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<h1>Transform input to minimum inhibitory concentrations (MIC)</h1>
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<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mic.R'><code>R/mic.R</code></a></small>
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<div class="hidden name"><code>as.mic.Rd</code></div>
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<div class="ref-description">
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<p>This transforms a vector to a new class <code>mic</code>, which is an ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with valid minimum inhibitory concentrations (MIC) as levels. Invalid MIC values will be translated as <code>NA</code> with a warning.</p>
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<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>
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<span class='fu'>is.mic</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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<colgroup><col class="name" /><col class="desc" /></colgroup>
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<tr>
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<th>x</th>
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<td><p>vector</p></td>
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</tr>
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<tr>
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<th>na.rm</th>
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<td><p>a logical indicating whether missing values should be removed</p></td>
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</tr>
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</table>
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<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
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<p>Ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with additional class <code>mic</code></p>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<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>
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<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
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<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
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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>
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<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>
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<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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<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>
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<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
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<div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><span class='va'>mic_data</span> <span class='op'><-</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'>">=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'>"<=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>
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<span class='fu'>is.mic</span><span class='op'>(</span><span class='va'>mic_data</span><span class='op'>)</span>
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<span class='co'># this can also coerce combined MIC/RSI values:</span>
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<span class='fu'>as.mic</span><span class='op'>(</span><span class='st'>"<=0.002; S"</span><span class='op'>)</span> <span class='co'># will return <=0.002</span>
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<span class='co'># interpret MIC values</span>
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<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>,
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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>,
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ab <span class='op'>=</span> <span class='st'>"AMX"</span>,
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guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span><span class='op'>)</span>
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<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>,
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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>,
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ab <span class='op'>=</span> <span class='st'>"AMX"</span>,
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guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span><span class='op'>)</span>
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<span class='fu'><a href='plot.html'>plot</a></span><span class='op'>(</span><span class='va'>mic_data</span><span class='op'>)</span>
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<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span><span class='op'>(</span><span class='va'>mic_data</span><span class='op'>)</span>
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</pre>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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