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@@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9001</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9002</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -167,9 +167,11 @@
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><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>, keep_operators <span class="op">=</span> <span class="st">"all"</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">is.mic</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span>
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<span></span>
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<span><span class="va">NA_mic_</span></span>
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<span></span>
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<span><span class="fu">is.mic</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span>
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<span><span class="fu">rescale_mic</span><span class="op">(</span><span class="va">x</span>, <span class="va">mic_range</span>, keep_operators <span class="op">=</span> <span class="st">"edges"</span>, as.mic <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
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<span></span>
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<span><span class="co"># S3 method for mic</span></span>
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<span><span class="fu"><a href="https://rdrr.io/r/base/droplevels.html" class="external-link">droplevels</a></span><span class="op">(</span><span class="va">x</span>, as.mic <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
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@@ -189,6 +191,10 @@
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<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> specifying how to handle operators (such as <code>></code> and <code><=</code>) in the input. Accepts one of three values: <code>"all"</code> (or <code>TRUE</code>) to keep all operators, <code>"none"</code> (or <code>FALSE</code>) to remove all operators, or <code>"edges"</code> to keep operators only at both ends of the range.</p></dd>
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<dt>mic_range</dt>
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<dd><p>a manual range to plot the MIC values, e.g., <code>mic_range = c(0.001, 32)</code>. Use <code>NA</code> to set no limit on one side, e.g., <code>mic_range = c(NA, 32)</code>.</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 - the default is <code>FALSE</code></p></dd>
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@@ -237,6 +243,7 @@
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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">IQLine truncated
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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>With <code>rescale_mic()</code>, existing MIC ranges can be rescaled to a defined range of MIC values. This can be useful to better compare MIC distributions.</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 class="section level2">
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@@ -267,6 +274,11 @@
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<span class="r-in"><span><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></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] TRUE</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># rescale MICs using rescale_mic()</span></span></span>
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<span class="r-in"><span><span class="fu">rescale_mic</span><span class="op">(</span><span class="va">mic_data</span>, mic_range <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="fl">4</span>, <span class="fl">16</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] >=16 <=4 <=4 <=4 8 <=4 8 >=16 >=16</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># interpret MIC values</span></span></span>
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<span class="r-in"><span><span class="fu"><a href="as.sir.html">as.sir</a></span><span class="op">(</span></span></span>
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<span class="r-in"><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>,</span></span>
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