2021578 0.2653193 NA NA 0.23373852</span></a>
<a class="sourceLine" id="cb4-19" data-line-number="19"><span class="co"># 17 2019 0.25412909 0.2168525 0.2914057 NA NA 0.25412909</span></a>
<a class="sourceLine" id="cb4-20" data-line-number="20"><span class="co"># 18 2020 0.27565854 0.2321869 0.3191302 NA NA 0.27565854</span></a>
<a class="sourceLine" id="cb4-21" data-line-number="21"><span class="co"># 19 2021 0.29828252 0.2481942 0.3483709 NA NA 0.29828252</span></a>
<a class="sourceLine" id="cb4-22" data-line-number="22"><span class="co"># 20 2022 0.32193804 0.2649008 0.3789753 NA NA 0.32193804</span></a>
<a class="sourceLine" id="cb4-23" data-line-number="23"><span class="co"># 21 2023 0.34654311 0.2823269 0.4107593 NA NA 0.34654311</span></a>
<a class="sourceLine" id="cb4-24" data-line-number="24"><span class="co"># 22 2024 0.37199700 0.3004860 0.4435080 NA NA 0.37199700</span></a>
<a class="sourceLine" id="cb4-25" data-line-number="25"><span class="co"># 23 2025 0.39818127 0.3193839 0.4769787 NA NA 0.39818127</span></a>
<a class="sourceLine" id="cb4-26" data-line-number="26"><span class="co"># 24 2026 0.42496142 0.3390173 0.5109056 NA NA 0.42496142</span></a>
<a class="sourceLine" id="cb4-27" data-line-number="27"><span class="co"># 25 2027 0.45218939 0.3593720 0.5450068 NA NA 0.45218939</span></a>
<a class="sourceLine" id="cb4-28" data-line-number="28"><span class="co"># 26 2028 0.47970658 0.3804212 0.5789920 NA NA 0.47970658</span></a>
<a class="sourceLine" id="cb4-29" data-line-number="29"><span class="co"># 27 2029 0.50734745 0.4021241 0.6125708 NA NA 0.50734745</span></a></code></pre></div>
<p>The function <code>plot</code> is available in base R, and can be extended by other packages to depend the output based on the type of input. We extended its function to cope with resistance predictions:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(predict_TZP)</a></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"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(predict_TZP)</a></code></pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-4-1.png" width="720"></p>
<p>This is the fastest way to plot the result. It automatically adds the right axes, error bars, titles, number of available observations and type of model.</p>
<p>We also support the <code>ggplot2</code> package with our custom function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> to create more appealing plots:</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(predict_TZP)</a></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="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(predict_TZP)</a></code></pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-5-1.png" width="720"></p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1"></a>
<a class="sourceLine" id="cb7-2" title="2"><span class="co"># choose for error bars instead of a ribbon</span></a>
<a class="sourceLine" id="cb7-3" title="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(predict_TZP, <span class="dt">ribbon =</span> <span class="ot">FALSE</span>)</a></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"></a>
<a class="sourceLine" id="cb7-2" data-line-number="2"><span class="co"># choose for error bars instead of a ribbon</span></a>
<a class="sourceLine" id="cb7-3" data-line-number="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(predict_TZP, <span class="dt">ribbon =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-5-2.png" width="720"></p>
<div id="choosing-the-right-model" class="section level3">
<h3 class="hasAnchor">
<a href="#choosing-the-right-model" class="anchor"></a>Choosing the right model</h3>
<p>Resistance is not easily predicted; if we look at vancomycin resistance in Gram positives, the spread (i.e. standard error) is enormous:</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb8-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(mo, <span class="dt">language =</span> <span class="ot">NULL</span>) <span class="op">==</span><span class="st"> "Gram-positive"</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb8-3" title="3"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">col_ab =</span> <span class="st">"VAN"</span>, <span class="dt">year_min =</span> <span class="dv">2010</span>, <span class="dt">info =</span> <span class="ot">FALSE</span>) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb8-4" title="4"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>()</a>
<a class="sourceLine" id="cb8-5" title="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a></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="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(mo, <span class="dt">language =</span> <span class="ot">NULL</span>) <span class="op">==</span><span class="st"> "Gram-positive"</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb8-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">col_ab =</span> <span class="st">"VAN"</span>, <span class="dt">year_min =</span> <span class="dv">2010</span>, <span class="dt">info =</span> <span class="ot">FALSE</span>) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb8-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>()</a>
<a class="sourceLine" id="cb8-5" data-line-number="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a></code></pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-6-1.png" width="720"></p>
<p>Vancomycin resistance could be 100% in ten years, but might also stay around 0%.</p>
<p>You can define the model with the <code>model</code> parameter. The default model is a generalised linear regression model using a binomial distribution, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance.</p>
@ -346,25 +346,25 @@
</tbody>
</table>
<p>For the vancomycin resistance in Gram positive bacteria, a linear model might be more appropriate since no (left half of a) binomial distribution is to be expected based on the observed years:</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="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(mo, <span class="dt">language =</span> <span class="ot">NULL</span>) <span class="op">==</span><span class="st"> "Gram-positive"</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb9-3" title="3"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">col_ab =</span> <span class="st">"VAN"</span>, <span class="dt">year_min =</span> <span class="dv">2010</span>, <span class="dt">info =</span> <span class="ot">FALSE</span>, <span class="dt">model =</span> <span class="st">"linear"</span>) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb9-4" title="4"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>()</a>
<a class="sourceLine" id="cb9-5" title="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a></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="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(mo, <span class="dt">language =</span> <span class="ot">NULL</span>) <span class="op">==</span><span class="st"> "Gram-positive"</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb9-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">col_ab =</span> <span class="st">"VAN"</span>, <span class="dt">year_min =</span> <span class="dv">2010</span>, <span class="dt">info =</span> <span class="ot">FALSE</span>, <span class="dt">model =</span> <span class="st">"linear"</span>) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb9-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>()</a>
<a class="sourceLine" id="cb9-5" data-line-number="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a></code></pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
<p>This seems more likely, doesn’t it?</p>
<p>The model itself is also available from the object, as an <code>attribute</code>:</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1">model &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/attributes">attributes</a></span>(predict_TZP)<span class="op">$</span>model</a>
<a class="sourceLine" id="cb10-2" title="2"></a>
<a class="sourceLine" id="cb10-3" title="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(model)<span class="op">$</span>family</a>
<a class="sourceLine" id="cb10-4" title="4"><span class="co"># </span></a>
<a class="sourceLine" id="cb10-5" title="5"><span class="co"># Family: binomial </span></a>
<a class="sourceLine" id="cb10-6" title="6"><span class="co"># Link function: logit</span></a>
<a class="sourceLine" id="cb10-7" title="7"></a>
<a class="sourceLine" id="cb10-8" title="8"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(model)<span class="op">$</span>coefficients</a>
<a class="sourceLine" id="cb10-9" title="9"><span class="co"># Estimate Std. Error z value Pr(&gt;|z|)</span></a>
<a class="sourceLine" id="cb10-10" title="10"><span class="co"># (Intercept) -224.3987194 48.0335384 -4.671709 2.987038e-06</span></a>
<a class="sourceLine" id="cb10-11" title="11"><span class="co"># year 0.1106102 0.0238753 4.632831 3.606990e-06</span></a></code></pre></div>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1">model &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/attributes">attributes</a></span>(predict_TZP)<span class="op">$</span>model</a>
<a class="sourceLine" id="cb10-2" data-line-number="2"></a>
<a class="sourceLine" id="cb10-3" data-line-number="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(model)<span class="op">$</span>family</a>
<a class="sourceLine" id="cb10-4" data-line-number="4"><span class="co"># </span></a>
<a class="sourceLine" id="cb10-5" data-line-number="5"><span class="co"># Family: binomial </span></a>
<a class="sourceLine" id="cb10-6" data-line-number="6"><span class="co"># Link function: logit</span></a>
<a class="sourceLine" id="cb10-7" data-line-number="7"></a>
<a class="sourceLine" id="cb10-8" data-line-number="8"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(model)<span class="op">$</span>coefficients</a>
<a class="sourceLine" id="cb10-9" data-line-number="9"><span class="co"># Estimate Std. Error z value Pr(&gt;|z|)</span></a>
<a class="sourceLine" id="cb10-10" data-line-number="10"><span class="co"># (Intercept) -224.3987194 48.0335384 -4.671709 2.987038e-06</span></a>
<a class="sourceLine" id="cb10-11" data-line-number="11"><span class="co"># year 0.1106102 0.0238753 4.632831 3.606990e-06</span></a></code></pre></div>
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