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(v1.8.1.9004) fix for table() on MICs

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dr. M.S. (Matthijs) Berends committed 2022-05-09 21:33:27 +02:00
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docs/404.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9004</span>
</span>
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docs/LICENSE-text.html
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</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="Released version">1.8.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9004</span>
</span>
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docs/articles/datasets.html
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@@ -44,7 +44,7 @@
</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="Released version">1.8.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9004</span>
</span>
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docs/authors.html
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</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="Released version">1.8.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9004</span>
</span>
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docs/index.html
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@@ -47,7 +47,7 @@
</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="Released version">1.8.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9004</span>
</span>
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docs/news/index.html
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</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="Released version">1.8.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9004</span>
</span>
</div>
@@ -157,12 +157,12 @@
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="1.8.1.9003" id="amr-1819003">
<code>AMR</code> 1.8.1.9003<a class="anchor" aria-label="anchor" href="#amr-1819003"></a></h2>
<h2 class="page-header" data-toc-text="1.8.1.9004" id="amr-1819004">
<code>AMR</code> 1.8.1.9004<a class="anchor" aria-label="anchor" href="#amr-1819004"></a></h2>
<div class="section level3">
<h3 id="last-updated-may-1-8-1-9003"><small>Last updated: 9 May 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-may-1-8-1-9003"></a></h3>
<h3 id="last-updated-may-1-8-1-9004"><small>Last updated: 9 May 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-may-1-8-1-9004"></a></h3>
<div class="section level4">
<h4 id="changed-1-8-1-9003">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9003"></a></h4>
<h4 id="changed-1-8-1-9004">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9004"></a></h4>
<ul><li>Removed <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> for MIC values, since MIC are not integer values and running <code><a href="https://rdrr.io/r/base/table.html" class="external-link">table()</a></code> on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on <code>factor</code>s work)</li>
<li>
<code><a href="https://rdrr.io/r/base/droplevels.html" class="external-link">droplevels()</a></code> on MIC will now return a common <code>factor</code> at default and will lose the <code>&lt;mic&gt;</code> class. Use <code>droplevels(..., as.mic = TRUE)</code> to keep the <code>&lt;mic&gt;</code> class.</li>
docs/reference/as.mic.html
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</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="Released version">1.8.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9004</span>
</span>
</div>
@@ -30,7 +30,7 @@
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
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How to
@@ -166,19 +166,27 @@
<span class="va">NA_mic_</span>
<span class="fu">is.mic</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></code></pre></div>
<span class="fu">is.mic</span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
<span class="co"># S3 method for mic</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>,
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>,
as.mic <span class="op">=</span> <span class="cn">FALSE</span>,
<span class="va">...</span>
<span class="op">)</span></code></pre></div>
</div>
<div id="format">
<h2>Format</h2>
<p>An object of class <code>mic</code> (inherits from <code>ordered</code>, <code>factor</code>) of length 1.</p>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>x</dt>
<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>
<dt>na.rm</dt>
<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>
<dt>exclude</dt>
<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>
<dt>as.mic</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the <code>&lt;mic&gt;</code> class should be kept, defaults to <code>FALSE</code></p></dd>
</dl></div>
<div id="value">
<h2>Value</h2>
@@ -186,7 +194,7 @@
</div>
<div id="details">
<h2>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>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 (2011-2021) and CLSI (2010-2021).</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" 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">&lt;-</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>
<span class="va">x</span>
<span class="co">#&gt; Class &lt;mic&gt;</span>
@@ -216,7 +224,9 @@
<span class="co">#&gt; 10 16 A</span></code></pre></div>
<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>&amp;</code>, <code>*</code>, <code>+</code>, <code>-</code>, <code>/</code>, <code>&lt;</code>, <code>&lt;=</code>, <code>==</code>, <code>&gt;</code>, <code>&gt;=</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
<p><code>NA_mic_</code> is a missing value of the new <code>&lt;mic&gt;</code> class.</p>
<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>
<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>&lt;mic&gt;</code> class.</p>
<p><code>NA_mic_</code> is a missing value of the new <code>&lt;mic&gt;</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>
</div>
<div id="stable-lifecycle">
<h2>Stable Lifecycle</h2>
@@ -277,7 +287,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
</div>
</footer></div>
docs/reference/as.rsi.html
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@@ -17,7 +17,7 @@
</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="Released version">1.8.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9004</span>
</span>
</div>
@@ -225,7 +225,7 @@
<dt>ab</dt>
<dd><p>any (vector of) text that can be coerced to a valid antimicrobial code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
<dt>guideline</dt>
<dd><p>defaults to the latest included EUCAST guideline, see <em>Details</em> for all options</p></dd>
<dd><p>defaults to the latest included EUCAST guideline, supports EUCAST (2011-2021) and CLSI (2010-2021), see <em>Details</em></p></dd>
<dt>uti</dt>
<dd><p>(Urinary Tract Infection) A vector with <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a>s (<code>TRUE</code> or <code>FALSE</code>) to specify whether a UTI specific interpretation from the guideline should be chosen. For using <code>as.rsi()</code> on a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, this can also be a column containing <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a>s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See <em>Examples</em>.</p></dd>
<dt>conserve_capped_values</dt>
@@ -289,7 +289,7 @@
<p>The function <code>is.rsi.eligible()</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> argument. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, it iterates over all columns and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
</div>
<p><code>NA_rsi_</code> is a missing value of the new <code>&lt;rsi&gt;</code> class.</p>
<p><code>NA_rsi_</code> is a missing value of the new <code>&lt;rsi&gt;</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>
</div>
<div id="interpretation-of-r-and-s-i">
<h2>Interpretation of R and S/I</h2>
@@ -408,7 +408,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.rsi.eligible</span>, <span class="va">as.rsi</span><span class="op">)</span>
<span class="co"># note: from dplyr 1.0.0 on, this will be: </span>
<span class="co"># since dplyr 1.0.0, this can also be: </span>
<span class="co"># example_isolates %&gt;%</span>
<span class="co"># mutate(across(where(is.rsi.eligible), as.rsi))</span>
<span class="op">}</span>
docs/reference/index.html
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@@ -17,7 +17,7 @@
</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="Released version">1.8.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9004</span>
</span>
</div>
@@ -200,7 +200,7 @@
</td>
<td><p>Interpret MIC and Disk Values, or Clean Raw R/SI Data</p></td>
</tr><tr><td>
<p><code><a href="as.mic.html">as.mic()</a></code> <code><a href="as.mic.html">NA_mic_</a></code> <code><a href="as.mic.html">is.mic()</a></code> </p>
<p><code><a href="as.mic.html">as.mic()</a></code> <code><a href="as.mic.html">NA_mic_</a></code> <code><a href="as.mic.html">is.mic()</a></code> <code><a href="as.mic.html">droplevels(<i>&lt;mic&gt;</i>)</a></code> </p>
</td>
<td><p>Transform Input to Minimum Inhibitory Concentrations (MIC)</p></td>
</tr><tr><td>
docs/survey.html
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@@ -17,7 +17,7 @@
</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="Released version">1.8.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9004</span>
</span>
</div>