<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic • AMR (for R)</title><!-- favicons --><linkrel="icon"type="image/png"sizes="16x16"href="../favicon-16x16.png"><linkrel="icon"type="image/png"sizes="32x32"href="../favicon-32x32.png"><linkrel="apple-touch-icon"type="image/png"sizes="180x180"href="../apple-touch-icon.png"><linkrel="apple-touch-icon"type="image/png"sizes="120x120"href="../apple-touch-icon-120x120.png"><linkrel="apple-touch-icon"type="image/png"sizes="76x76"href="../apple-touch-icon-76x76.png"><linkrel="apple-touch-icon"type="image/png"sizes="60x60"href="../apple-touch-icon-60x60.png"><!-- jquery --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js"integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo="crossorigin="anonymous"></script><!-- Bootstrap --><linkhref="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css"rel="stylesheet"crossorigin="anonymous"><scriptsrc="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 --><linkrel="stylesheet"href="../bootstrap-toc.css"><scriptsrc="../bootstrap-toc.js"></script><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="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 --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- pkgdown --><linkhref="../pkgdown.css"rel="stylesheet"><scriptsrc="../pkgdown.js"></script><linkhref="../extra.css"rel="stylesheet"><scriptsrc="../extra.js"></script><metaproperty="og:title"content="Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic"><metaproperty="og:description"content='This transforms vectors to a new class mic, 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.'><metaproperty="og:image"content="https://msberends.github.io/AMR/logo.svg"><metaname="twitter:card"content="summary_large_image"><metaname="twitter:creator"content="@msberends"><metaname="twitter:site"content="@univgroningen"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
<p>This transforms vectors to a new class <code>mic</code>, which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology.</p>
<dd><p>a <ahref="https://rdrr.io/r/base/character.html"class="external-link">character</a> or <ahref="https://rdrr.io/r/base/numeric.html"class="external-link">numeric</a> vector</p></dd>
<dt>na.rm</dt>
<dd><p>a <ahref="https://rdrr.io/r/base/logical.html"class="external-link">logical</a> indicating whether missing values should be removed</p></dd>
</dl></div>
<divid="value">
<h2>Value</h2>
<p>Ordered <ahref="https://rdrr.io/r/base/factor.html"class="external-link">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 <ahref="https://rdrr.io/r/base/numeric.html"class="external-link">numeric</a> value.</p>
</div>
<divid="details">
<h2>Details</h2>
<p>To interpret MIC values as RSI values, use <code><ahref="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 <ahref="https://rdrr.io/r/base/factor.html"class="external-link">factor</a> with valid MIC values as <ahref="https://rdrr.io/r/base/factor.html"class="external-link">factor</a> levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:</p><divclass="sourceCode"><pre><code><spanclass="va">x</span><spanclass="op"><-</span><spanclass="fu"><ahref="../reference/random.html">random_mic</a></span><spanclass="op">(</span><spanclass="fl">10</span><spanclass="op">)</span>
<p>This makes it possible to maintain operators that often come with MIC values, such ">=" and "<=", even when filtering using <ahref="https://rdrr.io/r/base/numeric.html"class="external-link">numeric</a> values in data analysis, e.g.:</p><divclass="sourceCode"><pre><code><spanclass="va">x</span><spanclass="op">[</span><spanclass="va">x</span><spanclass="op">></span><spanclass="fl">4</span><spanclass="op">]</span>
<spanclass="fu"><ahref="https://rdrr.io/r/base/subset.html"class="external-link">subset</a></span><spanclass="op">(</span><spanclass="va">df</span>, <spanclass="va">x</span><spanclass="op">></span><spanclass="fl">4</span><spanclass="op">)</span><spanclass="co"># or with dplyr: df %>% filter(x > 4)</span>
The <ahref="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, an 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>
<p>On our website <ahref="https://msberends.github.io/AMR/">https://msberends.github.io/AMR/</a> you can find <ahref="https://msberends.github.io/AMR/articles/AMR.html">a comprehensive tutorial</a> about how to conduct AMR data analysis, the <ahref="https://msberends.github.io/AMR/reference/">complete documentation of all functions</a> and <ahref="https://msberends.github.io/AMR/articles/WHONET.html">an example analysis using WHONET data</a>.</p>
<spanclass="co"># this can also coerce combined MIC/RSI values:</span>
<spanclass="fu">as.mic</span><spanclass="op">(</span><spanclass="st">"<=0.002; S"</span><spanclass="op">)</span><spanclass="co"># will return <=0.002</span>
<spanclass="co"># mathematical processing treats MICs as [numeric] values</span>
mo <spanclass="op">=</span><spanclass="fu"><ahref="as.mo.html">as.mo</a></span><spanclass="op">(</span><spanclass="st">"S. pneumoniae"</span><spanclass="op">)</span>,
ab <spanclass="op">=</span><spanclass="st">"AMX"</span>,
mo <spanclass="op">=</span><spanclass="fu"><ahref="as.mo.html">as.mo</a></span><spanclass="op">(</span><spanclass="st">"S. pneumoniae"</span><spanclass="op">)</span>,
ab <spanclass="op">=</span><spanclass="st">"AMX"</span>,
<spanclass="fu"><ahref="plot.html">plot</a></span><spanclass="op">(</span><spanclass="va">mic_data</span>, mo <spanclass="op">=</span><spanclass="st">"E. coli"</span>, ab <spanclass="op">=</span><spanclass="st">"cipro"</span><spanclass="op">)</span>
