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(v1.4.0.9037) random_* functions

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dr. M.S. (Matthijs) Berends
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9037</span>
</span>
</div>
@ -447,7 +447,7 @@
</tr><tr>
<td>
<p><code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">barplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;rsi&gt;</i>)</a></code> <code><a href="plot.html">barplot(<i>&lt;rsi&gt;</i>)</a></code> </p>
<p><code><a href="plot.html">plot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">barplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;rsi&gt;</i>)</a></code> <code><a href="plot.html">barplot(<i>&lt;rsi&gt;</i>)</a></code> </p>
</td>
<td><p>Plotting for classes <code>rsi</code> and <code>disk</code></p></td>
</tr>
@ -602,6 +602,12 @@
<p><code><a href="pca.html">pca()</a></code> </p>
</td>
<td><p>Principal Component Analysis (for AMR)</p></td>
</tr><tr>
<td>
<p><code><a href="random.html">random_mic()</a></code> <code><a href="random.html">random_disk()</a></code> <code><a href="random.html">random_rsi()</a></code> </p>
</td>
<td><p>Random MIC values/disk zones/RSI generation</p></td>
</tr>
</tbody><tbody>
<tr>

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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">1.4.0.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9037</span>
</span>
</div>
@ -267,13 +267,15 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Dates are first sorted from old to new. The oldest date will mark the start of the first episode. After this date, the next date will be marked that is at least <code>episode_days</code> days later than the start of the first episode. From that second marked date on, the next date will be marked that is at least <code>episode_days</code> days later than the start of the second episode which will be the start of the third episode, and so on. Before the vector is being returned, the original order will be restored.</p>
<p>The <code><a href='first_isolate.html'>first_isolate()</a></code> function is a wrapper around the <code>is_new_episode()</code> function, but more efficient for data sets containing microorganism codes or names.</p>
<p>The <code>dplyr</code> package is not required for this function to work, but this function works conveniently inside <code>dplyr</code> verbs such as <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>.</p>
<h2 class="hasAnchor" id="experimental-lifecycle"><a class="anchor" href="#experimental-lifecycle"></a>Experimental lifecycle</h2>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<p><img src='figures/lifecycle_experimental.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>experimental</strong>. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this <code>AMR</code> package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.</p>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

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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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9037</span>
</span>
</div>
@ -234,7 +234,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Plotting for classes <code>rsi</code> and <code>disk</code></h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/amr.R'><code>R/amr.R</code></a>, <a href='https://github.com/msberends/AMR/blob/master/R/mic.R'><code>R/mic.R</code></a>, <a href='https://github.com/msberends/AMR/blob/master/R/rsi.R'><code>R/rsi.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/amr.R'><code>R/amr.R</code></a>, <a href='https://github.com/msberends/AMR/blob/master/R/disk.R'><code>R/disk.R</code></a>, <a href='https://github.com/msberends/AMR/blob/master/R/mic.R'><code>R/mic.R</code></a>, and 1 more</small>
<div class="hidden name"><code>plot.Rd</code></div>
</div>
@ -242,7 +242,17 @@
<p>Functions to print classes of the <code>AMR</code> package.</p>
</div>
<pre class="usage"><span class='co'># S3 method for mic</span>
<pre class="usage"><span class='co'># S3 method for disk</span>
<span class='fu'>plot</span><span class='op'>(</span>
<span class='va'>x</span>,
main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Disk zones values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
xlab <span class='op'>=</span> <span class='st'>"Disk diffusion (mm)"</span>,
axes <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='co'># S3 method for mic</span>
<span class='fu'>plot</span><span class='op'>(</span>
<span class='va'>x</span>,
main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"MIC values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,

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<h1>Random MIC values/disk zones/RSI generation</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/random.R'><code>R/random.R</code></a></small>
<div class="hidden name"><code>random.Rd</code></div>
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<div class="ref-description">
<p>These functions can be used for generating random MIC values and disk diffusion diameters, for AMR analysis practice.</p>
</div>
<pre class="usage"><span class='fu'>random_mic</span><span class='op'>(</span><span class='va'>size</span>, mo <span class='op'>=</span> <span class='cn'>NULL</span>, ab <span class='op'>=</span> <span class='cn'>NULL</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>random_disk</span><span class='op'>(</span><span class='va'>size</span>, mo <span class='op'>=</span> <span class='cn'>NULL</span>, ab <span class='op'>=</span> <span class='cn'>NULL</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>random_rsi</span><span class='op'>(</span><span class='va'>size</span>, prob_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.33</span>, <span class='fl'>0.33</span>, <span class='fl'>0.33</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>size</th>
<td><p>desired size of the returned vector</p></td>
</tr>
<tr>
<th>mo</th>
<td><p>any character that can be coerced to a valid microorganism code with <code><a href='as.mo.html'>as.mo()</a></code></p></td>
</tr>
<tr>
<th>ab</th>
<td><p>any character that can be coerced to a valid antimicrobial agent code with <code><a href='as.ab.html'>as.ab()</a></code></p></td>
</tr>
<tr>
<th>...</th>
<td><p>extension for future versions, not used at the moment</p></td>
</tr>
<tr>
<th>prob_RSI</th>
<td><p>a vector of length 3: the probabilities for R (1st value), S (2nd value) and I (3rd value)</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>class <code>&lt;mic&gt;</code> for <code>random_mic()</code> (see <code><a href='as.mic.html'>as.mic()</a></code>) and class <code>&lt;disk&gt;</code> for <code>random_disk()</code> (see <code><a href='as.disk.html'>as.disk()</a></code>)</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The base R function <code><a href='https://rdrr.io/r/base/sample.html'>sample()</a></code> is used for generating values.</p>
<p>Generated values are based on the latest EUCAST guideline implemented in the <a href='rsi_translation.html'>rsi_translation</a> data set. To create specific generated values per bug or drug, set the <code>mo</code> and/or <code>ab</code> parameter.</p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'>random_mic</span><span class='op'>(</span><span class='fl'>100</span><span class='op'>)</span>
<span class='fu'>random_disk</span><span class='op'>(</span><span class='fl'>100</span><span class='op'>)</span>
<span class='fu'>random_rsi</span><span class='op'>(</span><span class='fl'>100</span><span class='op'>)</span>
<span class='co'># \donttest{</span>
<span class='co'># make the random generation more realistic by setting a bug and/or drug:</span>
<span class='fu'>random_mic</span><span class='op'>(</span><span class='fl'>100</span>, <span class='st'>"Klebsiella pneumoniae"</span><span class='op'>)</span> <span class='co'># range 0.0625-64</span>
<span class='fu'>random_mic</span><span class='op'>(</span><span class='fl'>100</span>, <span class='st'>"Klebsiella pneumoniae"</span>, <span class='st'>"meropenem"</span><span class='op'>)</span> <span class='co'># range 0.0625-16</span>
<span class='fu'>random_mic</span><span class='op'>(</span><span class='fl'>100</span>, <span class='st'>"Streptococcus pneumoniae"</span>, <span class='st'>"meropenem"</span><span class='op'>)</span> <span class='co'># range 0.0625-4</span>
<span class='fu'>random_disk</span><span class='op'>(</span><span class='fl'>100</span>, <span class='st'>"Klebsiella pneumoniae"</span><span class='op'>)</span> <span class='co'># range 11-50</span>
<span class='fu'>random_disk</span><span class='op'>(</span><span class='fl'>100</span>, <span class='st'>"Klebsiella pneumoniae"</span>, <span class='st'>"ampicillin"</span><span class='op'>)</span> <span class='co'># range 6-14</span>
<span class='fu'>random_disk</span><span class='op'>(</span><span class='fl'>100</span>, <span class='st'>"Streptococcus pneumoniae"</span>, <span class='st'>"ampicillin"</span><span class='op'>)</span> <span class='co'># range 16-22</span>
<span class='co'># }</span>
</pre>
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