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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/HEAD/R/mic.R" class="external-link"><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>
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<div class="ref-description">
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<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>
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</div>
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<div id="ref-usage">
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<div class="sourceCode"><pre class="sourceCode r"><code><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="va">NA_mic_</span>
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<span class="fu">is.mic</span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
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<span class="co"># S3 method for mic</span>
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<span class="fu"><a href="https://rdrr.io/r/base/droplevels.html" class="external-link">droplevels</a></span><span class="op">(</span>
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<span class="va">x</span>,
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exclude <span class="op">=</span> <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/levels.html" class="external-link">levels</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="cn">NULL</span> <span class="kw">else</span> <span class="cn">NA</span>,
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as.mic <span class="op">=</span> <span class="cn">FALSE</span>,
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<span class="va">...</span>
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<span class="op">)</span></code></pre></div>
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</div>
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<div id="arguments">
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<h2>Arguments</h2>
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<dl><dt>x</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> or <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector</p></dd>
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<dt>na.rm</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> indicating whether missing values should be removed</p></dd>
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<dt>exclude</dt>
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<dd><p>factor levels which should be excluded from the result even if present, see <a href="https://rdrr.io/r/base/droplevels.html" class="external-link">droplevels()</a></p></dd>
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<dt>as.mic</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the <code><mic></code> class should be kept, defaults to <code>FALSE</code></p></dd>
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</dl></div>
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<div id="value">
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<h2>Value</h2>
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<p>Ordered <a href="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 <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> value.</p>
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</div>
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<div id="details">
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<h2>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 (2011-2022) and CLSI (2011-2022).</p>
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<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" class="external-link">factor</a> with valid MIC values as <a href="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><div class="sourceCode"><pre><code><span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span>
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<span class="va">x</span>
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<span class="co">#> Class <mic></span>
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<span class="co">#> [1] 16 1 8 8 64 >=128 0.0625 32 32 16</span>
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<span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">is.factor</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
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<span class="co">#> [1] TRUE</span>
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<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>
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<span class="co">#> [1] 32</span>
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<span class="fu"><a href="https://rdrr.io/r/stats/median.html" class="external-link">median</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
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<span class="co">#> [1] 26</span></code></pre></div>
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<p>This makes it possible to maintain operators that often come with MIC values, such ">=" and "<=", even when filtering using <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> values in data analysis, e.g.:</p><div class="sourceCode"><pre><code><span class="va">x</span><span class="op">[</span><span class="va">x</span> <span class="op">></span> <span class="fl">4</span><span class="op">]</span>
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<span class="co">#> Class <mic></span>
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<span class="co">#> [1] 16 8 8 64 >=128 32 32 16</span>
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<span class="va">df</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">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>
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<span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">df</span>, <span class="va">x</span> <span class="op">></span> <span class="fl">4</span><span class="op">)</span> <span class="co"># or with dplyr: df %>% filter(x > 4)</span>
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<span class="co">#> x hospital</span>
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<span class="co">#> 1 16 A</span>
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<span class="co">#> 5 64 A</span>
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<span class="co">#> 6 >=128 A</span>
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<span class="co">#> 8 32 A</span>
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<span class="co">#> 9 32 A</span>
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<span class="co">#> 10 16 A</span></code></pre></div>
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<p>The following <a href="https://rdrr.io/r/base/groupGeneric.html" class="external-link">generic functions</a> are implemented for the MIC class: <code>!</code>, <code>!=</code>, <code>%%</code>, <code>%/%</code>, <code>&</code>, <code>*</code>, <code>+</code>, <code>-</code>, <code>/</code>, <code><</code>, <code><=</code>, <code>==</code>, <code>></code>, <code>>=</code>, <code>^</code>, <code>|</code>, <code><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs()</a></code>, <code><a href="https://rdrr.io/r/base/Trig.html" class="external-link">acos()</a></code>, <code><a href="https://rdrr.io/r/base/Hyperbolic.html" class="external-link">acosh()</a></code>, <code><a href="https://rdrr.io/r/base/all.html" class="external-link">all()</a></code>, <code><a href="https://rdrr.io/r/base/any.html" class="external-link">any()</a></code>, <code><a href="https://rdrr.io/r/base/Trig.html" class="external-link">asin()</a></code>, <code><a href="https://rdrr.io/r/base/Hyperbolic.html" class="external-link">asinh()</a></code>, <code><a href="https://rdrr.io/r/base/Trig.html" class="external-link">atan()</a></code>, <code><a href="https://rdrr.io/r/base/Hyperbolic.html" class="external-link">atanh()</a></code>, <code><a href="https://rdrr.io/r/base/Round.html" class="external-link">ceiling()</a></code>, <code><a href="https://rdrr.io/r/base/Trig.html" class="external-link">cos()</a></code>, <code><a href="https://rdrr.io/r/base/Hyperbolic.html" class="external-link">cosh()</a></code>, <code><a href="https://rdrr.io/r/base/Trig.html" class="external-link">cospi()</a></code>, <code><a href="https://rdrr.io/r/base/cumsum.html" class="external-link">cummax()</a></code>, <code><a href="https://rdrr.io/r/base/cumsum.html" class="external-link">cummin()</a></code>, <code><a href="https://rdrr.io/r/base/cumsum.html" class="external-link">cumprod()</a></code>, <code><a href="https://rdrr.io/r/base/cumsum.html" class="external-link">cumsum()</a></code>, <code><a href="https://rdrr.io/r/base/Special.html" class="external-link">digamma()</a></code>, <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">exp()</a></code>, <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">expm1()</a></code>, <code><a href="https://rdrr.io/r/base/Round.html" class="external-link">floor()</a></code>, <code><a href="https://rdrr.io/r/base/Special.html" class="external-link">gamma()</a></code>, <code><a href="https://rdrr.io/r/base/Special.html" class="external-link">lgamma()</a></code>, <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">log()</a></code>, <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">log1p()</a></code>, <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2()</a></code>, <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">log10()</a></code>, <code><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max()</a></code>, <code><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean()</a></code>, <code><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">min()</a></code>, <code><a href="https://rdrr.io/r/base/prod.html" class="external-link">prod()</a></code>, <code><a href="https://rdrr.io/r/base/range.html" class="external-link">range()</a></code>, <code><a href="https://rdrr.io/r/base/Round.html" class="external-link">round()</a></code>, <code><a href="https://rdrr.io/r/base/sign.html" class="external-link">sign()</a></code>, <code><a href="https://rdrr.io/r/base/Round.html" class="external-link">signif()</a></code>, <code><a href="https://rdrr.io/r/base/Trig.html" class="external-link">sin()</a></code>, <code><a href="https://rdrr.io/r/base/Hyperbolic.html" class="external-link">sinh()</a></code>, <code><a href="https://rdrr.io/r/base/Trig.html" class="external-link">sinpi()</a></code>, <code><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt()</a></code>, <code><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum()</a></code>, <code><a href="https://rdrr.io/r/base/Trig.html" class="external-link">tan()</a></code>, <code><a href="https://rdrr.io/r/base/Hyperbolic.html" class="external-link">tanh()</a></code>, <code><a href="https://rdrr.io/r/base/Trig.html" class="external-link">tanpi()</a></code>, <code><a href="https://rdrr.io/r/base/Special.html" class="external-link">trigamma()</a></code> and <code><a href="https://rdrr.io/r/base/Round.html" class="external-link">trunc()</a></code>. Some functions of the <code>stats</code> package are also implemented: <code><a href="https://rdrr.io/r/stats/median.html" class="external-link">median()</a></code>, <code><a href="https://rdrr.io/r/stats/quantile.html" class="external-link">quantile()</a></code>, <code><a href="https://rdrr.io/r/stats/mad.html" class="external-link">mad()</a></code>, <code><a href="https://rdrr.io/r/stats/IQR.html" class="external-link">IQR()</a></code>, <code><a href="https://rdrr.io/r/stats/fivenum.html" class="external-link">fivenum()</a></code>. Also, <code><a href="https://rdrr.io/r/grDevices/boxplot.stats.html" class="external-link">boxplot.stats()</a></code> is supported. Since <code><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd()</a></code> and <code><a href="https://rdrr.io/r/stats/cor.html" class="external-link">var()</a></code> are non-generic functions, these could not be extended. Use <code><a href="https://rdrr.io/r/stats/mad.html" class="external-link">mad()</a></code> as an alternative, or use e.g. <code>sd(as.numeric(x))</code> where <code>x</code> is your vector of MIC values.</p>
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<p>Using <code><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double()</a></code> or <code><a href="https://rdrr.io/r/base/numeric.html" class="external-link">as.numeric()</a></code> on MIC values will remove the operators and return a numeric vector. Do <strong>not</strong> use <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on MIC values as by the <span style="R">R</span> convention on <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a>s, it will return the index of the factor levels (which is often useless for regular users).</p>
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<p>Use <code><a href="https://rdrr.io/r/base/droplevels.html" class="external-link">droplevels()</a></code> to drop unused levels. At default, it will return a plain factor. Use <code>droplevels(..., as.mic = TRUE)</code> to maintain the <code><mic></code> class.</p>
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<p><code>NA_mic_</code> is a missing value of the new <code><mic></code> class, analogous to e.g. base <span style="R">R</span>'s <code><a href="https://rdrr.io/r/base/NA.html" class="external-link">NA_character_</a></code>.</p>
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</div>
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<div id="stable-lifecycle">
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<h2>Stable Lifecycle</h2>
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<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument will be deprecated and first continue to work, but will emit a 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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</div>
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<div id="read-more-on-our-website-">
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<h2>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 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>
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</div>
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<div id="see-also">
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<h2>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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</div>
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<div id="ref-examples">
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<h2>Examples</h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><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" class="external-link">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"># mathematical processing treats MICs as [numeric] values</span>
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<span class="fu"><a href="https://rdrr.io/r/stats/fivenum.html" class="external-link">fivenum</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/stats/quantile.html" class="external-link">quantile</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/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="va">mic_data</span> <span class="op"><</span> <span class="fl">512</span><span class="op">)</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="co"># plot MIC values, see ?plot</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="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>
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</code></pre></div>
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<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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