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dr. M.S. (Matthijs) Berends
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DESCRIPTION
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Package: AMR
Version: 1.0.1.9009
Version: 1.1.0
Date: 2020-04-15
Title: Antimicrobial Resistance Analysis
Authors@R: c(

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NEWS.md
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# AMR 1.0.1.9009
## <small>Last updated: 15-Apr-2020</small>
# AMR 1.1.0
### New
* Support for easy principal component analysis for AMR, using the new `pca()` function

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cran-comments.md
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# Version 0.10.0
* Although the previous release (1.0.1) is from 2020-02-23, this updates provides support for the upcoming dplyr 1.0.0 which is used (and relied upon) by probably all our users.
* For this specific version, nothing to mention.
* For this specific version, otherwise nothing to mention.
* Since version 0.3.0, CHECK returns a NOTE for having a data directory over 3 MB. This is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package.

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
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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">1.0.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
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@@ -38,7 +39,7 @@
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<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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -182,12 +183,12 @@
</header><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1>How to apply EUCAST rules</h1>
<h1 data-toc-skip>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">17 March 2020</h4>
<h4 class="date">15 April 2020</h4>
<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/EUCAST.Rmd"><code>vignettes/EUCAST.Rmd</code></a></small>
<div class="hidden name"><code>EUCAST.Rmd</code></div>
</div>
@@ -208,33 +209,33 @@
<a href="#examples" class="anchor"></a>Examples</h2>
<p>These rules can be used to discard impossible bug-drug combinations in your data. For example, <em>Klebsiella</em> produces beta-lactamase that prevents ampicillin (or amoxicillin) from working against it. In other words, practically every strain of <em>Klebsiella</em> is resistant to ampicillin.</p>
<p>Sometimes, laboratory data can still contain such strains with ampicillin being susceptible to ampicillin. This could be because an antibiogram is available before an identification is available, and the antibiogram is then not re-interpreted based on the identification (namely, <em>Klebsiella</em>). EUCAST expert rules solve this, that can be used with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a>oops &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="dt">mo =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Klebsiella"</span>, </span>
<span id="cb1-2"><a href="#cb1-2"></a> <span class="st">"Escherichia"</span>),</span>
<span id="cb1-3"><a href="#cb1-3"></a> <span class="dt">ampicillin =</span> <span class="st">"S"</span>)</span>
<span id="cb1-4"><a href="#cb1-4"></a>oops</span>
<span id="cb1-5"><a href="#cb1-5"></a><span class="co"># mo ampicillin</span></span>
<span id="cb1-6"><a href="#cb1-6"></a><span class="co"># 1 Klebsiella S</span></span>
<span id="cb1-7"><a href="#cb1-7"></a><span class="co"># 2 Escherichia S</span></span>
<span id="cb1-8"><a href="#cb1-8"></a></span>
<span id="cb1-9"><a href="#cb1-9"></a><span class="kw"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(oops, <span class="dt">info =</span> <span class="ot">FALSE</span>)</span>
<span id="cb1-10"><a href="#cb1-10"></a><span class="co"># mo ampicillin</span></span>
<span id="cb1-11"><a href="#cb1-11"></a><span class="co"># 1 Klebsiella R</span></span>
<span id="cb1-12"><a href="#cb1-12"></a><span class="co"># 2 Escherichia S</span></span></code></pre></div>
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="no">oops</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="kw">mo</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Klebsiella"</span>,
<span class="st">"Escherichia"</span>),
<span class="kw">ampicillin</span> <span class="kw">=</span> <span class="st">"S"</span>)
<span class="no">oops</span>
<span class="co"># mo ampicillin</span>
<span class="co"># 1 Klebsiella S</span>
<span class="co"># 2 Escherichia S</span>
<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="no">oops</span>, <span class="kw">info</span> <span class="kw">=</span> <span class="fl">FALSE</span>)
<span class="co"># mo ampicillin</span>
<span class="co"># 1 Klebsiella R</span>
<span class="co"># 2 Escherichia S</span></pre></body></html></div>
<p>EUCAST rules can not only be used for correction, they can also be used for filling in known resistance and susceptibility based on results of other antimicrobials drugs. This process is called <em>interpretive reading</em> and is part of the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function as well:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a>data &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="dt">mo =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Staphylococcus aureus"</span>,</span>
<span id="cb2-2"><a href="#cb2-2"></a> <span class="st">"Enterococcus faecalis"</span>,</span>
<span id="cb2-3"><a href="#cb2-3"></a> <span class="st">"Escherichia coli"</span>,</span>
<span id="cb2-4"><a href="#cb2-4"></a> <span class="st">"Klebsiella pneumoniae"</span>,</span>
<span id="cb2-5"><a href="#cb2-5"></a> <span class="st">"Pseudomonas aeruginosa"</span>),</span>
<span id="cb2-6"><a href="#cb2-6"></a> <span class="dt">VAN =</span> <span class="st">"-"</span>, <span class="co"># Vancomycin</span></span>
<span id="cb2-7"><a href="#cb2-7"></a> <span class="dt">AMX =</span> <span class="st">"-"</span>, <span class="co"># Amoxicillin</span></span>
<span id="cb2-8"><a href="#cb2-8"></a> <span class="dt">COL =</span> <span class="st">"-"</span>, <span class="co"># Colistin</span></span>
<span id="cb2-9"><a href="#cb2-9"></a> <span class="dt">CAZ =</span> <span class="st">"-"</span>, <span class="co"># Ceftazidime</span></span>
<span id="cb2-10"><a href="#cb2-10"></a> <span class="dt">CXM =</span> <span class="st">"-"</span>, <span class="co"># Cefuroxime</span></span>
<span id="cb2-11"><a href="#cb2-11"></a> <span class="dt">PEN =</span> <span class="st">"S"</span>, <span class="co"># Penicillin G</span></span>
<span id="cb2-12"><a href="#cb2-12"></a> <span class="dt">FOX =</span> <span class="st">"S"</span>, <span class="co"># Cefoxitin</span></span>
<span id="cb2-13"><a href="#cb2-13"></a> <span class="dt">stringsAsFactors =</span> <span class="ot">FALSE</span>)</span></code></pre></div>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1"></a>data</span></code></pre></div>
<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">data</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="kw">mo</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Staphylococcus aureus"</span>,
<span class="st">"Enterococcus faecalis"</span>,
<span class="st">"Escherichia coli"</span>,
<span class="st">"Klebsiella pneumoniae"</span>,
<span class="st">"Pseudomonas aeruginosa"</span>),
<span class="kw">VAN</span> <span class="kw">=</span> <span class="st">"-"</span>, <span class="co"># Vancomycin</span>
<span class="kw">AMX</span> <span class="kw">=</span> <span class="st">"-"</span>, <span class="co"># Amoxicillin</span>
<span class="kw">COL</span> <span class="kw">=</span> <span class="st">"-"</span>, <span class="co"># Colistin</span>
<span class="kw">CAZ</span> <span class="kw">=</span> <span class="st">"-"</span>, <span class="co"># Ceftazidime</span>
<span class="kw">CXM</span> <span class="kw">=</span> <span class="st">"-"</span>, <span class="co"># Cefuroxime</span>
<span class="kw">PEN</span> <span class="kw">=</span> <span class="st">"S"</span>, <span class="co"># Penicillin G</span>
<span class="kw">FOX</span> <span class="kw">=</span> <span class="st">"S"</span>, <span class="co"># Cefoxitin</span>
<span class="kw">stringsAsFactors</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">data</span></pre></body></html></div>
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<th align="left">mo</th>
@@ -299,7 +300,7 @@
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<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1"></a><span class="kw"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(data)</span></code></pre></div>
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="no">data</span>)</pre></body></html></div>
<table class="table">
<thead><tr class="header">
<th align="left">mo</th>
@@ -369,15 +370,9 @@
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@@ -388,7 +383,7 @@
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<h1>How to determine multi-drug resistance (MDR)</h1>
<h1 data-toc-skip>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">17 March 2020</h4>
<h4 class="date">15 April 2020</h4>
<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/MDR.Rmd"><code>vignettes/MDR.Rmd</code></a></small>
<div class="hidden name"><code>MDR.Rmd</code></div>
</div>
@@ -233,15 +234,15 @@
<a href="#examples" class="anchor"></a>Examples</h4>
<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function always returns an ordered <code>factor</code>. For example, the output of the default guideline by Magiorakos <em>et al.</em> returns a <code>factor</code> with levels ‘Negative’, ‘MDR’, ‘XDR’ or ‘PDR’ in that order.</p>
<p>The next example uses the <code>example_isolates</code> data set. This is a data set included with this package and contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practice AMR analysis. If we test the MDR/XDR/PDR guideline on this data set, we get:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(dplyr) <span class="co"># to support pipes: %&gt;%</span></span></code></pre></div>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a>example_isolates <span class="op">%&gt;%</span><span class="st"> </span></span>
<span id="cb2-2"><a href="#cb2-2"></a><span class="st"> </span><span class="kw"><a href="../reference/mdro.html">mdro</a></span>() <span class="op">%&gt;%</span><span class="st"> </span></span>
<span id="cb2-3"><a href="#cb2-3"></a><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>() <span class="co"># show frequency table of the result</span></span>
<span id="cb2-4"><a href="#cb2-4"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `mo` as input for `col_mo`.</span></span>
<span id="cb2-5"><a href="#cb2-5"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Auto-guessing columns suitable for analysis...OK.</span></span>
<span id="cb2-6"><a href="#cb2-6"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Reliability will be improved if these antimicrobial results would be available too: SAM (ampicillin/sulbactam), ATM (aztreonam), CTT (cefotetan), CPT (ceftaroline), DAP (daptomycin), DOR (doripenem), ETP (ertapenem), FUS (fusidic acid), GEH (gentamicin-high), LVX (levofloxacin), MNO (minocycline), NET (netilmicin), PLB (polymyxin B), QDA (quinupristin/dalfopristin), STH (streptomycin-high), TLV (telavancin), TCC (ticarcillin/clavulanic acid)</span></span>
<span id="cb2-7"><a href="#cb2-7"></a><span class="co"># Warning in mdro(.): NA introduced for isolates where the available percentage of</span></span>
<span id="cb2-8"><a href="#cb2-8"></a><span class="co"># antimicrobial classes was below 50% (set with `pct_required_classes`)</span></span></code></pre></div>
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>) <span class="co"># to support pipes: %&gt;%</span></pre></body></html></div>
<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">example_isolates</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="../reference/mdro.html">mdro</a></span>() <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>() <span class="co"># show frequency table of the result</span>
<span class="co"># NOTE: Using column `mo` as input for `col_mo`.</span>
<span class="co"># NOTE: Auto-guessing columns suitable for analysis...OK.</span>
<span class="co"># NOTE: Reliability will be improved if these antimicrobial results would be available too: SAM (ampicillin/sulbactam), ATM (aztreonam), CTT (cefotetan), CPT (ceftaroline), DAP (daptomycin), DOR (doripenem), ETP (ertapenem), FUS (fusidic acid), GEH (gentamicin-high), LVX (levofloxacin), MNO (minocycline), NET (netilmicin), PLB (polymyxin B), QDA (quinupristin/dalfopristin), STH (streptomycin-high), TLV (telavancin), TCC (ticarcillin/clavulanic acid)</span>
<span class="co"># Warning in mdro(.): NA introduced for isolates where the available percentage of</span>
<span class="co"># antimicrobial classes was below 50% (set with `pct_required_classes`)</span></pre></body></html></div>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered (numeric)<br>
Length: 2,000<br>
@@ -277,55 +278,55 @@ Unique: 2</p>
</tbody>
</table>
<p>For another example, I will create a data set to determine multi-drug resistant TB:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1"></a><span class="co"># a helper function to get a random vector with values S, I and R</span></span>
<span id="cb3-2"><a href="#cb3-2"></a><span class="co"># with the probabilities 50% - 10% - 40%</span></span>
<span id="cb3-3"><a href="#cb3-3"></a>sample_rsi &lt;-<span class="st"> </span><span class="cf">function</span>() {</span>
<span id="cb3-4"><a href="#cb3-4"></a> <span class="kw"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>),</span>
<span id="cb3-5"><a href="#cb3-5"></a> <span class="dt">size =</span> <span class="dv">5000</span>,</span>
<span id="cb3-6"><a href="#cb3-6"></a> <span class="dt">prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.1</span>, <span class="fl">0.4</span>),</span>
<span id="cb3-7"><a href="#cb3-7"></a> <span class="dt">replace =</span> <span class="ot">TRUE</span>)</span>
<span id="cb3-8"><a href="#cb3-8"></a>}</span>
<span id="cb3-9"><a href="#cb3-9"></a></span>
<span id="cb3-10"><a href="#cb3-10"></a>my_TB_data &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="dt">rifampicin =</span> <span class="kw">sample_rsi</span>(),</span>
<span id="cb3-11"><a href="#cb3-11"></a> <span class="dt">isoniazid =</span> <span class="kw">sample_rsi</span>(),</span>
<span id="cb3-12"><a href="#cb3-12"></a> <span class="dt">gatifloxacin =</span> <span class="kw">sample_rsi</span>(),</span>
<span id="cb3-13"><a href="#cb3-13"></a> <span class="dt">ethambutol =</span> <span class="kw">sample_rsi</span>(),</span>
<span id="cb3-14"><a href="#cb3-14"></a> <span class="dt">pyrazinamide =</span> <span class="kw">sample_rsi</span>(),</span>
<span id="cb3-15"><a href="#cb3-15"></a> <span class="dt">moxifloxacin =</span> <span class="kw">sample_rsi</span>(),</span>
<span id="cb3-16"><a href="#cb3-16"></a> <span class="dt">kanamycin =</span> <span class="kw">sample_rsi</span>())</span></code></pre></div>
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="co"># a helper function to get a random vector with values S, I and R</span>
<span class="co"># with the probabilities 50% - 10% - 40%</span>
<span class="no">sample_rsi</span> <span class="kw">&lt;-</span> <span class="kw">function</span>() {
<span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>),
<span class="kw">size</span> <span class="kw">=</span> <span class="fl">5000</span>,
<span class="kw">prob</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.1</span>, <span class="fl">0.4</span>),
<span class="kw">replace</span> <span class="kw">=</span> <span class="fl">TRUE</span>)
}
<span class="no">my_TB_data</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="kw">rifampicin</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">isoniazid</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">gatifloxacin</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">ethambutol</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">pyrazinamide</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">moxifloxacin</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">kanamycin</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>())</pre></body></html></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="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1"></a>my_TB_data &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="dt">RIF =</span> <span class="kw">sample_rsi</span>(),</span>
<span id="cb4-2"><a href="#cb4-2"></a> <span class="dt">INH =</span> <span class="kw">sample_rsi</span>(),</span>
<span id="cb4-3"><a href="#cb4-3"></a> <span class="dt">GAT =</span> <span class="kw">sample_rsi</span>(),</span>
<span id="cb4-4"><a href="#cb4-4"></a> <span class="dt">ETH =</span> <span class="kw">sample_rsi</span>(),</span>
<span id="cb4-5"><a href="#cb4-5"></a> <span class="dt">PZA =</span> <span class="kw">sample_rsi</span>(),</span>
<span id="cb4-6"><a href="#cb4-6"></a> <span class="dt">MFX =</span> <span class="kw">sample_rsi</span>(),</span>
<span id="cb4-7"><a href="#cb4-7"></a> <span class="dt">KAN =</span> <span class="kw">sample_rsi</span>())</span></code></pre></div>
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="no">my_TB_data</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="kw">RIF</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">INH</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">GAT</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">ETH</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">PZA</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">MFX</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">KAN</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>())</pre></body></html></div>
<p>The data set now looks like this:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1"></a><span class="kw"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(my_TB_data)</span>
<span id="cb5-2"><a href="#cb5-2"></a><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span id="cb5-3"><a href="#cb5-3"></a><span class="co"># 1 S R R I R R</span></span>
<span id="cb5-4"><a href="#cb5-4"></a><span class="co"># 2 I R R R S R</span></span>
<span id="cb5-5"><a href="#cb5-5"></a><span class="co"># 3 R R R S R S</span></span>
<span id="cb5-6"><a href="#cb5-6"></a><span class="co"># 4 S S R R R S</span></span>
<span id="cb5-7"><a href="#cb5-7"></a><span class="co"># 5 S R S R S S</span></span>
<span id="cb5-8"><a href="#cb5-8"></a><span class="co"># 6 R S S S R S</span></span>
<span id="cb5-9"><a href="#cb5-9"></a><span class="co"># kanamycin</span></span>
<span id="cb5-10"><a href="#cb5-10"></a><span class="co"># 1 S</span></span>
<span id="cb5-11"><a href="#cb5-11"></a><span class="co"># 2 S</span></span>
<span id="cb5-12"><a href="#cb5-12"></a><span class="co"># 3 R</span></span>
<span id="cb5-13"><a href="#cb5-13"></a><span class="co"># 4 R</span></span>
<span id="cb5-14"><a href="#cb5-14"></a><span class="co"># 5 R</span></span>
<span id="cb5-15"><a href="#cb5-15"></a><span class="co"># 6 R</span></span></code></pre></div>
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="no">my_TB_data</span>)
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
<span class="co"># 1 S I R R S I</span>
<span class="co"># 2 R S S R S S</span>
<span class="co"># 3 R S S R R I</span>
<span class="co"># 4 I S S R R S</span>
<span class="co"># 5 R R S R I R</span>
<span class="co"># 6 R I S I R S</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 S</span>
<span class="co"># 2 S</span>
<span class="co"># 3 R</span>
<span class="co"># 4 S</span>
<span class="co"># 5 I</span>
<span class="co"># 6 I</span></pre></body></html></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1"></a><span class="kw"><a href="../reference/mdro.html">mdro</a></span>(my_TB_data, <span class="dt">guideline =</span> <span class="st">"TB"</span>)</span></code></pre></div>
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="fu"><a href="../reference/mdro.html">mdro</a></span>(<span class="no">my_TB_data</span>, <span class="kw">guideline</span> <span class="kw">=</span> <span class="st">"TB"</span>)</pre></body></html></div>
<p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1"></a>my_TB_data<span class="op">$</span>mdr &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mdro.html">mdr_tb</a></span>(my_TB_data)</span>
<span id="cb7-2"><a href="#cb7-2"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span></span>
<span id="cb7-3"><a href="#cb7-3"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Auto-guessing columns suitable for analysis...OK.</span></span>
<span id="cb7-4"><a href="#cb7-4"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Reliability will be improved if these antimicrobial results would be available too: CAP (capreomycin), RIB (rifabutin), RFP (rifapentine)</span></span></code></pre></div>
<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="no">my_TB_data</span>$<span class="no">mdr</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">mdr_tb</a></span>(<span class="no">my_TB_data</span>)
<span class="co"># NOTE: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span>
<span class="co"># NOTE: Auto-guessing columns suitable for analysis...OK.</span>
<span class="co"># NOTE: Reliability will be improved if these antimicrobial results would be available too: CAP (capreomycin), RIB (rifabutin), RFP (rifapentine)</span></pre></body></html></div>
<p>Create a frequency table of the results:</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1"></a><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(my_TB_data<span class="op">$</span>mdr)</span></code></pre></div>
<div class="sourceCode" id="cb8"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">my_TB_data</span>$<span class="no">mdr</span>)</pre></body></html></div>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered (numeric)<br>
Length: 5,000<br>
@@ -345,40 +346,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3312</td>
<td align="right">66.24%</td>
<td align="right">3312</td>
<td align="right">66.24%</td>
<td align="right">3310</td>
<td align="right">66.20%</td>
<td align="right">3310</td>
<td align="right">66.20%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">634</td>
<td align="right">12.68%</td>
<td align="right">3946</td>
<td align="right">78.92%</td>
<td align="right">637</td>
<td align="right">12.74%</td>
<td align="right">3947</td>
<td align="right">78.94%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">554</td>
<td align="right">11.08%</td>
<td align="right">4500</td>
<td align="right">90.00%</td>
<td align="right">569</td>
<td align="right">11.38%</td>
<td align="right">4516</td>
<td align="right">90.32%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">291</td>
<td align="right">5.82%</td>
<td align="right">4791</td>
<td align="right">95.82%</td>
<td align="right">283</td>
<td align="right">5.66%</td>
<td align="right">4799</td>
<td align="right">95.98%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">209</td>
<td align="right">4.18%</td>
<td align="right">201</td>
<td align="right">4.02%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>
@@ -400,7 +401,7 @@ Unique: 5</p>
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<h1>How to import data from SPSS / SAS / Stata</h1>
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">17 March 2020</h4>
<h4 class="date">15 April 2020</h4>
<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="hidden name"><code>SPSS.Rmd</code></div>
</div>
@@ -239,39 +240,38 @@
</li>
</ul>
<p>To demonstrate the first point:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a><span class="co"># not all values are valid MIC values:</span></span>
<span id="cb1-2"><a href="#cb1-2"></a><span class="kw"><a href="../reference/as.mic.html">as.mic</a></span>(<span class="fl">0.125</span>)</span>
<span id="cb1-3"><a href="#cb1-3"></a><span class="co"># Class 'mic'</span></span>
<span id="cb1-4"><a href="#cb1-4"></a><span class="co"># [1] 0.125</span></span>
<span id="cb1-5"><a href="#cb1-5"></a><span class="kw"><a href="../reference/as.mic.html">as.mic</a></span>(<span class="st">"testvalue"</span>)</span>
<span id="cb1-6"><a href="#cb1-6"></a><span class="co"># Class 'mic'</span></span>
<span id="cb1-7"><a href="#cb1-7"></a><span class="co"># [1] &lt;NA&gt;</span></span>
<span id="cb1-8"><a href="#cb1-8"></a></span>
<span id="cb1-9"><a href="#cb1-9"></a><span class="co"># the Gram stain is avaiable for all bacteria:</span></span>
<span id="cb1-10"><a href="#cb1-10"></a><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</span>
<span id="cb1-11"><a href="#cb1-11"></a><span class="co"># [1] "Gram-negative"</span></span>
<span id="cb1-12"><a href="#cb1-12"></a></span>
<span id="cb1-13"><a href="#cb1-13"></a><span class="co"># Klebsiella is intrinsic resistant to amoxicllin, according to EUCAST:</span></span>
<span id="cb1-14"><a href="#cb1-14"></a>klebsiella_test &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="dt">mo =</span> <span class="st">"klebsiella"</span>, </span>
<span id="cb1-15"><a href="#cb1-15"></a> <span class="dt">amox =</span> <span class="st">"S"</span>,</span>
<span id="cb1-16"><a href="#cb1-16"></a> <span class="dt">stringsAsFactors =</span> <span class="ot">FALSE</span>)</span>
<span id="cb1-17"><a href="#cb1-17"></a>klebsiella_test <span class="co"># (our original data)</span></span>
<span id="cb1-18"><a href="#cb1-18"></a><span class="co"># mo amox</span></span>
<span id="cb1-19"><a href="#cb1-19"></a><span class="co"># 1 klebsiella S</span></span>
<span id="cb1-20"><a href="#cb1-20"></a><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>) <span class="co"># (the edited data by EUCAST rules)</span></span>
<span id="cb1-21"><a href="#cb1-21"></a><span class="co"># mo amox</span></span>
<span id="cb1-22"><a href="#cb1-22"></a><span class="co"># 1 klebsiella R</span></span>
<span id="cb1-23"><a href="#cb1-23"></a></span>
<span id="cb1-24"><a href="#cb1-24"></a><span class="co"># hundreds of trade names can be translated to a name, trade name or an ATC code:</span></span>
<span id="cb1-25"><a href="#cb1-25"></a><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="st">"floxapen"</span>)</span>
<span id="cb1-26"><a href="#cb1-26"></a><span class="co"># [1] "Flucloxacillin"</span></span>
<span id="cb1-27"><a href="#cb1-27"></a><span class="kw"><a href="../reference/ab_property.html">ab_tradenames</a></span>(<span class="st">"floxapen"</span>)</span>
<span id="cb1-28"><a href="#cb1-28"></a><span class="co"># [1] "Floxacillin" "FLOXACILLIN" "Floxapen" </span></span>
<span id="cb1-29"><a href="#cb1-29"></a><span class="co"># [4] "Floxapen sodium salt" "Fluclox" "Flucloxacilina" </span></span>
<span id="cb1-30"><a href="#cb1-30"></a><span class="co"># [7] "Flucloxacillin" "Flucloxacilline" "Flucloxacillinum" </span></span>
<span id="cb1-31"><a href="#cb1-31"></a><span class="co"># [10] "Fluorochloroxacillin"</span></span>
<span id="cb1-32"><a href="#cb1-32"></a><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="st">"floxapen"</span>)</span>
<span id="cb1-33"><a href="#cb1-33"></a><span class="co"># [1] "J01CF05"</span></span></code></pre></div>
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="co"># not all values are valid MIC values:</span>
<span class="fu"><a href="../reference/as.mic.html">as.mic</a></span>(<span class="fl">0.125</span>)
<span class="co"># Class 'mic'</span>
<span class="co"># [1] 0.125</span>
<span class="fu"><a href="../reference/as.mic.html">as.mic</a></span>(<span class="st">"testvalue"</span>)
<span class="co"># Class 'mic'</span>
<span class="co"># [1] &lt;NA&gt;</span>
<span class="co"># the Gram stain is avaiable for all bacteria:</span>
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)
<span class="co"># [1] "Gram-negative"</span>
<span class="co"># Klebsiella is intrinsic resistant to amoxicllin, according to EUCAST:</span>
<span class="no">klebsiella_test</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="kw">mo</span> <span class="kw">=</span> <span class="st">"klebsiella"</span>,
<span class="kw">amox</span> <span class="kw">=</span> <span class="st">"S"</span>,
<span class="kw">stringsAsFactors</span> <span class="kw">=</span> <span class="fl">FALSE</span>)
<span class="no">klebsiella_test</span> <span class="co"># (our original data)</span>
<span class="co"># mo amox</span>
<span class="co"># 1 klebsiella S</span>
<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="no">klebsiella_test</span>, <span class="kw">info</span> <span class="kw">=</span> <span class="fl">FALSE</span>) <span class="co"># (the edited data by EUCAST rules)</span>
<span class="co"># mo amox</span>
<span class="co"># 1 klebsiella R</span>
<span class="co"># hundreds of trade names can be translated to a name, trade name or an ATC code:</span>
<span class="fu"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="st">"floxapen"</span>)
<span class="co"># [1] "Flucloxacillin"</span>
<span class="fu"><a href="../reference/ab_property.html">ab_tradenames</a></span>(<span class="st">"floxapen"</span>)
<span class="co"># [1] "floxacillin" "floxapen" "floxapen sodium salt"</span>
<span class="co"># [4] "fluclox" "flucloxacilina" "flucloxacillin" </span>
<span class="co"># [7] "flucloxacilline" "flucloxacillinum" "fluorochloroxacillin"</span>
<span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="st">"floxapen"</span>)
<span class="co"># [1] "J01CF05"</span></pre></body></html></div>
</div>
<div id="import-data-from-spsssasstata" class="section level2">
<h2 class="hasAnchor">
@@ -287,97 +287,97 @@
<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"><span id="cb2-1"><a href="#cb2-1"></a>SPSS_data</span>
<span id="cb2-2"><a href="#cb2-2"></a><span class="co"># # A tibble: 4,203 x 4</span></span>
<span id="cb2-3"><a href="#cb2-3"></a><span class="co"># v001 sex status statusage</span></span>
<span id="cb2-4"><a href="#cb2-4"></a><span class="co"># &lt;dbl&gt; &lt;dbl+lbl&gt; &lt;dbl+lbl&gt; &lt;dbl&gt;</span></span>
<span id="cb2-5"><a href="#cb2-5"></a><span class="co"># 1 10002 1 1 76.6</span></span>
<span id="cb2-6"><a href="#cb2-6"></a><span class="co"># 2 10004 0 1 59.1</span></span>
<span id="cb2-7"><a href="#cb2-7"></a><span class="co"># 3 10005 1 1 54.5</span></span>
<span id="cb2-8"><a href="#cb2-8"></a><span class="co"># 4 10006 1 1 54.1</span></span>
<span id="cb2-9"><a href="#cb2-9"></a><span class="co"># 5 10007 1 1 57.7</span></span>
<span id="cb2-10"><a href="#cb2-10"></a><span class="co"># 6 10008 1 1 62.8</span></span>
<span id="cb2-11"><a href="#cb2-11"></a><span class="co"># 7 10010 0 1 63.7</span></span>
<span id="cb2-12"><a href="#cb2-12"></a><span class="co"># 8 10011 1 1 73.1</span></span>
<span id="cb2-13"><a href="#cb2-13"></a><span class="co"># 9 10017 1 1 56.7</span></span>
<span id="cb2-14"><a href="#cb2-14"></a><span class="co"># 10 10018 0 1 66.6</span></span>
<span id="cb2-15"><a href="#cb2-15"></a><span class="co"># # … with 4,193 more rows</span></span>
<span id="cb2-16"><a href="#cb2-16"></a></span>
<span id="cb2-17"><a href="#cb2-17"></a><span class="kw">as_factor</span>(SPSS_data)</span>
<span id="cb2-18"><a href="#cb2-18"></a><span class="co"># # A tibble: 4,203 x 4</span></span>
<span id="cb2-19"><a href="#cb2-19"></a><span class="co"># v001 sex status statusage</span></span>
<span id="cb2-20"><a href="#cb2-20"></a><span class="co"># &lt;dbl&gt; &lt;fct&gt; &lt;fct&gt; &lt;dbl&gt;</span></span>
<span id="cb2-21"><a href="#cb2-21"></a><span class="co"># 1 10002 Male alive 76.6</span></span>
<span id="cb2-22"><a href="#cb2-22"></a><span class="co"># 2 10004 Female alive 59.1</span></span>
<span id="cb2-23"><a href="#cb2-23"></a><span class="co"># 3 10005 Male alive 54.5</span></span>
<span id="cb2-24"><a href="#cb2-24"></a><span class="co"># 4 10006 Male alive 54.1</span></span>
<span id="cb2-25"><a href="#cb2-25"></a><span class="co"># 5 10007 Male alive 57.7</span></span>
<span id="cb2-26"><a href="#cb2-26"></a><span class="co"># 6 10008 Male alive 62.8</span></span>
<span id="cb2-27"><a href="#cb2-27"></a><span class="co"># 7 10010 Female alive 63.7</span></span>
<span id="cb2-28"><a href="#cb2-28"></a><span class="co"># 8 10011 Male alive 73.1</span></span>
<span id="cb2-29"><a href="#cb2-29"></a><span class="co"># 9 10017 Male alive 56.7</span></span>
<span id="cb2-30"><a href="#cb2-30"></a><span class="co"># 10 10018 Female alive 66.6</span></span>
<span id="cb2-31"><a href="#cb2-31"></a><span class="co"># # … with 4,193 more rows</span></span></code></pre></div>
<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">SPSS_data</span>
<span class="co"># # A tibble: 4,203 x 4</span>
<span class="co"># v001 sex status statusage</span>
<span class="co"># &lt;dbl&gt; &lt;dbl+lbl&gt; &lt;dbl+lbl&gt; &lt;dbl&gt;</span>
<span class="co"># 1 10002 1 1 76.6</span>
<span class="co"># 2 10004 0 1 59.1</span>
<span class="co"># 3 10005 1 1 54.5</span>
<span class="co"># 4 10006 1 1 54.1</span>
<span class="co"># 5 10007 1 1 57.7</span>
<span class="co"># 6 10008 1 1 62.8</span>
<span class="co"># 7 10010 0 1 63.7</span>
<span class="co"># 8 10011 1 1 73.1</span>
<span class="co"># 9 10017 1 1 56.7</span>
<span class="co"># 10 10018 0 1 66.6</span>
<span class="co"># # … with 4,193 more rows</span>
<span class="fu">as_factor</span>(<span class="no">SPSS_data</span>)
<span class="co"># # A tibble: 4,203 x 4</span>
<span class="co"># v001 sex status statusage</span>
<span class="co"># &lt;dbl&gt; &lt;fct&gt; &lt;fct&gt; &lt;dbl&gt;</span>
<span class="co"># 1 10002 Male alive 76.6</span>
<span class="co"># 2 10004 Female alive 59.1</span>
<span class="co"># 3 10005 Male alive 54.5</span>
<span class="co"># 4 10006 Male alive 54.1</span>
<span class="co"># 5 10007 Male alive 57.7</span>
<span class="co"># 6 10008 Male alive 62.8</span>
<span class="co"># 7 10010 Female alive 63.7</span>
<span class="co"># 8 10011 Male alive 73.1</span>
<span class="co"># 9 10017 Male alive 56.7</span>
<span class="co"># 10 10018 Female alive 66.6</span>
<span class="co"># # … with 4,193 more rows</span></pre></body></html></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"><span id="cb3-1"><a href="#cb3-1"></a><span class="co"># download and install the latest version:</span></span>
<span id="cb3-2"><a href="#cb3-2"></a><span class="kw"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"haven"</span>)</span>
<span id="cb3-3"><a href="#cb3-3"></a><span class="co"># load the package you just installed:</span></span>
<span id="cb3-4"><a href="#cb3-4"></a><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(haven) </span></code></pre></div>
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="co"># download and install the latest version:</span>
<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"haven"</span>)
<span class="co"># load the package you just installed:</span>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">haven</span>)</pre></body></html></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"><span id="cb4-1"><a href="#cb4-1"></a><span class="co"># read any SPSS file based on file extension (best way):</span></span>
<span id="cb4-2"><a href="#cb4-2"></a><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>)</span>
<span id="cb4-3"><a href="#cb4-3"></a></span>
<span id="cb4-4"><a href="#cb4-4"></a><span class="co"># read .sav or .zsav file:</span></span>
<span id="cb4-5"><a href="#cb4-5"></a><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>)</span>
<span id="cb4-6"><a href="#cb4-6"></a></span>
<span id="cb4-7"><a href="#cb4-7"></a><span class="co"># read .por file:</span></span>
<span id="cb4-8"><a href="#cb4-8"></a><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>)</span></code></pre></div>
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="co"># read any SPSS file based on file extension (best way):</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_spss</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)
<span class="co"># read .sav or .zsav file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_sav</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)
<span class="co"># read .por file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_por</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)</pre></body></html></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"><span id="cb5-1"><a href="#cb5-1"></a><span class="co"># save as .sav file:</span></span>
<span id="cb5-2"><a href="#cb5-2"></a><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>
<span id="cb5-3"><a href="#cb5-3"></a></span>
<span id="cb5-4"><a href="#cb5-4"></a><span class="co"># save as compressed .zsav file:</span></span>
<span id="cb5-5"><a href="#cb5-5"></a><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>)</span></code></pre></div>
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="co"># save as .sav file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span>(<span class="kw">data</span> <span class="kw">=</span> <span class="no">yourdata</span>, <span class="kw">path</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)
<span class="co"># save as compressed .zsav file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span>(<span class="kw">data</span> <span class="kw">=</span> <span class="no">yourdata</span>, <span class="kw">path</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>, <span class="kw">compress</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></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"><span id="cb6-1"><a href="#cb6-1"></a><span class="co"># read .sas7bdat + .sas7bcat files:</span></span>
<span id="cb6-2"><a href="#cb6-2"></a><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>)</span>
<span id="cb6-3"><a href="#cb6-3"></a></span>
<span id="cb6-4"><a href="#cb6-4"></a><span class="co"># read SAS transport files (version 5 and version 8):</span></span>
<span id="cb6-5"><a href="#cb6-5"></a><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>)</span></code></pre></div>
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="co"># read .sas7bdat + .sas7bcat files:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html">read_sas</a></span>(<span class="kw">data_file</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>, <span class="kw">catalog_file</span> <span class="kw">=</span> <span class="kw">NULL</span>)
<span class="co"># read SAS transport files (version 5 and version 8):</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html">read_xpt</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)</pre></body></html></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"><span id="cb7-1"><a href="#cb7-1"></a><span class="co"># save as regular SAS file:</span></span>
<span id="cb7-2"><a href="#cb7-2"></a><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>)</span>
<span id="cb7-3"><a href="#cb7-3"></a></span>
<span id="cb7-4"><a href="#cb7-4"></a><span class="co"># the SAS transport format is an open format </span></span>
<span id="cb7-5"><a href="#cb7-5"></a><span class="co"># (required for submission of the data to the FDA)</span></span>
<span id="cb7-6"><a href="#cb7-6"></a><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>)</span></code></pre></div>
<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="co"># save as regular SAS file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html">write_sas</a></span>(<span class="kw">data</span> <span class="kw">=</span> <span class="no">yourdata</span>, <span class="kw">path</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)
<span class="co"># the SAS transport format is an open format </span>
<span class="co"># (required for submission of the data to the FDA)</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html">write_xpt</a></span>(<span class="kw">data</span> <span class="kw">=</span> <span class="no">yourdata</span>, <span class="kw">path</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>, <span class="kw">version</span> <span class="kw">=</span> <span class="fl">8</span>)</pre></body></html></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"><span id="cb8-1"><a href="#cb8-1"></a><span class="co"># read .dta file:</span></span>
<span id="cb8-2"><a href="#cb8-2"></a><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>)</span>
<span id="cb8-3"><a href="#cb8-3"></a></span>
<span id="cb8-4"><a href="#cb8-4"></a><span class="co"># works exactly the same:</span></span>
<span id="cb8-5"><a href="#cb8-5"></a><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>)</span></code></pre></div>
<div class="sourceCode" id="cb8"><html><body><pre class="r"><span class="co"># read .dta file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_stata</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"/path/to/file"</span>)
<span class="co"># works exactly the same:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_dta</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"/path/to/file"</span>)</pre></body></html></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"><span id="cb9-1"><a href="#cb9-1"></a><span class="co"># save as .dta file, Stata version 14:</span></span>
<span id="cb9-2"><a href="#cb9-2"></a><span class="co"># (supports Stata v8 until v15 at the time of writing)</span></span>
<span id="cb9-3"><a href="#cb9-3"></a><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>)</span></code></pre></div>
<div class="sourceCode" id="cb9"><html><body><pre class="r"><span class="co"># save as .dta file, Stata version 14:</span>
<span class="co"># (supports Stata v8 until v15 at the time of writing)</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">write_dta</a></span>(<span class="kw">data</span> <span class="kw">=</span> <span class="no">yourdata</span>, <span class="kw">path</span> <span class="kw">=</span> <span class="st">"/path/to/file"</span>, <span class="kw">version</span> <span class="kw">=</span> <span class="fl">14</span>)</pre></body></html></div>
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@@ -385,16 +385,9 @@
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@@ -182,12 +183,12 @@
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<h1>How to work with WHONET data</h1>
<h1 data-toc-skip>How to work with WHONET data</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">17 March 2020</h4>
<h4 class="date">15 April 2020</h4>
<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/WHONET.Rmd"><code>vignettes/WHONET.Rmd</code></a></small>
<div class="hidden name"><code>WHONET.Rmd</code></div>
</div>
@@ -199,33 +200,33 @@
<a href="#import-of-data" class="anchor"></a>Import of data</h3>
<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"><span id="cb1-1"><a href="#cb1-1"></a><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(readxl)</span>
<span id="cb1-2"><a href="#cb1-2"></a>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>)</span></code></pre></div>
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">readxl</span>)
<span class="no">data</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://readxl.tidyverse.org/reference/read_excel.html">read_excel</a></span>(<span class="kw">path</span> <span class="kw">=</span> <span class="st">"path/to/your/file.xlsx"</span>)</pre></body></html></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 level3">
<h3 class="hasAnchor">
<a href="#preparation" class="anchor"></a>Preparation</h3>
<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"><span id="cb2-1"><a href="#cb2-1"></a><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(dplyr) <span class="co"># part of tidyverse</span></span>
<span id="cb2-2"><a href="#cb2-2"></a><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(ggplot2) <span class="co"># part of tidyverse</span></span>
<span id="cb2-3"><a href="#cb2-3"></a><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(AMR) <span class="co"># this package</span></span></code></pre></div>
<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>) <span class="co"># part of tidyverse</span>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">ggplot2</span>) <span class="co"># part of tidyverse</span>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">AMR</span>) <span class="co"># this package</span></pre></body></html></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/catalogue_of_life">our Catalogue of Life reference data set</a>, which contains all ~70,000 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"><span id="cb3-1"><a href="#cb3-1"></a><span class="co"># transform variables</span></span>
<span id="cb3-2"><a href="#cb3-2"></a>data &lt;-<span class="st"> </span>WHONET <span class="op">%&gt;%</span></span>
<span id="cb3-3"><a href="#cb3-3"></a><span class="st"> </span><span class="co"># get microbial ID based on given organism</span></span>
<span id="cb3-4"><a href="#cb3-4"></a><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></span>
<span id="cb3-5"><a href="#cb3-5"></a><span class="st"> </span><span class="co"># transform everything from "AMP_ND10" to "CIP_EE" to the new `rsi` class</span></span>
<span id="cb3-6"><a href="#cb3-6"></a><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)</span></code></pre></div>
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="co"># transform variables</span>
<span class="no">data</span> <span class="kw">&lt;-</span> <span class="no">WHONET</span> <span class="kw">%&gt;%</span>
<span class="co"># get microbial ID based on given organism</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="kw">mo</span> <span class="kw">=</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="no">Organism</span>)) <span class="kw">%&gt;%</span>
<span class="co"># transform everything from "AMP_ND10" to "CIP_EE" to the new `rsi` class</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(<span class="no">AMP_ND10</span>:<span class="no">CIP_EE</span>), <span class="no">as.rsi</span>)</pre></body></html></div>
<p>No errors or warnings, so all values are transformed succesfully.</p>
<p>We also created a package dedicated to data cleaning and checking, called the <code>cleaner</code> package. It gets automatically installed with the <code>AMR</code> package. For its <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function to create frequency tables, you don’t even need to load it yourself as it is available through the <code>AMR</code> package as well.</p>
<p>So let’s check our data, with a couple of frequency tables:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1"></a><span class="co"># our newly created `mo` variable, put in the mo_name() function</span></span>
<span id="cb4-2"><a href="#cb4-2"></a>data <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(mo), <span class="dt">nmax =</span> <span class="dv">10</span>)</span></code></pre></div>
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="co"># our newly created `mo` variable, put in the mo_name() function</span>
<span class="no">data</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="no">mo</span>), <span class="kw">nmax</span> <span class="kw">=</span> <span class="fl">10</span>)</pre></body></html></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 500<br>
@@ -326,9 +327,9 @@ Longest: 40</p>
</tbody>
</table>
<p>(omitted 29 entries, n = 57 [11.40%])</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1"></a><span class="co"># our transformed antibiotic columns</span></span>
<span id="cb5-2"><a href="#cb5-2"></a><span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span></span>
<span id="cb5-3"><a href="#cb5-3"></a>data <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(AMC_ND2)</span></code></pre></div>
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="co"># our transformed antibiotic columns</span>
<span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span>
<span class="no">data</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">AMC_ND2</span>)</pre></body></html></div>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered &gt; rsi (numeric)<br>
Length: 500<br>
@@ -377,10 +378,10 @@ Unique: 3</p>
<h3 class="hasAnchor">
<a href="#a-first-glimpse-at-results" class="anchor"></a>A first glimpse at results</h3>
<p>An easy <code>ggplot</code> will already give a lot of information, using the included <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> function:</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1"></a>data <span class="op">%&gt;%</span></span>
<span id="cb6-2"><a href="#cb6-2"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(Country) <span class="op">%&gt;%</span></span>
<span id="cb6-3"><a href="#cb6-3"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(Country, AMP_ND2, AMC_ED20, CAZ_ED10, CIP_ED5) <span class="op">%&gt;%</span></span>
<span id="cb6-4"><a href="#cb6-4"></a><span class="st"> </span><span class="kw"><a href="../reference/ggplot_rsi.html">ggplot_rsi</a></span>(<span class="dt">translate_ab =</span> <span class="st">'ab'</span>, <span class="dt">facet =</span> <span class="st">"Country"</span>, <span class="dt">datalabels =</span> <span class="ot">FALSE</span>)</span></code></pre></div>
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="no">data</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="no">Country</span>) <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="no">Country</span>, <span class="no">AMP_ND2</span>, <span class="no">AMC_ED20</span>, <span class="no">CAZ_ED10</span>, <span class="no">CIP_ED5</span>) <span class="kw">%&gt;%</span>
<span class="fu"><a href="../reference/ggplot_rsi.html">ggplot_rsi</a></span>(<span class="kw">translate_ab</span> <span class="kw">=</span> <span class="st">'ab'</span>, <span class="kw">facet</span> <span class="kw">=</span> <span class="st">"Country"</span>, <span class="kw">datalabels</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
<p><img src="WHONET_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
</div>
</div>
@@ -398,7 +399,7 @@ Unique: 3</p>
</div>
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@@ -13,19 +13,20 @@
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<script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script><meta property="og:title" content="Benchmarks">
<meta property="og:description" content="AMR">
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@@ -38,7 +39,7 @@
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<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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
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@@ -182,12 +183,12 @@
</header><div class="row">
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<h1>Benchmarks</h1>
<h1 data-toc-skip>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">17 March 2020</h4>
<h4 class="date">15 April 2020</h4>
<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd"><code>vignettes/benchmarks.Rmd</code></a></small>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
</div>
@@ -196,83 +197,68 @@
<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://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">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"><span id="cb1-1"><a href="#cb1-1"></a><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(microbenchmark)</span>
<span id="cb1-2"><a href="#cb1-2"></a><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(AMR)</span></code></pre></div>
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">microbenchmark</span>)
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">AMR</span>)</pre></body></html></div>
<p>In the next test, we try to ‘coerce’ different input values into the microbial code of <em>Staphylococcus aureus</em>. Coercion is a computational process of forcing output based on an input. For microorganism names, coercing user input to taxonomically valid microorganism names is crucial to ensure correct interpretation and to enable grouping based on taxonomic properties.</p>
<p>The actual result is the same every time: it returns its microorganism code <code>B_STPHY_AURS</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"><span id="cb2-1"><a href="#cb2-1"></a>S.aureus &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(</span>
<span id="cb2-2"><a href="#cb2-2"></a> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"sau"</span>), <span class="co"># WHONET code</span></span>
<span id="cb2-3"><a href="#cb2-3"></a> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"stau"</span>),</span>
<span id="cb2-4"><a href="#cb2-4"></a> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"STAU"</span>),</span>
<span id="cb2-5"><a href="#cb2-5"></a> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"staaur"</span>),</span>
<span id="cb2-6"><a href="#cb2-6"></a> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"STAAUR"</span>),</span>
<span id="cb2-7"><a href="#cb2-7"></a> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. aureus"</span>),</span>
<span id="cb2-8"><a href="#cb2-8"></a> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S aureus"</span>),</span>
<span id="cb2-9"><a href="#cb2-9"></a> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus"</span>), <span class="co"># official taxonomic name</span></span>
<span id="cb2-10"><a href="#cb2-10"></a> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus (MRSA)"</span>), <span class="co"># additional text</span></span>
<span id="cb2-11"><a href="#cb2-11"></a> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Sthafilokkockus aaureuz"</span>), <span class="co"># incorrect spelling</span></span>
<span id="cb2-12"><a href="#cb2-12"></a> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>), <span class="co"># Methicillin Resistant S. aureus</span></span>
<span id="cb2-13"><a href="#cb2-13"></a> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"VISA"</span>), <span class="co"># Vancomycin Intermediate S. aureus</span></span>
<span id="cb2-14"><a href="#cb2-14"></a> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"VRSA"</span>), <span class="co"># Vancomycin Resistant S. aureus</span></span>
<span id="cb2-15"><a href="#cb2-15"></a> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="dv">22242419</span>), <span class="co"># Catalogue of Life ID</span></span>
<span id="cb2-16"><a href="#cb2-16"></a> <span class="dt">times =</span> <span class="dv">10</span>)</span>
<span id="cb2-17"><a href="#cb2-17"></a><span class="kw"><a href="https://rdrr.io/r/base/print.html">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>)</span>
<span id="cb2-18"><a href="#cb2-18"></a><span class="co"># Unit: milliseconds</span></span>
<span id="cb2-19"><a href="#cb2-19"></a><span class="co"># expr min lq mean median uq max</span></span>
<span id="cb2-20"><a href="#cb2-20"></a><span class="co"># as.mo("sau") 9.1 9.5 12.0 9.8 10.0 34.0</span></span>
<span id="cb2-21"><a href="#cb2-21"></a><span class="co"># as.mo("stau") 38.0 41.0 55.0 41.0 42.0 160.0</span></span>
<span id="cb2-22"><a href="#cb2-22"></a><span class="co"># as.mo("STAU") 41.0 41.0 50.0 44.0 63.0 67.0</span></span>
<span id="cb2-23"><a href="#cb2-23"></a><span class="co"># as.mo("staaur") 8.6 8.8 9.4 9.4 9.6 10.0</span></span>
<span id="cb2-24"><a href="#cb2-24"></a><span class="co"># as.mo("STAAUR") 8.6 8.8 12.0 9.3 9.8 37.0</span></span>
<span id="cb2-25"><a href="#cb2-25"></a><span class="co"># as.mo("S. aureus") 14.0 15.0 51.0 27.0 43.0 250.0</span></span>
<span id="cb2-26"><a href="#cb2-26"></a><span class="co"># as.mo("S aureus") 14.0 15.0 16.0 15.0 16.0 18.0</span></span>
<span id="cb2-27"><a href="#cb2-27"></a><span class="co"># as.mo("Staphylococcus aureus") 5.1 5.3 5.7 5.5 6.0 6.6</span></span>
<span id="cb2-28"><a href="#cb2-28"></a><span class="co"># as.mo("Staphylococcus aureus (MRSA)") 640.0 670.0 700.0 690.0 730.0 760.0</span></span>
<span id="cb2-29"><a href="#cb2-29"></a><span class="co"># as.mo("Sthafilokkockus aaureuz") 370.0 380.0 420.0 400.0 440.0 510.0</span></span>
<span id="cb2-30"><a href="#cb2-30"></a><span class="co"># as.mo("MRSA") 8.6 8.7 11.0 9.1 9.6 32.0</span></span>
<span id="cb2-31"><a href="#cb2-31"></a><span class="co"># as.mo("VISA") 24.0 25.0 38.0 38.0 50.0 53.0</span></span>
<span id="cb2-32"><a href="#cb2-32"></a><span class="co"># as.mo("VRSA") 24.0 25.0 49.0 37.0 52.0 150.0</span></span>
<span id="cb2-33"><a href="#cb2-33"></a><span class="co"># as.mo(22242419) 130.0 140.0 150.0 140.0 160.0 160.0</span></span>
<span id="cb2-34"><a href="#cb2-34"></a><span class="co"># neval</span></span>
<span id="cb2-35"><a href="#cb2-35"></a><span class="co"># 10</span></span>
<span id="cb2-36"><a href="#cb2-36"></a><span class="co"># 10</span></span>
<span id="cb2-37"><a href="#cb2-37"></a><span class="co"># 10</span></span>
<span id="cb2-38"><a href="#cb2-38"></a><span class="co"># 10</span></span>
<span id="cb2-39"><a href="#cb2-39"></a><span class="co"># 10</span></span>
<span id="cb2-40"><a href="#cb2-40"></a><span class="co"># 10</span></span>
<span id="cb2-41"><a href="#cb2-41"></a><span class="co"># 10</span></span>
<span id="cb2-42"><a href="#cb2-42"></a><span class="co"># 10</span></span>
<span id="cb2-43"><a href="#cb2-43"></a><span class="co"># 10</span></span>
<span id="cb2-44"><a href="#cb2-44"></a><span class="co"># 10</span></span>
<span id="cb2-45"><a href="#cb2-45"></a><span class="co"># 10</span></span>
<span id="cb2-46"><a href="#cb2-46"></a><span class="co"># 10</span></span>
<span id="cb2-47"><a href="#cb2-47"></a><span class="co"># 10</span></span>
<span id="cb2-48"><a href="#cb2-48"></a><span class="co"># 10</span></span></code></pre></div>
<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">S.aureus</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"sau"</span>), <span class="co"># WHONET code</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"stau"</span>),
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"STAU"</span>),
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"staaur"</span>),
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"STAAUR"</span>),
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. aureus"</span>),
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S aureus"</span>),
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus"</span>), <span class="co"># official taxonomic name</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus (MRSA)"</span>), <span class="co"># additional text</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Sthafilokkockus aaureuz"</span>), <span class="co"># incorrect spelling</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>), <span class="co"># Methicillin Resistant S. aureus</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"VISA"</span>), <span class="co"># Vancomycin Intermediate S. aureus</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"VRSA"</span>), <span class="co"># Vancomycin Resistant S. aureus</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="fl">22242419</span>), <span class="co"># Catalogue of Life ID</span>
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">S.aureus</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">2</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 10.0 11.0 11 11.0 11.0 11 10</span>
<span class="co"># as.mo("stau") 39.0 43.0 54 44.0 70.0 72 10</span>
<span class="co"># as.mo("STAU") 43.0 44.0 52 47.0 68.0 71 10</span>
<span class="co"># as.mo("staaur") 9.6 9.8 11 11.0 12.0 13 10</span>
<span class="co"># as.mo("STAAUR") 9.6 11.0 17 11.0 11.0 45 10</span>
<span class="co"># as.mo("S. aureus") 15.0 17.0 26 18.0 43.0 50 10</span>
<span class="co"># as.mo("S aureus") 16.0 17.0 23 18.0 21.0 44 10</span>
<span class="co"># as.mo("Staphylococcus aureus") 6.0 6.0 12 6.9 7.2 40 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 660.0 740.0 780 780.0 810.0 870 10</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 370.0 430.0 470 450.0 460.0 760 10</span>
<span class="co"># as.mo("MRSA") 9.5 9.6 13 11.0 11.0 35 10</span>
<span class="co"># as.mo("VISA") 25.0 26.0 38 30.0 50.0 58 10</span>
<span class="co"># as.mo("VRSA") 25.0 29.0 55 55.0 56.0 150 10</span>
<span class="co"># as.mo(22242419) 130.0 150.0 160 160.0 170.0 170 10</span></pre></body></html></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="562.5"></p>
<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.</p>
<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside of this is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Methanosarcina semesiae</em> (<code>B_MTHNSR_SEMS</code>), a bug probably never found before in humans:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1"></a>M.semesiae &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"metsem"</span>),</span>
<span id="cb3-2"><a href="#cb3-2"></a> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"METSEM"</span>),</span>
<span id="cb3-3"><a href="#cb3-3"></a> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"M. semesiae"</span>),</span>
<span id="cb3-4"><a href="#cb3-4"></a> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"M. semesiae"</span>),</span>
<span id="cb3-5"><a href="#cb3-5"></a> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Methanosarcina semesiae"</span>),</span>
<span id="cb3-6"><a href="#cb3-6"></a> <span class="dt">times =</span> <span class="dv">10</span>)</span>
<span id="cb3-7"><a href="#cb3-7"></a><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(M.semesiae, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</span>
<span id="cb3-8"><a href="#cb3-8"></a><span class="co"># Unit: milliseconds</span></span>
<span id="cb3-9"><a href="#cb3-9"></a><span class="co"># expr min lq mean median uq</span></span>
<span id="cb3-10"><a href="#cb3-10"></a><span class="co"># as.mo("metsem") 1530.00 1561.000 1618.00 1620.000 1665.000</span></span>
<span id="cb3-11"><a href="#cb3-11"></a><span class="co"># as.mo("METSEM") 1482.00 1523.000 1544.00 1555.000 1567.000</span></span>
<span id="cb3-12"><a href="#cb3-12"></a><span class="co"># as.mo("M. semesiae") 15.01 16.140 27.85 17.080 43.620</span></span>
<span id="cb3-13"><a href="#cb3-13"></a><span class="co"># as.mo("M. semesiae") 15.54 16.200 19.30 16.570 17.040</span></span>
<span id="cb3-14"><a href="#cb3-14"></a><span class="co"># as.mo("Methanosarcina semesiae") 6.05 6.307 9.35 6.437 7.649</span></span>
<span id="cb3-15"><a href="#cb3-15"></a><span class="co"># max neval</span></span>
<span id="cb3-16"><a href="#cb3-16"></a><span class="co"># 1710.00 10</span></span>
<span id="cb3-17"><a href="#cb3-17"></a><span class="co"># 1586.00 10</span></span>
<span id="cb3-18"><a href="#cb3-18"></a><span class="co"># 50.39 10</span></span>
<span id="cb3-19"><a href="#cb3-19"></a><span class="co"># 42.95 10</span></span>
<span id="cb3-20"><a href="#cb3-20"></a><span class="co"># 33.42 10</span></span></code></pre></div>
<p>That takes 5.7 times as much time on average. 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>Methanosarcina semesiae</em>) are always very fast and only take some thousands of seconds to coerce - they are the most probable input from most data sets.</p>
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">M.semesiae</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"metsem"</span>),
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"METSEM"</span>),
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"M. semesiae"</span>),
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"M. semesiae"</span>),
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Methanosarcina semesiae"</span>),
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">M.semesiae</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">4</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq</span>
<span class="co"># as.mo("metsem") 1629.000 1648.000 1694.000 1681.000 1734.000</span>
<span class="co"># as.mo("METSEM") 1577.000 1604.000 1675.000 1685.000 1700.000</span>
<span class="co"># as.mo("M. semesiae") 17.390 17.470 26.150 18.020 43.560</span>
<span class="co"># as.mo("M. semesiae") 17.390 17.880 27.570 18.310 45.910</span>
<span class="co"># as.mo("Methanosarcina semesiae") 6.988 7.067 7.443 7.262 7.733</span>
<span class="co"># max neval</span>
<span class="co"># 1825.000 10</span>
<span class="co"># 1793.000 10</span>
<span class="co"># 48.390 10</span>
<span class="co"># 50.960 10</span>
<span class="co"># 8.381 10</span></pre></body></html></div>
<p>That takes 5.6 times as much time on average. 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>Methanosarcina semesiae</em>) are always very fast and only take some thousands of seconds to coerce - they 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>Methanosarcina semesiae</em> (which is uncommon):</p>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-6-1.png" width="900"></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>
@@ -280,103 +266,103 @@
<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_name()</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="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1"></a><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(dplyr)</span>
<span id="cb4-2"><a href="#cb4-2"></a><span class="co"># take all MO codes from the example_isolates data set</span></span>
<span id="cb4-3"><a href="#cb4-3"></a>x &lt;-<span class="st"> </span>example_isolates<span class="op">$</span>mo <span class="op">%&gt;%</span></span>
<span id="cb4-4"><a href="#cb4-4"></a><span class="st"> </span><span class="co"># keep only the unique ones</span></span>
<span id="cb4-5"><a href="#cb4-5"></a><span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/unique.html">unique</a></span>() <span class="op">%&gt;%</span></span>
<span id="cb4-6"><a href="#cb4-6"></a><span class="st"> </span><span class="co"># pick 50 of them at random</span></span>
<span id="cb4-7"><a href="#cb4-7"></a><span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="dv">50</span>) <span class="op">%&gt;%</span></span>
<span id="cb4-8"><a href="#cb4-8"></a><span class="st"> </span><span class="co"># paste that 10,000 times</span></span>
<span id="cb4-9"><a href="#cb4-9"></a><span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="dv">10000</span>) <span class="op">%&gt;%</span></span>
<span id="cb4-10"><a href="#cb4-10"></a><span class="st"> </span><span class="co"># scramble it</span></span>
<span id="cb4-11"><a href="#cb4-11"></a><span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>()</span>
<span id="cb4-12"><a href="#cb4-12"></a> </span>
<span id="cb4-13"><a href="#cb4-13"></a><span class="co"># got indeed 50 times 10,000 = half a million?</span></span>
<span id="cb4-14"><a href="#cb4-14"></a><span class="kw"><a href="https://rdrr.io/r/base/length.html">length</a></span>(x)</span>
<span id="cb4-15"><a href="#cb4-15"></a><span class="co"># [1] 500000</span></span>
<span id="cb4-16"><a href="#cb4-16"></a></span>
<span id="cb4-17"><a href="#cb4-17"></a><span class="co"># and how many unique values do we have?</span></span>
<span id="cb4-18"><a href="#cb4-18"></a><span class="kw"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(x)</span>
<span id="cb4-19"><a href="#cb4-19"></a><span class="co"># [1] 50</span></span>
<span id="cb4-20"><a href="#cb4-20"></a></span>
<span id="cb4-21"><a href="#cb4-21"></a><span class="co"># now let's see:</span></span>
<span id="cb4-22"><a href="#cb4-22"></a>run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(x),</span>
<span id="cb4-23"><a href="#cb4-23"></a> <span class="dt">times =</span> <span class="dv">100</span>)</span>
<span id="cb4-24"><a href="#cb4-24"></a><span class="kw"><a href="https://rdrr.io/r/base/print.html">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>)</span>
<span id="cb4-25"><a href="#cb4-25"></a><span class="co"># Unit: milliseconds</span></span>
<span id="cb4-26"><a href="#cb4-26"></a><span class="co"># expr min lq mean median uq max neval</span></span>
<span id="cb4-27"><a href="#cb4-27"></a><span class="co"># mo_name(x) 572 626 648 645 666 792 100</span></span></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.64 seconds (644 ms). You only lose time on your unique input values.</p>
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
<span class="co"># take all MO codes from the example_isolates data set</span>
<span class="no">x</span> <span class="kw">&lt;-</span> <span class="no">example_isolates</span>$<span class="no">mo</span> <span class="kw">%&gt;%</span>
<span class="co"># keep only the unique ones</span>
<span class="fu"><a href="https://rdrr.io/r/base/unique.html">unique</a></span>() <span class="kw">%&gt;%</span>
<span class="co"># pick 50 of them at random</span>
<span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="fl">50</span>) <span class="kw">%&gt;%</span>
<span class="co"># paste that 10,000 times</span>
<span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="fl">10000</span>) <span class="kw">%&gt;%</span>
<span class="co"># scramble it</span>
<span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>()
<span class="co"># got indeed 50 times 10,000 = half a million?</span>
<span class="fu"><a href="https://rdrr.io/r/base/length.html">length</a></span>(<span class="no">x</span>)
<span class="co"># [1] 500000</span>
<span class="co"># and how many unique values do we have?</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(<span class="no">x</span>)
<span class="co"># [1] 50</span>
<span class="co"># now let's see:</span>
<span class="no">run_it</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="no">x</span>),
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">100</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># mo_name(x) 1730 1790 1830 1810 1860 2030 100</span></pre></body></html></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.81 seconds (1814 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_name()</a></code>, it almost doesn’t take any time at all (see ‘C’ below):</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1"></a>run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"B_STPHY_AURS"</span>),</span>
<span id="cb5-2"><a href="#cb5-2"></a> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"S. aureus"</span>),</span>
<span id="cb5-3"><a href="#cb5-3"></a> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),</span>
<span id="cb5-4"><a href="#cb5-4"></a> <span class="dt">times =</span> <span class="dv">10</span>)</span>
<span id="cb5-5"><a href="#cb5-5"></a><span class="kw"><a href="https://rdrr.io/r/base/print.html">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>)</span>
<span id="cb5-6"><a href="#cb5-6"></a><span class="co"># Unit: milliseconds</span></span>
<span id="cb5-7"><a href="#cb5-7"></a><span class="co"># expr min lq mean median uq max neval</span></span>
<span id="cb5-8"><a href="#cb5-8"></a><span class="co"># A 6.730 6.860 7.110 6.950 7.170 8.47 10</span></span>
<span id="cb5-9"><a href="#cb5-9"></a><span class="co"># B 14.500 14.800 18.100 15.500 15.900 43.10 10</span></span>
<span id="cb5-10"><a href="#cb5-10"></a><span class="co"># C 0.726 0.753 0.821 0.791 0.882 1.04 10</span></span></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0008 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="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1"></a>run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">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>),</span>
<span id="cb6-2"><a href="#cb6-2"></a> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</span>
<span id="cb6-3"><a href="#cb6-3"></a> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),</span>
<span id="cb6-4"><a href="#cb6-4"></a> <span class="dt">D =</span> <span class="kw"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="st">"Staphylococcaceae"</span>),</span>
<span id="cb6-5"><a href="#cb6-5"></a> <span class="dt">E =</span> <span class="kw"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="st">"Bacillales"</span>),</span>
<span id="cb6-6"><a href="#cb6-6"></a> <span class="dt">F =</span> <span class="kw"><a href="../reference/mo_property.html">mo_class</a></span>(<span class="st">"Bacilli"</span>),</span>
<span id="cb6-7"><a href="#cb6-7"></a> <span class="dt">G =</span> <span class="kw"><a href="../reference/mo_property.html">mo_phylum</a></span>(<span class="st">"Firmicutes"</span>),</span>
<span id="cb6-8"><a href="#cb6-8"></a> <span class="dt">H =</span> <span class="kw"><a href="../reference/mo_property.html">mo_kingdom</a></span>(<span class="st">"Bacteria"</span>),</span>
<span id="cb6-9"><a href="#cb6-9"></a> <span class="dt">times =</span> <span class="dv">10</span>)</span>
<span id="cb6-10"><a href="#cb6-10"></a><span class="kw"><a href="https://rdrr.io/r/base/print.html">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>)</span>
<span id="cb6-11"><a href="#cb6-11"></a><span class="co"># Unit: milliseconds</span></span>
<span id="cb6-12"><a href="#cb6-12"></a><span class="co"># expr min lq mean median uq max neval</span></span>
<span id="cb6-13"><a href="#cb6-13"></a><span class="co"># A 0.348 0.398 0.405 0.404 0.419 0.438 10</span></span>
<span id="cb6-14"><a href="#cb6-14"></a><span class="co"># B 0.407 0.416 0.461 0.426 0.490 0.667 10</span></span>
<span id="cb6-15"><a href="#cb6-15"></a><span class="co"># C 0.701 0.745 0.757 0.754 0.769 0.814 10</span></span>
<span id="cb6-16"><a href="#cb6-16"></a><span class="co"># D 0.435 0.440 0.497 0.464 0.569 0.588 10</span></span>
<span id="cb6-17"><a href="#cb6-17"></a><span class="co"># E 0.351 0.397 0.435 0.419 0.489 0.520 10</span></span>
<span id="cb6-18"><a href="#cb6-18"></a><span class="co"># F 0.358 0.385 0.396 0.393 0.420 0.430 10</span></span>
<span id="cb6-19"><a href="#cb6-19"></a><span class="co"># G 0.322 0.363 0.409 0.401 0.450 0.508 10</span></span>
<span id="cb6-20"><a href="#cb6-20"></a><span class="co"># H 0.340 0.372 0.384 0.385 0.403 0.432 10</span></span></code></pre></div>
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="no">run_it</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="kw">A</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"B_STPHY_AURS"</span>),
<span class="kw">B</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"S. aureus"</span>),
<span class="kw">C</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 7.26 7.390 8.020 7.450 7.500 11.100 10</span>
<span class="co"># B 15.30 15.700 20.500 15.800 17.000 56.300 10</span>
<span class="co"># C 0.58 0.718 0.735 0.726 0.747 0.927 10</span></pre></body></html></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0007 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="cb6"><html><body><pre class="r"><span class="no">run_it</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="kw">A</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),
<span class="kw">B</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),
<span class="kw">C</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),
<span class="kw">D</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="st">"Staphylococcaceae"</span>),
<span class="kw">E</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="st">"Bacillales"</span>),
<span class="kw">F</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_class</a></span>(<span class="st">"Bacilli"</span>),
<span class="kw">G</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_phylum</a></span>(<span class="st">"Firmicutes"</span>),
<span class="kw">H</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span>(<span class="st">"Bacteria"</span>),
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 0.380 0.386 0.397 0.394 0.397 0.434 10</span>
<span class="co"># B 0.413 0.417 0.444 0.424 0.430 0.627 10</span>
<span class="co"># C 0.574 0.680 0.707 0.730 0.735 0.776 10</span>
<span class="co"># D 0.407 0.419 0.430 0.430 0.435 0.470 10</span>
<span class="co"># E 0.374 0.381 0.401 0.397 0.424 0.438 10</span>
<span class="co"># F 0.366 0.380 0.389 0.387 0.395 0.422 10</span>
<span class="co"># G 0.367 0.377 0.388 0.383 0.392 0.420 10</span>
<span class="co"># H 0.368 0.374 0.386 0.382 0.390 0.430 10</span></pre></body></html></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> anyway, 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="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1"></a><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>) <span class="co"># or just mo_name("CoNS") on an English system</span></span>
<span id="cb7-2"><a href="#cb7-2"></a><span class="co"># [1] "Coagulase-negative Staphylococcus (CoNS)"</span></span>
<span id="cb7-3"><a href="#cb7-3"></a></span>
<span id="cb7-4"><a href="#cb7-4"></a><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># or just mo_name("CoNS") on a Spanish system</span></span>
<span id="cb7-5"><a href="#cb7-5"></a><span class="co"># [1] "Staphylococcus coagulasa negativo (SCN)"</span></span>
<span id="cb7-6"><a href="#cb7-6"></a></span>
<span id="cb7-7"><a href="#cb7-7"></a><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"nl"</span>) <span class="co"># or just mo_name("CoNS") on a Dutch system</span></span>
<span id="cb7-8"><a href="#cb7-8"></a><span class="co"># [1] "Coagulase-negatieve Staphylococcus (CNS)"</span></span>
<span id="cb7-9"><a href="#cb7-9"></a></span>
<span id="cb7-10"><a href="#cb7-10"></a>run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="dt">en =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>),</span>
<span id="cb7-11"><a href="#cb7-11"></a> <span class="dt">de =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"de"</span>),</span>
<span id="cb7-12"><a href="#cb7-12"></a> <span class="dt">nl =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"nl"</span>),</span>
<span id="cb7-13"><a href="#cb7-13"></a> <span class="dt">es =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"es"</span>),</span>
<span id="cb7-14"><a href="#cb7-14"></a> <span class="dt">it =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"it"</span>),</span>
<span id="cb7-15"><a href="#cb7-15"></a> <span class="dt">fr =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"fr"</span>),</span>
<span id="cb7-16"><a href="#cb7-16"></a> <span class="dt">pt =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>),</span>
<span id="cb7-17"><a href="#cb7-17"></a> <span class="dt">times =</span> <span class="dv">100</span>)</span>
<span id="cb7-18"><a href="#cb7-18"></a><span class="kw"><a href="https://rdrr.io/r/base/print.html">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>)</span>
<span id="cb7-19"><a href="#cb7-19"></a><span class="co"># Unit: milliseconds</span></span>
<span id="cb7-20"><a href="#cb7-20"></a><span class="co"># expr min lq mean median uq max neval</span></span>
<span id="cb7-21"><a href="#cb7-21"></a><span class="co"># en 25.28 26.99 33.53 27.88 29.51 61.96 100</span></span>
<span id="cb7-22"><a href="#cb7-22"></a><span class="co"># de 26.99 29.27 36.92 30.02 33.09 160.30 100</span></span>
<span id="cb7-23"><a href="#cb7-23"></a><span class="co"># nl 32.37 34.58 40.59 35.88 37.10 67.43 100</span></span>
<span id="cb7-24"><a href="#cb7-24"></a><span class="co"># es 27.54 29.14 34.40 29.88 31.45 61.89 100</span></span>
<span id="cb7-25"><a href="#cb7-25"></a><span class="co"># it 26.77 28.79 34.28 29.73 31.30 69.41 100</span></span>
<span id="cb7-26"><a href="#cb7-26"></a><span class="co"># fr 27.01 28.81 34.96 29.39 30.79 161.10 100</span></span>
<span id="cb7-27"><a href="#cb7-27"></a><span class="co"># pt 26.76 28.85 34.13 29.69 31.74 63.08 100</span></span></code></pre></div>
<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"en"</span>) <span class="co"># or just mo_name("CoNS") on an English system</span>
<span class="co"># [1] "Coagulase-negative Staphylococcus (CoNS)"</span>
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"es"</span>) <span class="co"># or just mo_name("CoNS") on a Spanish system</span>
<span class="co"># [1] "Staphylococcus coagulasa negativo (SCN)"</span>
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"nl"</span>) <span class="co"># or just mo_name("CoNS") on a Dutch system</span>
<span class="co"># [1] "Coagulase-negatieve Staphylococcus (CNS)"</span>
<span class="no">run_it</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="kw">en</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"en"</span>),
<span class="kw">de</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"de"</span>),
<span class="kw">nl</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"nl"</span>),
<span class="kw">es</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"es"</span>),
<span class="kw">it</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"it"</span>),
<span class="kw">fr</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"fr"</span>),
<span class="kw">pt</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"pt"</span>),
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">100</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">4</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 26.72 28.52 32.86 29.31 30.18 69.18 100</span>
<span class="co"># de 27.86 30.67 40.23 31.44 46.42 170.40 100</span>
<span class="co"># nl 34.45 36.94 44.89 37.95 40.54 76.41 100</span>
<span class="co"># es 27.89 30.51 38.46 31.33 32.89 170.10 100</span>
<span class="co"># it 29.15 30.37 35.85 31.04 32.39 65.33 100</span>
<span class="co"># fr 28.18 30.37 35.80 31.11 32.25 78.14 100</span>
<span class="co"># pt 28.23 30.55 36.89 31.32 32.77 67.79 100</span></pre></body></html></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>
@@ -394,7 +380,7 @@
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<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">1.0.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
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<script src="../extra.js"></script><meta property="og:title" content="How to predict antimicrobial resistance">
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@@ -38,7 +39,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -182,12 +183,12 @@
</header><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1>How to predict antimicrobial resistance</h1>
<h1 data-toc-skip>How to predict antimicrobial resistance</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">17 March 2020</h4>
<h4 class="date">15 April 2020</h4>
<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/resistance_predict.Rmd"><code>vignettes/resistance_predict.Rmd</code></a></small>
<div class="hidden name"><code>resistance_predict.Rmd</code></div>
</div>
@@ -199,84 +200,84 @@
<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"><span id="cb1-1"><a href="#cb1-1"></a><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(dplyr)</span>
<span id="cb1-2"><a href="#cb1-2"></a><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(ggplot2)</span>
<span id="cb1-3"><a href="#cb1-3"></a><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(AMR)</span>
<span id="cb1-4"><a href="#cb1-4"></a></span>
<span id="cb1-5"><a href="#cb1-5"></a><span class="co"># (if not yet installed, install with:)</span></span>
<span id="cb1-6"><a href="#cb1-6"></a><span class="co"># install.packages(c("tidyverse", "AMR"))</span></span></code></pre></div>
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">ggplot2</span>)
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">AMR</span>)
<span class="co"># (if not yet installed, install with:)</span>
<span class="co"># install.packages(c("tidyverse", "AMR"))</span></pre></body></html></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"><span id="cb2-1"><a href="#cb2-1"></a><span class="co"># resistance prediction of piperacillin/tazobactam (TZP):</span></span>
<span id="cb2-2"><a href="#cb2-2"></a><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">tbl =</span> example_isolates, <span class="dt">col_date =</span> <span class="st">"date"</span>, <span class="dt">col_ab =</span> <span class="st">"TZP"</span>, <span class="dt">model =</span> <span class="st">"binomial"</span>)</span>
<span id="cb2-3"><a href="#cb2-3"></a></span>
<span id="cb2-4"><a href="#cb2-4"></a><span class="co"># or:</span></span>
<span id="cb2-5"><a href="#cb2-5"></a>example_isolates <span class="op">%&gt;%</span><span class="st"> </span></span>
<span id="cb2-6"><a href="#cb2-6"></a><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>,</span>
<span id="cb2-7"><a href="#cb2-7"></a> model <span class="st">"binomial"</span>)</span>
<span id="cb2-8"><a href="#cb2-8"></a></span>
<span id="cb2-9"><a href="#cb2-9"></a><span class="co"># to bind it to object 'predict_TZP' for example:</span></span>
<span id="cb2-10"><a href="#cb2-10"></a>predict_TZP &lt;-<span class="st"> </span>example_isolates <span class="op">%&gt;%</span><span class="st"> </span></span>
<span id="cb2-11"><a href="#cb2-11"></a><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>,</span>
<span id="cb2-12"><a href="#cb2-12"></a> <span class="dt">model =</span> <span class="st">"binomial"</span>)</span></code></pre></div>
<div class="sourceCode" id="cb2"><html><body><pre class="r"># resistance prediction of piperacillin/tazobactam (TZP):
resistance_predict(tbl = example_isolates, col_date = "date", col_ab = "TZP", model = "binomial")
# or:
example_isolates %&gt;%
resistance_predict(col_ab = "TZP",
model "binomial")
# to bind it to object 'predict_TZP' for example:
predict_TZP %
resistance_predict(col_ab = "TZP",
model = "binomial")</pre></body></html></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`.</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"><span id="cb4-1"><a href="#cb4-1"></a>predict_TZP</span>
<span id="cb4-2"><a href="#cb4-2"></a><span class="co"># year value se_min se_max observations observed estimated</span></span>
<span id="cb4-3"><a href="#cb4-3"></a><span class="co"># 1 2003 0.06250000 NA NA 32 0.06250000 0.05486389</span></span>
<span id="cb4-4"><a href="#cb4-4"></a><span class="co"># 2 2004 0.08536585 NA NA 82 0.08536585 0.06089002</span></span>
<span id="cb4-5"><a href="#cb4-5"></a><span class="co"># 3 2005 0.05000000 NA NA 60 0.05000000 0.06753075</span></span>
<span id="cb4-6"><a href="#cb4-6"></a><span class="co"># 4 2006 0.05084746 NA NA 59 0.05084746 0.07483801</span></span>
<span id="cb4-7"><a href="#cb4-7"></a><span class="co"># 5 2007 0.12121212 NA NA 66 0.12121212 0.08286570</span></span>
<span id="cb4-8"><a href="#cb4-8"></a><span class="co"># 6 2008 0.04166667 NA NA 72 0.04166667 0.09166918</span></span>
<span id="cb4-9"><a href="#cb4-9"></a><span class="co"># 7 2009 0.01639344 NA NA 61 0.01639344 0.10130461</span></span>
<span id="cb4-10"><a href="#cb4-10"></a><span class="co"># 8 2010 0.05660377 NA NA 53 0.05660377 0.11182814</span></span>
<span id="cb4-11"><a href="#cb4-11"></a><span class="co"># 9 2011 0.18279570 NA NA 93 0.18279570 0.12329488</span></span>
<span id="cb4-12"><a href="#cb4-12"></a><span class="co"># 10 2012 0.30769231 NA NA 65 0.30769231 0.13575768</span></span>
<span id="cb4-13"><a href="#cb4-13"></a><span class="co"># 11 2013 0.06896552 NA NA 58 0.06896552 0.14926576</span></span>
<span id="cb4-14"><a href="#cb4-14"></a><span class="co"># 12 2014 0.10000000 NA NA 60 0.10000000 0.16386307</span></span>
<span id="cb4-15"><a href="#cb4-15"></a><span class="co"># 13 2015 0.23636364 NA NA 55 0.23636364 0.17958657</span></span>
<span id="cb4-16"><a href="#cb4-16"></a><span class="co"># 14 2016 0.22619048 NA NA 84 0.22619048 0.19646431</span></span>
<span id="cb4-17"><a href="#cb4-17"></a><span class="co"># 15 2017 0.16279070 NA NA 86 0.16279070 0.21451350</span></span>
<span id="cb4-18"><a href="#cb4-18"></a><span class="co"># 16 2018 0.23373852 0.2021578 0.2653193 NA NA 0.23373852</span></span>
<span id="cb4-19"><a href="#cb4-19"></a><span class="co"># 17 2019 0.25412909 0.2168525 0.2914057 NA NA 0.25412909</span></span>
<span id="cb4-20"><a href="#cb4-20"></a><span class="co"># 18 2020 0.27565854 0.2321869 0.3191302 NA NA 0.27565854</span></span>
<span id="cb4-21"><a href="#cb4-21"></a><span class="co"># 19 2021 0.29828252 0.2481942 0.3483709 NA NA 0.29828252</span></span>
<span id="cb4-22"><a href="#cb4-22"></a><span class="co"># 20 2022 0.32193804 0.2649008 0.3789753 NA NA 0.32193804</span></span>
<span id="cb4-23"><a href="#cb4-23"></a><span class="co"># 21 2023 0.34654311 0.2823269 0.4107593 NA NA 0.34654311</span></span>
<span id="cb4-24"><a href="#cb4-24"></a><span class="co"># 22 2024 0.37199700 0.3004860 0.4435080 NA NA 0.37199700</span></span>
<span id="cb4-25"><a href="#cb4-25"></a><span class="co"># 23 2025 0.39818127 0.3193839 0.4769787 NA NA 0.39818127</span></span>
<span id="cb4-26"><a href="#cb4-26"></a><span class="co"># 24 2026 0.42496142 0.3390173 0.5109056 NA NA 0.42496142</span></span>
<span id="cb4-27"><a href="#cb4-27"></a><span class="co"># 25 2027 0.45218939 0.3593720 0.5450068 NA NA 0.45218939</span></span>
<span id="cb4-28"><a href="#cb4-28"></a><span class="co"># 26 2028 0.47970658 0.3804212 0.5789920 NA NA 0.47970658</span></span>
<span id="cb4-29"><a href="#cb4-29"></a><span class="co"># 27 2029 0.50734745 0.4021241 0.6125708 NA NA 0.50734745</span></span>
<span id="cb4-30"><a href="#cb4-30"></a><span class="co"># 28 2030 0.53494347 0.4244247 0.6454622 NA NA 0.53494347</span></span></code></pre></div>
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="no">predict_TZP</span>
<span class="co"># year value se_min se_max observations observed estimated</span>
<span class="co"># 1 2003 0.06250000 NA NA 32 0.06250000 0.05486389</span>
<span class="co"># 2 2004 0.08536585 NA NA 82 0.08536585 0.06089002</span>
<span class="co"># 3 2005 0.05000000 NA NA 60 0.05000000 0.06753075</span>
<span class="co"># 4 2006 0.05084746 NA NA 59 0.05084746 0.07483801</span>
<span class="co"># 5 2007 0.12121212 NA NA 66 0.12121212 0.08286570</span>
<span class="co"># 6 2008 0.04166667 NA NA 72 0.04166667 0.09166918</span>
<span class="co"># 7 2009 0.01639344 NA NA 61 0.01639344 0.10130461</span>
<span class="co"># 8 2010 0.05660377 NA NA 53 0.05660377 0.11182814</span>
<span class="co"># 9 2011 0.18279570 NA NA 93 0.18279570 0.12329488</span>
<span class="co"># 10 2012 0.30769231 NA NA 65 0.30769231 0.13575768</span>
<span class="co"># 11 2013 0.06896552 NA NA 58 0.06896552 0.14926576</span>
<span class="co"># 12 2014 0.10000000 NA NA 60 0.10000000 0.16386307</span>
<span class="co"># 13 2015 0.23636364 NA NA 55 0.23636364 0.17958657</span>
<span class="co"># 14 2016 0.22619048 NA NA 84 0.22619048 0.19646431</span>
<span class="co"># 15 2017 0.16279070 NA NA 86 0.16279070 0.21451350</span>
<span class="co"># 16 2018 0.23373852 0.2021578 0.2653193 NA NA 0.23373852</span>
<span class="co"># 17 2019 0.25412909 0.2168525 0.2914057 NA NA 0.25412909</span>
<span class="co"># 18 2020 0.27565854 0.2321869 0.3191302 NA NA 0.27565854</span>
<span class="co"># 19 2021 0.29828252 0.2481942 0.3483709 NA NA 0.29828252</span>
<span class="co"># 20 2022 0.32193804 0.2649008 0.3789753 NA NA 0.32193804</span>
<span class="co"># 21 2023 0.34654311 0.2823269 0.4107593 NA NA 0.34654311</span>
<span class="co"># 22 2024 0.37199700 0.3004860 0.4435080 NA NA 0.37199700</span>
<span class="co"># 23 2025 0.39818127 0.3193839 0.4769787 NA NA 0.39818127</span>
<span class="co"># 24 2026 0.42496142 0.3390173 0.5109056 NA NA 0.42496142</span>
<span class="co"># 25 2027 0.45218939 0.3593720 0.5450068 NA NA 0.45218939</span>
<span class="co"># 26 2028 0.47970658 0.3804212 0.5789920 NA NA 0.47970658</span>
<span class="co"># 27 2029 0.50734745 0.4021241 0.6125708 NA NA 0.50734745</span>
<span class="co"># 28 2030 0.53494347 0.4244247 0.6454622 NA NA 0.53494347</span></pre></body></html></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"><span id="cb5-1"><a href="#cb5-1"></a><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(predict_TZP)</span></code></pre></div>
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(<span class="no">predict_TZP</span>)</pre></body></html></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"><span id="cb6-1"><a href="#cb6-1"></a><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(predict_TZP)</span></code></pre></div>
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(<span class="no">predict_TZP</span>)</pre></body></html></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"><span id="cb7-1"><a href="#cb7-1"></a></span>
<span id="cb7-2"><a href="#cb7-2"></a><span class="co"># choose for error bars instead of a ribbon</span></span>
<span id="cb7-3"><a href="#cb7-3"></a><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>)</span></code></pre></div>
<div class="sourceCode" id="cb7"><html><body><pre class="r">
<span class="co"># choose for error bars instead of a ribbon</span>
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(<span class="no">predict_TZP</span>, <span class="kw">ribbon</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></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"><span id="cb8-1"><a href="#cb8-1"></a>example_isolates <span class="op">%&gt;%</span></span>
<span id="cb8-2"><a href="#cb8-2"></a><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></span>
<span id="cb8-3"><a href="#cb8-3"></a><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">"binomial"</span>) <span class="op">%&gt;%</span><span class="st"> </span></span>
<span id="cb8-4"><a href="#cb8-4"></a><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>()</span>
<span id="cb8-5"><a href="#cb8-5"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></span></code></pre></div>
<div class="sourceCode" id="cb8"><html><body><pre class="r"><span class="no">example_isolates</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="no">mo</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="kw">NULL</span>) <span class="kw">==</span> <span class="st">"Gram-positive"</span>) <span class="kw">%&gt;%</span>
<span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="kw">col_ab</span> <span class="kw">=</span> <span class="st">"VAN"</span>, <span class="kw">year_min</span> <span class="kw">=</span> <span class="fl">2010</span>, <span class="kw">info</span> <span class="kw">=</span> <span class="fl">FALSE</span>, <span class="kw">model</span> <span class="kw">=</span> <span class="st">"binomial"</span>) <span class="kw">%&gt;%</span>
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>()
<span class="co"># NOTE: Using column `date` as input for `col_date`.</span></pre></body></html></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 model chosen above 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>
@@ -317,40 +318,34 @@
</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"><span id="cb9-1"><a href="#cb9-1"></a>example_isolates <span class="op">%&gt;%</span></span>
<span id="cb9-2"><a href="#cb9-2"></a><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></span>
<span id="cb9-3"><a href="#cb9-3"></a><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></span>
<span id="cb9-4"><a href="#cb9-4"></a><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>()</span>
<span id="cb9-5"><a href="#cb9-5"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></span></code></pre></div>
<div class="sourceCode" id="cb9"><html><body><pre class="r"><span class="no">example_isolates</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="no">mo</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="kw">NULL</span>) <span class="kw">==</span> <span class="st">"Gram-positive"</span>) <span class="kw">%&gt;%</span>
<span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="kw">col_ab</span> <span class="kw">=</span> <span class="st">"VAN"</span>, <span class="kw">year_min</span> <span class="kw">=</span> <span class="fl">2010</span>, <span class="kw">info</span> <span class="kw">=</span> <span class="fl">FALSE</span>, <span class="kw">model</span> <span class="kw">=</span> <span class="st">"linear"</span>) <span class="kw">%&gt;%</span>
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>()
<span class="co"># NOTE: Using column `date` as input for `col_date`.</span></pre></body></html></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"><span id="cb10-1"><a href="#cb10-1"></a>model &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/attributes.html">attributes</a></span>(predict_TZP)<span class="op">$</span>model</span>
<span id="cb10-2"><a href="#cb10-2"></a></span>
<span id="cb10-3"><a href="#cb10-3"></a><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(model)<span class="op">$</span>family</span>
<span id="cb10-4"><a href="#cb10-4"></a><span class="co"># </span></span>
<span id="cb10-5"><a href="#cb10-5"></a><span class="co"># Family: binomial </span></span>
<span id="cb10-6"><a href="#cb10-6"></a><span class="co"># Link function: logit</span></span>
<span id="cb10-7"><a href="#cb10-7"></a></span>
<span id="cb10-8"><a href="#cb10-8"></a><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(model)<span class="op">$</span>coefficients</span>
<span id="cb10-9"><a href="#cb10-9"></a><span class="co"># Estimate Std. Error z value Pr(&gt;|z|)</span></span>
<span id="cb10-10"><a href="#cb10-10"></a><span class="co"># (Intercept) -224.3987194 48.0335384 -4.671709 2.987038e-06</span></span>
<span id="cb10-11"><a href="#cb10-11"></a><span class="co"># year 0.1106102 0.0238753 4.632831 3.606990e-06</span></span></code></pre></div>
<div class="sourceCode" id="cb10"><html><body><pre class="r"><span class="no">model</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/attributes.html">attributes</a></span>(<span class="no">predict_TZP</span>)$<span class="no">model</span>
<span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">model</span>)$<span class="no">family</span>
<span class="co"># </span>
<span class="co"># Family: binomial </span>
<span class="co"># Link function: logit</span>
<span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">model</span>)$<span class="no">coefficients</span>
<span class="co"># Estimate Std. Error z value Pr(&gt;|z|)</span>
<span class="co"># (Intercept) -224.3987194 48.0335384 -4.671709 2.987038e-06</span>
<span class="co"># year 0.1106102 0.0238753 4.632831 3.606990e-06</span></pre></body></html></div>
</div>
</div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<div id="tocnav">
<h2 class="hasAnchor">
<a href="#tocnav" class="anchor"></a>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#needed-r-packages">Needed R packages</a></li>
<li><a href="#prediction-analysis">Prediction analysis</a></li>
</ul>
<nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2>
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@@ -361,7 +356,7 @@
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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2
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@@ -81,7 +81,7 @@
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<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">1.0.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>

2
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@@ -43,7 +43,7 @@
</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">1.0.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>

13
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@@ -81,7 +81,7 @@
</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">1.0.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -229,14 +229,10 @@
<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1019009" class="section level1">
<h1 class="page-header" data-toc-text="1.0.1.9009">
<a href="#amr-1019009" class="anchor"></a>AMR 1.0.1.9009<small> Unreleased </small>
<div id="amr-110" class="section level1">
<h1 class="page-header" data-toc-text="1.1.0">
<a href="#amr-110" class="anchor"></a>AMR 1.1.0<small> Unreleased </small>
</h1>
<div id="last-updated-15-apr-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-15-apr-2020" class="anchor"></a><small>Last updated: 15-Apr-2020</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h3>
@@ -274,7 +270,6 @@
</li>
</ul>
</div>
</div>
</div>
<div id="amr-101" class="section level1">
<h1 class="page-header" data-toc-text="1.0.1">

2
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@@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html
benchmarks: benchmarks.html
resistance_predict: resistance_predict.html
last_built: 2020-04-15T09:25Z
last_built: 2020-04-15T12:29Z
urls:
reference: https://msberends.gitlab.io/AMR/reference
article: https://msberends.gitlab.io/AMR/articles

33
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@@ -24,16 +24,20 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<!-- pkgdown -->
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@@ -46,7 +50,7 @@
<meta property="og:title" content="Deprecated functions — AMR-deprecated" />
<meta property="og:description" content="These functions are so-called 'Deprecated'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one)." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
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<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
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<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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Deprecated functions</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/deprecated.R'><code>R/deprecated.R</code></a></small>
<div class="hidden name"><code>AMR-deprecated.Rd</code></div>
</div>
@@ -260,12 +264,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
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@@ -276,7 +277,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
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@@ -24,16 +24,20 @@
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@@ -46,7 +50,7 @@
<meta property="og:title" content="The <code>AMR</code> Package — AMR" />
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@@ -64,7 +68,7 @@
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@@ -78,7 +82,7 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>The <code>AMR</code> Package</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/amr.R'><code>R/amr.R</code></a></small>
<div class="hidden name"><code>AMR.Rd</code></div>
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@@ -276,13 +280,9 @@ The Netherlands</p>
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@@ -293,7 +293,7 @@ The Netherlands</p>
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@@ -24,16 +24,20 @@
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@@ -46,7 +50,7 @@
<meta property="og:title" content="WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC" />
<meta property="og:description" content="All antimicrobial drugs and their official names, ATC codes, ATC groups and defined daily dose (DDD) are included in this package, using the WHO Collaborating Centre for Drug Statistics Methodology." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
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<div class="container template-reference-topic">
<header>
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@@ -78,7 +82,7 @@
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<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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/whocc.R'><code>R/whocc.R</code></a></small>
<div class="hidden name"><code>WHOCC.Rd</code></div>
</div>
@@ -255,13 +259,9 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<span class='fu'><a href='ab_property.html'>ab_tradenames</a></span>(<span class='st'>"flucloxacillin"</span>)</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#whocc">WHOCC</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
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@@ -272,7 +272,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
</div>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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@@ -82,7 +82,7 @@
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<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">1.0.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
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@@ -24,16 +24,20 @@
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@@ -46,7 +50,7 @@
<meta property="og:title" content="Property of an antibiotic — ab_property" />
<meta property="og:description" content="Use these functions to return a specific property of an antibiotic from the antibiotics data set. All input values will be evaluated internally with as.ab()." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Property of an antibiotic</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ab_property.R'><code>R/ab_property.R</code></a></small>
<div class="hidden name"><code>ab_property.Rd</code></div>
</div>
@@ -362,18 +366,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='fu'>ab_atc</span>(<span class='st'>"seephthriaaksone"</span>)</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
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@@ -384,7 +379,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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37
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@@ -24,16 +24,20 @@
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@@ -46,7 +50,7 @@
<meta property="og:title" content="Age in years of individuals — age" />
<meta property="og:description" content="Calculates age in years based on a reference date, which is the sytem date at default." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Age in years of individuals</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/age.R'><code>R/age.R</code></a></small>
<div class="hidden name"><code>age.Rd</code></div>
</div>
@@ -284,16 +288,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='no'>df</span></pre>
</div>
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<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
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@@ -304,7 +301,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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38
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@@ -24,16 +24,20 @@
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@@ -46,7 +50,7 @@
<meta property="og:title" content="Split ages into age groups — age_groups" />
<meta property="og:description" content="Split ages into age groups defined by the split parameter. This allows for easier demographic (antimicrobial resistance) analysis." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Split ages into age groups</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/age.R'><code>R/age.R</code></a></small>
<div class="hidden name"><code>age_groups.Rd</code></div>
</div>
@@ -316,17 +320,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -337,7 +333,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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2
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@@ -82,7 +82,7 @@
</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">1.0.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>

40
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@@ -24,16 +24,20 @@
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<link href="../pkgdown.css" rel="stylesheet">
@@ -46,7 +50,7 @@
<meta property="og:title" content="Transform to antibiotic ID — as.ab" />
<meta property="og:description" content="Use this function to determine the antibiotic code of one or more antibiotics. The data set antibiotics will be searched for abbreviations, official names and synonyms (brand names)." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Transform to antibiotic ID</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ab.R'><code>R/ab.R</code></a></small>
<div class="hidden name"><code>as.ab.Rd</code></div>
</div>
@@ -311,19 +315,9 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"eryt"</span>) <span class='co'># "Erythromycin"</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#whocc">WHOCC</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -334,7 +328,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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@@ -24,16 +24,20 @@
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -46,7 +50,7 @@
<meta property="og:title" content="Class 'disk' — as.disk" />
<meta property="og:description" content="This transforms a vector to a new class disk, which is a growth zone size (around an antibiotic disk) in millimetres between 6 and 50." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Class 'disk'</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/disk.R'><code>R/disk.R</code></a></small>
<div class="hidden name"><code>as.disk.Rd</code></div>
</div>
@@ -290,17 +294,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='no'>df</span>)</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -311,7 +307,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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38
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@@ -24,16 +24,20 @@
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<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -46,7 +50,7 @@
<meta property="og:title" content="Class 'mic' — as.mic" />
<meta property="og:description" content="This transforms a vector to a new class mic, which is an ordered factor with valid MIC values as levels. Invalid MIC values will be translated as NA with a warning." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Class 'mic'</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mic.R'><code>R/mic.R</code></a></small>
<div class="hidden name"><code>as.mic.Rd</code></div>
</div>
@@ -292,17 +296,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>mic_data</span>)</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -313,7 +309,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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40
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@@ -24,16 +24,20 @@
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<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -46,7 +50,7 @@
<meta property="og:title" content="Transform to microorganism ID — as.mo" />
<meta property="og:description" content="Use this function to determine a valid microorganism ID (mo). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like &quot;Staphylococcus aureus&quot;), an abbreviated name (like &quot;S. aureus&quot;), an abbreviation known in the field (like &quot;MRSA&quot;), or just a genus. Please see Examples." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Transform to microorganism ID</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mo.R'><code>R/mo.R</code></a></small>
<div class="hidden name"><code>as.mo.Rd</code></div>
</div>
@@ -438,19 +442,9 @@ This package contains the complete taxonomic tree of almost all microorganisms (
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#catalogue-of-life">Catalogue of Life</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -461,7 +455,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
</div>
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39
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@@ -24,16 +24,20 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -46,7 +50,7 @@
<meta property="og:title" content="Class 'rsi' — as.rsi" />
<meta property="og:description" content="Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class rsi, which is an ordered factor with levels S &amp;lt; I &amp;lt; R. Invalid antimicrobial interpretations will be translated as NA with a warning." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Class 'rsi'</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/rsi.R'><code>R/rsi.R</code></a></small>
<div class="hidden name"><code>as.rsi.Rd</code></div>
</div>
@@ -413,18 +417,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'>is.rsi.eligible</span>(<span class='no'>WHONET</span>$<span class='no'>`First name`</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>0.99</span>) <span class='co'># succeeds</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -435,7 +430,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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37
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@@ -24,16 +24,20 @@
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<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -47,7 +51,7 @@
<meta property="og:title" content="Get ATC properties from WHOCC website — atc_online_property" />
<meta property="og:description" content="Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit.
This function requires an internet connection." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -65,7 +69,7 @@ This function requires an internet connection." />
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -79,7 +83,7 @@ This function requires an internet connection." />
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -224,7 +228,7 @@ This function requires an internet connection." />
<div class="col-md-9 contents">
<div class="page-header">
<h1>Get ATC properties from WHOCC website</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/atc_online.R'><code>R/atc_online.R</code></a></small>
<div class="hidden name"><code>atc_online.Rd</code></div>
</div>
@@ -325,16 +329,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#questioning-lifecycle">Questioning lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -345,7 +342,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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</footer>

37
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@@ -24,16 +24,20 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<!-- pkgdown -->
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@@ -46,7 +50,7 @@
<meta property="og:title" content="Check availability of columns — availability" />
<meta property="og:description" content="Easy check for data availability of all columns in a data set. This makes it easy to get an idea of which antimicrobial combinations can be used for calculation with e.g. susceptibility() and resistance()." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Check availability of columns</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/availability.R'><code>R/availability.R</code></a></small>
<div class="hidden name"><code>availability.Rd</code></div>
</div>
@@ -281,16 +285,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'>availability</span>()</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -301,7 +298,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
</div>
</footer>

38
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@@ -24,16 +24,20 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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@@ -46,7 +50,7 @@
<meta property="og:title" content="Determine bug-drug combinations — bug_drug_combinations" />
<meta property="og:description" content="Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use format() on the result to prettify it to a publicable/printable format, see Examples." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Determine bug-drug combinations</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/bug_drug_combinations.R'><code>R/bug_drug_combinations.R</code></a></small>
<div class="hidden name"><code>bug_drug_combinations.Rd</code></div>
</div>
@@ -348,17 +352,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -369,7 +365,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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36
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@@ -24,16 +24,20 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<script src="../bootstrap-toc.js"></script>
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@@ -46,7 +50,7 @@
<meta property="og:title" content="The Catalogue of Life — catalogue_of_life" />
<meta property="og:description" content="This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>The Catalogue of Life</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
<div class="hidden name"><code>catalogue_of_life.Rd</code></div>
</div>
@@ -296,15 +300,9 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
<span class='co'># [1] "Chroococcus limneticus elegans" # Because a microorganism was found</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#catalogue-of-life">Catalogue of Life</a></li>
<li><a href="#included-taxa">Included taxa</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -315,7 +313,7 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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37
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@@ -24,16 +24,20 @@
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@@ -46,7 +50,7 @@
<meta property="og:title" content="Version info of included Catalogue of Life — catalogue_of_life_version" />
<meta property="og:description" content="This function returns information about the included data from the Catalogue of Life." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Version info of included Catalogue of Life</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
<div class="hidden name"><code>catalogue_of_life_version.Rd</code></div>
</div>
@@ -262,16 +266,9 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='no'>microorganisms</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>kingdom</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>phylum</span>, <span class='kw'>nmax</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#catalogue-of-life">Catalogue of Life</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -282,7 +279,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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40
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@@ -24,16 +24,20 @@
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@@ -47,7 +51,7 @@
<meta property="og:title" content="Count available isolates — count" />
<meta property="og:description" content="These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in summarise() and support grouped variables, see Examples.
count_resistant() should be used to count resistant isolates, count_susceptible() should be used to count susceptible isolates." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -65,7 +69,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -79,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -224,7 +228,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<div class="col-md-9 contents">
<div class="page-header">
<h1>Count available isolates</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/count.R'><code>R/count.R</code></a></small>
<div class="hidden name"><code>count.Rd</code></div>
</div>
@@ -420,19 +424,9 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#combination-therapy">Combination therapy</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -443,7 +437,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</div>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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39
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@@ -24,16 +24,20 @@
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@@ -47,7 +51,7 @@
<meta property="og:title" content="Apply EUCAST rules — eucast_rules" />
<meta property="og:description" content="Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, http://eucast.org), see Source. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.
To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -65,7 +69,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -79,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -224,7 +228,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<div class="col-md-9 contents">
<div class="page-header">
<h1>Apply EUCAST rules</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/eucast_rules.R'><code>R/eucast_rules.R</code></a></small>
<div class="hidden name"><code>eucast_rules.Rd</code></div>
</div>
@@ -444,18 +448,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#antibiotics">Antibiotics</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -466,7 +461,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
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33
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@@ -24,16 +24,20 @@
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<!-- pkgdown -->
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@@ -46,7 +50,7 @@
<meta property="og:title" content="Data set with 2,000 example isolates — example_isolates" />
<meta property="og:description" content="A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read the tutorial on our website." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
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<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data set with 2,000 example isolates</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>example_isolates.Rd</code></div>
</div>
@@ -257,12 +261,9 @@
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#format">Format</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
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@@ -273,7 +274,7 @@
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33
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@@ -24,16 +24,20 @@
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@@ -46,7 +50,7 @@
<meta property="og:title" content="Data set with unclean data — example_isolates_unclean" />
<meta property="og:description" content="A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR analysis. This data set can be used for practice." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
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@@ -78,7 +82,7 @@
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<span class="navbar-brand">
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
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@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data set with unclean data</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>example_isolates_unclean.Rd</code></div>
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@@ -252,12 +256,9 @@
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@@ -268,7 +269,7 @@
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@@ -46,7 +50,7 @@
<meta property="og:title" content="Extended functions — extended-functions" />
<meta property="og:description" content="These functions are extensions of functions in other packages." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
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@@ -78,7 +82,7 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
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@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Extended functions</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/extended.R'><code>R/extended.R</code></a></small>
<div class="hidden name"><code>extended-functions.Rd</code></div>
</div>
@@ -251,12 +255,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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@@ -267,7 +268,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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@@ -46,7 +50,7 @@
<meta property="og:title" content="Filter isolates on result in antibiotic class — filter_ab_class" />
<meta property="og:description" content="Filter isolates on results in specific antibiotic variables based on their antibiotic class. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
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@@ -78,7 +82,7 @@
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<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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Filter isolates on result in antibiotic class</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/filter_ab_class.R'><code>R/filter_ab_class.R</code></a></small>
<div class="hidden name"><code>filter_ab_class.Rd</code></div>
</div>
@@ -324,14 +328,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'>filter_fluoroquinolones</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>)</pre>
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<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
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<h2 data-toc-skip>Contents</h2>
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@@ -342,7 +341,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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@@ -82,7 +82,7 @@
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<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">1.0.1.9009</span>
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</span>
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40
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@@ -24,16 +24,20 @@
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@@ -46,7 +50,7 @@
<meta property="og:title" content="<em>G</em>-test for Count Data — g.test" />
<meta property="og:description" content="g.test() performs chi-squared contingency table tests and goodness-of-fit tests, just like chisq.test() but is more reliable (1). A G-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a G-test of goodness-of-fit), or to see whether the proportions of one variable are different for different values of the other variable (called a G-test of independence)." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
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@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1><em>G</em>-test for Count Data</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/g.test.R'><code>R/g.test.R</code></a></small>
<div class="hidden name"><code>g.test.Rd</code></div>
</div>
@@ -376,19 +380,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<span class='co'># Meaning: there are significantly more left-billed birds.</span></pre>
</div>
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<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#questioning-lifecycle">Questioning lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#references">References</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
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<h2 data-toc-skip>Contents</h2>
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@@ -399,7 +393,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
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@@ -82,7 +82,7 @@
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -46,7 +50,7 @@
<meta property="og:title" content="AMR plots with <code>ggplot2</code> — ggplot_rsi" />
<meta property="og:description" content="Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal ggplot2 functions." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>AMR plots with <code>ggplot2</code></h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ggplot_rsi.R'><code>R/ggplot_rsi.R</code></a></small>
<div class="hidden name"><code>ggplot_rsi.Rd</code></div>
</div>
@@ -507,15 +511,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -526,7 +524,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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37
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@@ -24,16 +24,20 @@
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@@ -46,7 +50,7 @@
<meta property="og:title" content="Guess antibiotic column — guess_ab_col" />
<meta property="og:description" content="This tries to find a column name in a data set based on information from the antibiotics data set. Also supports WHONET abbreviations." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Guess antibiotic column</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/guess_ab_col.R'><code>R/guess_ab_col.R</code></a></small>
<div class="hidden name"><code>guess_ab_col.Rd</code></div>
</div>
@@ -298,16 +302,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='co'># [1] "AMP_ED20"</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -318,7 +315,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
</div>
</footer>

2
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@@ -81,7 +81,7 @@
</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">1.0.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>

36
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@@ -24,16 +24,20 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
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@@ -46,7 +50,7 @@
<meta property="og:title" content="Join a table with <a href='microorganisms.html'>microorganisms</a> — join" />
<meta property="og:description" content="Join the data set microorganisms easily to an existing table or character vector." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Join a table with <a href='microorganisms.html'>microorganisms</a></h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/join_microorganisms.R'><code>R/join_microorganisms.R</code></a></small>
<div class="hidden name"><code>join.Rd</code></div>
</div>
@@ -298,15 +302,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></span>(<span class='no'>df_joined</span>)</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -317,7 +315,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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38
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@@ -24,16 +24,20 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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@@ -46,7 +50,7 @@
<meta property="og:title" content="Key antibiotics for first <em>weighted</em> isolates — key_antibiotics" />
<meta property="og:description" content="These function can be used to determine first isolates (see first_isolate()). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first weighted isolates." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Key antibiotics for first <em>weighted</em> isolates</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/key_antibiotics.R'><code>R/key_antibiotics.R</code></a></small>
<div class="hidden name"><code>key_antibiotics.Rd</code></div>
</div>
@@ -410,17 +414,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># FALSE, because I is not ignored and so the 4th value differs</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#key-antibiotics">Key antibiotics</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -431,7 +427,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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35
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@@ -24,16 +24,20 @@
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@@ -46,7 +50,7 @@
<meta property="og:title" content="Kurtosis of the sample — kurtosis" />
<meta property="og:description" content="Kurtosis is a measure of the &quot;tailedness&quot; of the probability distribution of a real-valued random variable." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
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@@ -78,7 +82,7 @@
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<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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Kurtosis of the sample</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/kurtosis.R'><code>R/kurtosis.R</code></a></small>
<div class="hidden name"><code>kurtosis.Rd</code></div>
</div>
@@ -272,14 +276,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
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<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#questioning-lifecycle">Questioning lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
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@@ -290,7 +289,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
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@@ -48,7 +52,7 @@
<meta property="og:description" content="Our functions are categorised using the lifecycle circle of the tidyverse as found on www.tidyverse.org/lifecycle.
This page contains a section for every lifecycle (with text borrowed from the aforementioned tidyverse website), so they can be used in the manual pages of our functions." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -66,7 +70,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -80,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -225,7 +229,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
<div class="col-md-9 contents">
<div class="page-header">
<h1>Lifecycles of functions in the <code>AMR</code> package</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/lifecycle.R'><code>R/lifecycle.R</code></a></small>
<div class="hidden name"><code>lifecycle.Rd</code></div>
</div>
@@ -283,17 +287,9 @@ The lifecycle of this function is <strong>questioning</strong>. We are no longer
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#experimental-lifecycle">Experimental lifecycle</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#retired-lifecycle">Retired lifecycle</a></li>
<li><a href="#archived-lifecycle">Archived lifecycle</a></li>
<li><a href="#dormant-lifecycle">Dormant lifecycle</a></li>
<li><a href="#questioning-lifecycle">Questioning lifecycle</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
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@@ -304,7 +300,7 @@ The lifecycle of this function is <strong>questioning</strong>. We are no longer
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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">1.0.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>

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@@ -24,16 +24,20 @@
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@@ -46,7 +50,7 @@
<meta property="og:title" content="Determine multidrug-resistant organisms (MDRO) — mdro" />
<meta property="og:description" content="Determine which isolates are multidrug-resistant organisms (MDRO) according to international and national guidelines." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
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<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Determine multidrug-resistant organisms (MDRO)</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mdro.R'><code>R/mdro.R</code></a></small>
<div class="hidden name"><code>mdro.Rd</code></div>
</div>
@@ -450,19 +454,9 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#antibiotics">Antibiotics</a></li>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -473,7 +467,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</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">1.0.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>

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<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">1.0.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>

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<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">1.0.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>

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@@ -46,7 +50,7 @@
<meta property="og:title" content="Property of a microorganism — mo_property" />
<meta property="og:description" content="Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with as.mo(), which makes it possible to use microbial abbreviations, codes and names as input. Please see Examples." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
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<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Property of a microorganism</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mo_property.R'><code>R/mo_property.R</code></a></small>
<div class="hidden name"><code>mo_property.Rd</code></div>
</div>
@@ -437,18 +441,9 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#catalogue-of-life">Catalogue of Life</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -459,7 +454,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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@@ -24,16 +24,20 @@
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<link href="../pkgdown.css" rel="stylesheet">
@@ -47,7 +51,7 @@
<meta property="og:title" content="Use predefined reference data set — mo_source" />
<meta property="og:description" content="These functions can be used to predefine your own reference to be used in as.mo() and consequently all mo_* functions like mo_genus() and mo_gramstain().
This is the fastest way to have your organisation (or analysis) specific codes picked up and translated by this package." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -65,7 +69,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -79,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -224,7 +228,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<div class="col-md-9 contents">
<div class="page-header">
<h1>Use predefined reference data set</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mo_source.R'><code>R/mo_source.R</code></a></small>
<div class="hidden name"><code>mo_source.Rd</code></div>
</div>
@@ -313,14 +317,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -331,7 +330,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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@@ -24,16 +24,20 @@
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@@ -46,7 +50,7 @@
<meta property="og:title" content="Symbol of a p-value — p_symbol" />
<meta property="og:description" content="Return the symbol related to the p-value: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1. Values above p = 1 will return NA." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Symbol of a p-value</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/p_symbol.R'><code>R/p_symbol.R</code></a></small>
<div class="hidden name"><code>p_symbol.Rd</code></div>
</div>
@@ -263,14 +267,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#questioning-lifecycle">Questioning lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -281,7 +280,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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@@ -24,16 +24,20 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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@@ -46,7 +50,7 @@
<meta property="og:title" content="Principal Component Analysis (for AMR) — pca" />
<meta property="og:description" content="Performs a principal component analysis (PCA) based on a data set with automatic determination for afterwards plotting the groups and labels, and automatic filtering on only suitable (i.e. non-empty and numeric) variables." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Principal Component Analysis (for AMR)</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/pca.R'><code>R/pca.R</code></a></small>
<div class="hidden name"><code>pca.Rd</code></div>
</div>
@@ -328,15 +332,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='fu'><a href='ggplot_pca.html'>ggplot_pca</a></span>(<span class='no'>pca_result</span>) <span class='co'># a new and convenient plot function</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -347,7 +345,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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41
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@@ -24,16 +24,20 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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@@ -47,7 +51,7 @@
<meta property="og:title" content="Calculate microbial resistance — proportion" />
<meta property="og:description" content="These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in summarise()][dplyr::summarise()] and also support grouped variables, please see Examples.
resistance() should be used to calculate resistance, susceptibility() should be used to calculate susceptibility." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -65,7 +69,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -79,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -224,7 +228,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<div class="col-md-9 contents">
<div class="page-header">
<h1>Calculate microbial resistance</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/proportion.R'><code>R/proportion.R</code></a>, <a href='https://gitlab.com/msberends/AMR/blob/master/R/rsi_df.R'><code>R/rsi_df.R</code></a></small>
<div class="hidden name"><code>proportion.Rd</code></div>
</div>
@@ -463,20 +467,9 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#combination-therapy">Combination therapy</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
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@@ -487,7 +480,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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@@ -46,7 +50,7 @@
<meta property="og:title" content="Read data from 4D database — read.4D" />
<meta property="og:description" content="This function is only useful for the MMB department of the UMCG. Use this function to import data by just defining the file parameter. It will automatically transform birth dates and calculate patients age, translate the column names to English, transform the MO codes with as.mo() and transform all antimicrobial columns with as.rsi()." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Read data from 4D database</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/read.4d.R'><code>R/read.4d.R</code></a></small>
<div class="hidden name"><code>read.4D.Rd</code></div>
</div>
@@ -401,14 +405,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>dormant</
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#dormant-lifecycle">Dormant lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
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@@ -419,7 +418,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>dormant</
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@@ -51,7 +55,7 @@ below to see their documentation.
cleanerfreq
" />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -69,7 +73,7 @@ below to see their documentation.
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<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -83,7 +87,7 @@ below to see their documentation.
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -228,14 +232,14 @@ below to see their documentation.
<div class="col-md-9 contents">
<div class="page-header">
<h1>Objects exported from other packages</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/freq.R'><code>R/freq.R</code></a></small>
<div class="hidden name"><code>reexports.Rd</code></div>
</div>
<div class="ref-description">
<p>These objects are imported from other packages. Follow the links
below to see their documentation.</p>
<dl class='dl-horizontal'>
<dl'>
<dt>cleaner</dt><dd><p><code><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></code></p></dd>
</dl>
@@ -246,10 +250,9 @@ below to see their documentation.</p>
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@@ -260,7 +263,7 @@ below to see their documentation.</p>
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@@ -46,7 +50,7 @@
<meta property="og:title" content="Predict antimicrobial resistance — resistance_predict" />
<meta property="og:description" content="Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns se_min and se_max. See Examples for a real live example." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
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<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Predict antimicrobial resistance</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/resistance_predict.R'><code>R/resistance_predict.R</code></a></small>
<div class="hidden name"><code>resistance_predict.Rd</code></div>
</div>
@@ -434,18 +438,9 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
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@@ -456,7 +451,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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@@ -82,7 +82,7 @@
</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">1.0.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>

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@@ -24,16 +24,20 @@
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@@ -47,7 +51,7 @@
<meta property="og:title" content="Skewness of the sample — skewness" />
<meta property="og:description" content="Skewness is a measure of the asymmetry of the probability distribution of a real-valued random variable about its mean.
When negative: the left tail is longer; the mass of the distribution is concentrated on the right of the figure. When positive: the right tail is longer; the mass of the distribution is concentrated on the left of the figure." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -65,7 +69,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
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@@ -79,7 +83,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -224,7 +228,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
<div class="col-md-9 contents">
<div class="page-header">
<h1>Skewness of the sample</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/skewness.R'><code>R/skewness.R</code></a></small>
<div class="hidden name"><code>skewness.Rd</code></div>
</div>
@@ -274,14 +278,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
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<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#questioning-lifecycle">Questioning lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
</ul>
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@@ -292,7 +291,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
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</div>
</footer>

35
docs/reference/translate.html
View File

@@ -24,16 +24,20 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -46,7 +50,7 @@
<meta property="og:title" content="Translate strings from AMR package — translate" />
<meta property="og:description" content="For language-dependent output of AMR functions, like mo_name(), mo_type() and ab_name()." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Translate strings from AMR package</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/translate.R'><code>R/translate.R</code></a></small>
<div class="hidden name"><code>translate.Rd</code></div>
</div>
@@ -284,14 +288,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'>#&gt; "Staphylococcus coagulase negativo (CoNS)"</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@@ -302,7 +301,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
</div>
</footer>

35
git_merge.sh
View File

@@ -19,17 +19,28 @@
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#######################################################################
# To push new commits to the premaster branch, run: #
# bash git_premaster.sh "commit message" #
# This creates auto version numbering in DESCRIPTION and NEWS.md. #
# #
# After successful CRAN checks, merge it to the master branch with: #
# bash git_merge.sh #
# #
# To prerelease a new version number, run: #
# bash git_premaster.sh "v0.x.x" FALSE "0.x.x" #
#######################################################################
########################################################################
# `git_premaster.sh` takes 3 parameters: #
# 1. Commit message (character) [mandatory] #
# 2. Lazy website generation (logical), with FALSE only changed #
# files will be processed [defaults to TRUE] #
# 3. Version number to be used in DESCRIPTION and NEWS.md #
# [defaults to current tag and last commit number + 9000] #
# #
# To push new commits to the premaster branch, run: #
# bash git_premaster.sh "commit message" #
# This creates auto version numbering in DESCRIPTION and NEWS.md. #
# #
# After successful test checks, merge it to the master branch with: #
# bash git_merge.sh #
# #
# To prerelease a new version number, run: #
# bash git_premaster.sh "v1.x.x" FALSE "1.x.x" #
# #
# To only update the website, run: #
# bash git_siteonly.sh #
# (which is short for 'bash git_premaster.sh "website update" FALSE') #
########################################################################
# stash current changes
# git stash --quiet
@@ -55,7 +66,7 @@ case "$choice" in
y|Y|j|J ) ;;
* ) exit 1;;
esac
Rscript -e "rhub::check(devtools::build(), platform = c('debian-clang-devel', 'debian-gcc-devel', 'fedora-clang-devel', 'fedora-gcc-devel', 'windows-x86_64-devel', 'debian-gcc-patched', 'solaris-x86-patched', 'debian-gcc-release', 'windows-x86_64-release', 'macos-elcapitan-release', 'windows-x86_64-oldrel'))"
Rscript -e "rhub::check(devtools::build(), platform = rhub::platforms()[!is.na(rhub::platforms()$`cran-name`), 'name'])"
echo
# and get stashed changes back

39
git_premaster.sh
View File

@@ -19,17 +19,28 @@
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#######################################################################
# To push new commits to the premaster branch, run: #
# bash git_premaster.sh "commit message" #
# This creates auto version numbering in DESCRIPTION and NEWS.md. #
# #
# After successful CRAN checks, merge it to the master branch with: #
# bash git_merge.sh #
# #
# To prerelease a new version number, run: #
# bash git_premaster.sh "v0.x.x" FALSE "0.x.x" #
#######################################################################
########################################################################
# `git_premaster.sh` takes 3 parameters: #
# 1. Commit message (character) [mandatory] #
# 2. Lazy website generation (logical), with FALSE only changed #
# files will be processed [defaults to TRUE] #
# 3. Version number to be used in DESCRIPTION and NEWS.md #
# [defaults to current tag and last commit number + 9000] #
# #
# To push new commits to the premaster branch, run: #
# bash git_premaster.sh "commit message" #
# This creates auto version numbering in DESCRIPTION and NEWS.md. #
# #
# After successful test checks, merge it to the master branch with: #
# bash git_merge.sh #
# #
# To prerelease a new version number, run: #
# bash git_premaster.sh "v1.x.x" FALSE "1.x.x" #
# #
# To only update the website, run: #
# bash git_siteonly.sh #
# (which is short for 'bash git_premaster.sh "website update" FALSE') #
########################################################################
if [ -z "$1" ]; then
echo "FATAL - no commit message"
@@ -41,6 +52,9 @@ else
lazy=$2
fi
# be sure to be on premaster branch
git checkout premaster --quiet
echo "••••••••••••••••••••••••••••••••••••••••••••"
echo "• Updating package date and version number •"
echo "••••••••••••••••••••••••••••••••••••••••••••"
@@ -70,6 +84,7 @@ if [ -z "$3" ]; then
# add date to 2nd line of NEWS.md when no version number was set
sed -i -- "2s/.*/## \<small\>Last updated: $(date '+%d-%b-%Y')\<\/small\>/" NEWS.md
else
# version number set in command
new_version=$3
# rmove 2nd line of NEWS.md (the last changed date)
sed -i -- "2s/.*//" NEWS.md
@@ -136,5 +151,5 @@ case "$choice" in
y|Y|j|J ) ;;
* ) exit 1;;
esac
Rscript -e "rhub::check(devtools::build(), platform = c('debian-clang-devel', 'debian-gcc-devel', 'fedora-clang-devel', 'fedora-gcc-devel', 'windows-x86_64-devel', 'debian-gcc-patched', 'solaris-x86-patched', 'debian-gcc-release', 'windows-x86_64-release', 'macos-elcapitan-release', 'windows-x86_64-oldrel'))"
Rscript -e "rhub::check(devtools::build(), platform = rhub::platforms()[!is.na(rhub::platforms()$`cran-name`), 'name'])"
echo

33
git_siteonly.sh
View File

@@ -19,17 +19,28 @@
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#######################################################################
# To push new commits to the premaster branch, run: #
# bash git_premaster.sh "commit message" #
# This creates auto version numbering in DESCRIPTION and NEWS.md. #
# #
# After successful CRAN checks, merge it to the master branch with: #
# bash git_merge.sh #
# #
# To prerelease a new version number, run: #
# bash git_premaster.sh "v0.x.x" FALSE "0.x.x" #
#######################################################################
########################################################################
# `git_premaster.sh` takes 3 parameters: #
# 1. Commit message (character) [mandatory] #
# 2. Lazy website generation (logical), with FALSE only changed #
# files will be processed [defaults to TRUE] #
# 3. Version number to be used in DESCRIPTION and NEWS.md #
# [defaults to current tag and last commit number + 9000] #
# #
# To push new commits to the premaster branch, run: #
# bash git_premaster.sh "commit message" #
# This creates auto version numbering in DESCRIPTION and NEWS.md. #
# #
# After successful test checks, merge it to the master branch with: #
# bash git_merge.sh #
# #
# To prerelease a new version number, run: #
# bash git_premaster.sh "v1.x.x" FALSE "1.x.x" #
# #
# To only update the website, run: #
# bash git_siteonly.sh #
# (which is short for 'bash git_premaster.sh "website update" FALSE') #
########################################################################
bash git_premaster.sh "website update" FALSE