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<h1>Transform Input to Minimum Inhibitory Concentrations (MIC)</h1>
<small class="dont-index">Source: <a href='https://github.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>
<div class="ref-description">
<p>This transforms vectors to a new class <code>mic</code>, which treats the input as decimal numbers, while maintaining operators (such as "&gt;=") and only allowing valid MIC values known to the field of (medical) microbiology.</p>
</div>
<pre class="usage"><span class='fu'>as.mic</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='va'>NA_mic_</span>
<span class='fu'>is.mic</span><span class='op'>(</span><span class='va'>x</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>x</th>
<td><p>a <a href='https://rdrr.io/r/base/character.html'>character</a> or <a href='https://rdrr.io/r/base/numeric.html'>numeric</a> vector</p></td>
</tr>
<tr>
<th>na.rm</th>
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> indicating whether missing values should be removed</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>An object of class <code>mic</code> (inherits from <code>ordered</code>, <code>factor</code>) of length 1.</p>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with additional class <code>mic</code>, that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a <a href='https://rdrr.io/r/base/numeric.html'>numeric</a> value.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>To interpret MIC values as RSI values, use <code><a href='as.rsi.html'>as.rsi()</a></code> on MIC values. It supports guidelines from EUCAST and CLSI.</p>
<p>This class for MIC values is a quite a special data type: formally it is an ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with valid MIC values as <a href='https://rdrr.io/r/base/factor.html'>factor</a> levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:</p><pre><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'><a href='random.html'>random_mic</a></span><span class='op'>(</span><span class='fl'>10</span><span class='op'>)</span>
<span class='va'>x</span>
<span class='co'>#&gt; Class &lt;mic&gt;</span>
<span class='co'>#&gt; [1] 16 1 8 8 64 &gt;=128 0.0625 32 32 16</span>
<span class='fu'><a href='https://rdrr.io/r/base/factor.html'>is.factor</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
<span class='co'>#&gt; [1] TRUE</span>
<span class='va'>x</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>]</span> <span class='op'>*</span> <span class='fl'>2</span>
<span class='co'>#&gt; [1] 32</span>
<span class='fu'><a href='https://rdrr.io/r/stats/median.html'>median</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
<span class='co'>#&gt; [1] 26</span>
</pre>
<p>This makes it possible to maintain operators that often come with MIC values, such "&gt;=" and "&lt;=", even when filtering using <a href='https://rdrr.io/r/base/numeric.html'>numeric</a> values in data analysis, e.g.:</p><pre><span class='va'>x</span><span class='op'>[</span><span class='va'>x</span> <span class='op'>&gt;</span> <span class='fl'>4</span><span class='op'>]</span>
<span class='co'>#&gt; Class &lt;mic&gt;</span>
<span class='co'>#&gt; [1] 16 8 8 64 &gt;=128 32 32 16</span>
<span class='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span><span class='va'>x</span>, hospital <span class='op'>=</span> <span class='st'>"A"</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>df</span>, <span class='va'>x</span> <span class='op'>&gt;</span> <span class='fl'>4</span><span class='op'>)</span> <span class='co'># or with dplyr: df %&gt;% filter(x &gt; 4)</span>
<span class='co'>#&gt; x hospital</span>
<span class='co'>#&gt; 1 16 A</span>
<span class='co'>#&gt; 5 64 A</span>
<span class='co'>#&gt; 6 &gt;=128 A</span>
<span class='co'>#&gt; 8 32 A</span>
<span class='co'>#&gt; 9 32 A</span>
<span class='co'>#&gt; 10 16 A</span>
</pre>
<p>The following <a href='https://rdrr.io/r/base/groupGeneric.html'>generic functions</a> are implemented for the MIC class: <code><a href='https://rdrr.io/r/base/Logic.html'>!</a></code>, <code><a href='https://rdrr.io/r/base/Comparison.html'>!=</a></code>, <code><a href='https://rdrr.io/r/base/Arithmetic.html'>%%</a></code>, <code><a href='https://rdrr.io/r/base/Arithmetic.html'>%/%</a></code>, <code>&amp;</code>, <code><a href='https://rdrr.io/r/base/Arithmetic.html'>*</a></code>, <code><a href='https://rdrr.io/r/base/Arithmetic.html'>+</a></code>, <code><a href='https://rdrr.io/r/base/Arithmetic.html'>-</a></code>, <code><a href='https://rdrr.io/r/base/Arithmetic.html'>/</a></code>, <code>&lt;</code>, <code>&lt;=</code>, <code><a href='https://rdrr.io/r/base/Comparison.html'>==</a></code>, <code>&gt;</code>, <code>&gt;=</code>, <code><a href='https://rdrr.io/r/base/Arithmetic.html'>^</a></code>, <code><a href='https://rdrr.io/r/base/Logic.html'>|</a></code>, <code><a href='https://rdrr.io/r/base/MathFun.html'>abs()</a></code>, <code><a href='https://rdrr.io/r/base/Trig.html'>acos()</a></code>, <code><a href='https://rdrr.io/r/base/Hyperbolic.html'>acosh()</a></code>, <code><a href='https://rdrr.io/r/base/all.html'>all()</a></code>, <code><a href='https://rdrr.io/r/base/any.html'>any()</a></code>, <code><a href='https://rdrr.io/r/base/Trig.html'>asin()</a></code>, <code><a href='https://rdrr.io/r/base/Hyperbolic.html'>asinh()</a></code>, <code><a href='https://rdrr.io/r/base/Trig.html'>atan()</a></code>, <code><a href='https://rdrr.io/r/base/Hyperbolic.html'>atanh()</a></code>, <code><a href='https://rdrr.io/r/base/Round.html'>ceiling()</a></code>, <code><a href='https://rdrr.io/r/base/Trig.html'>cos()</a></code>, <code><a href='https://rdrr.io/r/base/Hyperbolic.html'>cosh()</a></code>, <code><a href='https://rdrr.io/r/base/Trig.html'>cospi()</a></code>, <code><a href='https://rdrr.io/r/base/cumsum.html'>cummax()</a></code>, <code><a href='https://rdrr.io/r/base/cumsum.html'>cummin()</a></code>, <code><a href='https://rdrr.io/r/base/cumsum.html'>cumprod()</a></code>, <code><a href='https://rdrr.io/r/base/cumsum.html'>cumsum()</a></code>, <code><a href='https://rdrr.io/r/base/Special.html'>digamma()</a></code>, <code><a href='https://rdrr.io/r/base/Log.html'>exp()</a></code>, <code><a href='https://rdrr.io/r/base/Log.html'>expm1()</a></code>, <code><a href='https://rdrr.io/r/base/Round.html'>floor()</a></code>, <code><a href='https://rdrr.io/r/base/Special.html'>gamma()</a></code>, <code><a href='https://rdrr.io/r/base/Special.html'>lgamma()</a></code>, <code><a href='https://rdrr.io/r/base/Log.html'>log()</a></code>, <code><a href='https://rdrr.io/r/base/Log.html'>log1p()</a></code>, <code><a href='https://rdrr.io/r/base/Log.html'>log2()</a></code>, <code><a href='https://rdrr.io/r/base/Log.html'>log10()</a></code>, <code><a href='https://rdrr.io/r/base/Extremes.html'>max()</a></code>, <code><a href='https://rdrr.io/r/base/mean.html'>mean()</a></code>, <code><a href='https://rdrr.io/r/base/Extremes.html'>min()</a></code>, <code><a href='https://rdrr.io/r/base/prod.html'>prod()</a></code>, <code><a href='https://rdrr.io/r/base/range.html'>range()</a></code>, <code><a href='https://rdrr.io/r/base/Round.html'>round()</a></code>, <code><a href='https://rdrr.io/r/base/sign.html'>sign()</a></code>, <code><a href='https://rdrr.io/r/base/Round.html'>signif()</a></code>, <code><a href='https://rdrr.io/r/base/Trig.html'>sin()</a></code>, <code><a href='https://rdrr.io/r/base/Hyperbolic.html'>sinh()</a></code>, <code><a href='https://rdrr.io/r/base/Trig.html'>sinpi()</a></code>, <code><a href='https://rdrr.io/r/base/MathFun.html'>sqrt()</a></code>, <code><a href='https://rdrr.io/r/base/sum.html'>sum()</a></code>, <code><a href='https://rdrr.io/r/base/Trig.html'>tan()</a></code>, <code><a href='https://rdrr.io/r/base/Hyperbolic.html'>tanh()</a></code>, <code><a href='https://rdrr.io/r/base/Trig.html'>tanpi()</a></code>, <code><a href='https://rdrr.io/r/base/Special.html'>trigamma()</a></code> and <code><a href='https://rdrr.io/r/base/Round.html'>trunc()</a></code>. Some functions of the <code>stats</code> package are also implemented: <code><a href='https://rdrr.io/r/stats/median.html'>median()</a></code>, <code><a href='https://rdrr.io/r/stats/quantile.html'>quantile()</a></code>, <code><a href='https://rdrr.io/r/stats/mad.html'>mad()</a></code>, <code><a href='https://rdrr.io/r/stats/IQR.html'>IQR()</a></code>, <code><a href='https://rdrr.io/r/stats/fivenum.html'>fivenum()</a></code>. Also, <code><a href='https://rdrr.io/r/grDevices/boxplot.stats.html'>boxplot.stats()</a></code> is supported. Since <code><a href='https://rdrr.io/r/stats/sd.html'>sd()</a></code> and <code><a href='https://rdrr.io/r/stats/cor.html'>var()</a></code> are non-generic functions, these could not be extended. Use <code><a href='https://rdrr.io/r/stats/mad.html'>mad()</a></code> as an alternative, or use e.g. <code><a href='https://rdrr.io/r/stats/sd.html'>sd(as.numeric(x))</a></code> where <code>x</code> is your vector of MIC values.</p>
<p><code>NA_mic_</code> is a missing value of the new <code>&lt;mic&gt;</code> class.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
<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 argument 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>
<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 data 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>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='va'>mic_data</span> <span class='op'>&lt;-</span> <span class='fu'>as.mic</span><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='st'>"&gt;=32"</span>, <span class='st'>"1.0"</span>, <span class='st'>"1"</span>, <span class='st'>"1.00"</span>, <span class='fl'>8</span>, <span class='st'>"&lt;=0.128"</span>, <span class='st'>"8"</span>, <span class='st'>"16"</span>, <span class='st'>"16"</span><span class='op'>)</span><span class='op'>)</span>
<span class='fu'>is.mic</span><span class='op'>(</span><span class='va'>mic_data</span><span class='op'>)</span>
<span class='co'># this can also coerce combined MIC/RSI values:</span>
<span class='fu'>as.mic</span><span class='op'>(</span><span class='st'>"&lt;=0.002; S"</span><span class='op'>)</span> <span class='co'># will return &lt;=0.002</span>
<span class='co'># mathematical processing treats MICs as [numeric] values</span>
<span class='fu'><a href='https://rdrr.io/r/stats/fivenum.html'>fivenum</a></span><span class='op'>(</span><span class='va'>mic_data</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/stats/quantile.html'>quantile</a></span><span class='op'>(</span><span class='va'>mic_data</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/all.html'>all</a></span><span class='op'>(</span><span class='va'>mic_data</span> <span class='op'>&lt;</span> <span class='fl'>512</span><span class='op'>)</span>
<span class='co'># interpret MIC values</span>
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span><span class='op'>(</span>x <span class='op'>=</span> <span class='fu'>as.mic</span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span>,
mo <span class='op'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"S. pneumoniae"</span><span class='op'>)</span>,
ab <span class='op'>=</span> <span class='st'>"AMX"</span>,
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span><span class='op'>)</span>
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span><span class='op'>(</span>x <span class='op'>=</span> <span class='fu'>as.mic</span><span class='op'>(</span><span class='fl'>4</span><span class='op'>)</span>,
mo <span class='op'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"S. pneumoniae"</span><span class='op'>)</span>,
ab <span class='op'>=</span> <span class='st'>"AMX"</span>,
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span><span class='op'>)</span>
<span class='co'># plot MIC values, see ?plot</span>
<span class='fu'><a href='plot.html'>plot</a></span><span class='op'>(</span><span class='va'>mic_data</span><span class='op'>)</span>
<span class='fu'><a href='plot.html'>plot</a></span><span class='op'>(</span><span class='va'>mic_data</span>, mo <span class='op'>=</span> <span class='st'>"E. coli"</span>, ab <span class='op'>=</span> <span class='st'>"cipro"</span><span class='op'>)</span>
</pre>
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