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(v1.7.1.9022) rely on vctrs for ab selectors

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dr. M.S. (Matthijs) Berends committed 2021-07-23 21:42:11 +02:00
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docs/reference/as.mic.html
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@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
<ul class="nav navbar-nav">
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<span class="fa fa-question-circle"></span>
How to
@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span>
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
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<li>
<a href="../articles/datasets.html">
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Data sets for download / own use
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<a href="../articles/PCA.html">
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Conduct principal component analysis for AMR
</a>
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<li>
<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
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<a href="../articles/WHONET.html">
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Work with WHONET data
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Import data from SPSS/SAS/Stata
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<a href="../articles/EUCAST.html">
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Apply EUCAST rules
</a>
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<a href="../reference/mo_property.html">
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Get properties of a microorganism
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Get properties of an antibiotic
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Other: benchmarks
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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Survey
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@@ -242,9 +250,9 @@
<p>This ransforms 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>
<div class="ref-usage 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>
<span class='fu'>is.mic</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></pre>
<span class='fu'>is.mic</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -265,7 +273,7 @@
<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>
<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 class='sourceCode r'><code><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>
@@ -278,9 +286,9 @@
<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>
</code></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>
<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 class='sourceCode r'><code><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>
@@ -293,7 +301,7 @@
<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>
</code></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.iLine truncated
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
@@ -313,7 +321,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><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>
@@ -337,7 +345,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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>
</code></pre></div>
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@@ -349,11 +357,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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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>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -362,6 +370,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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