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(v1.6.0.9021) join functions update

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dr. M.S. (Matthijs) Berends
2021-05-12 18:15:03 +02:00
parent 3319fbae58
commit 29dbfa2f49
119 changed files with 973 additions and 1040 deletions
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docs/reference/as.mic.html
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@ -82,7 +82,7 @@
</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">1.6.0.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9021</span>
</span>
</div>
@ -90,14 +90,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
<span class="fas fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-question-circle"></span>
<span class="fas fa-question-circle"></span>
How to
@ -106,77 +106,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@ -185,21 +185,21 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
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<span class="fas fa-users"></span>
Authors
</a>
</li>
<li>
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
<span class="far fa-newspaper"></span>
Changelog
</a>
@ -208,14 +208,14 @@
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
<span class="fab fa-github"></span>
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
<span class="fas fa-clipboard-list"></span>
Survey
</a>
@ -251,21 +251,21 @@
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>character or numeric vector</p></td>
<td><p>a <a href='https://rdrr.io/r/base/character.html'>character</a> or <a href='https://rdrr.io/r/base/numeric.html'>numeric</a> vector</p></td>
</tr>
<tr>
<th>na.rm</th>
<td><p>a logical indicating whether missing values should be removed</p></td>
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> indicating whether missing values should be removed</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Ordered <a href='https://rdrr.io/r/base/factor.html'>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 numeric value.</p>
<p>Ordered <a href='https://rdrr.io/r/base/factor.html'>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'>numeric</a> value.</p>
<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 factor with valid MIC values as factor 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><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>
@ -280,7 +280,7 @@
<span class='co'>#&gt; [1] 26</span>
</pre>
<p>This makes it possible to maintain operators that often come with MIC values, such "&gt;=" and "&lt;=", even when filtering using numeric 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><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>
@ -319,7 +319,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># this can also coerce combined MIC/RSI values:</span>
<span class='fu'>as.mic</span><span class='op'>(</span><span class='st'>"&lt;=0.002; S"</span><span class='op'>)</span> <span class='co'># will return &lt;=0.002</span>
<span class='co'># mathematical processing treats MICs as numeric values</span>
<span class='co'># mathematical processing treats MICs as [numeric] values</span>
<span class='fu'><a href='https://rdrr.io/r/stats/fivenum.html'>fivenum</a></span><span class='op'>(</span><span class='va'>mic_data</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/stats/quantile.html'>quantile</a></span><span class='op'>(</span><span class='va'>mic_data</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/all.html'>all</a></span><span class='op'>(</span><span class='va'>mic_data</span> <span class='op'>&lt;</span> <span class='fl'>512</span><span class='op'>)</span>