Commit ba2da118 authored by Armin Rauschenberger's avatar Armin Rauschenberger
Browse files

automation

parent 46553707
# Generated by roxygen2: do not edit by hand # Generated by roxygen2: do not edit by hand
S3method(coef,bilasso)
S3method(plot,bilasso)
S3method(predict,bilasso)
export() export()
export(bilasso) export(bilasso)
export(bilasso_compare) export(bilasso_compare)
......
## spliceQTL 0.0.0 (2018-06-12) ## colasso 0.0.0 (2019-01-08)
* Added functions * Added functions
\ No newline at end of file
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...@@ -101,9 +101,9 @@ ...@@ -101,9 +101,9 @@
<small>Source: <a href='https://github.com/rauschenberger/colasso/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/rauschenberger/colasso/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="spliceqtl-0-0-0-2018-06-12" class="section level2"> <div id="colasso-0-0-0-2019-01-08" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#spliceqtl-0-0-0-2018-06-12" class="anchor"></a>spliceQTL 0.0.0 (2018-06-12)</h2> <a href="#colasso-0-0-0-2019-01-08" class="anchor"></a>colasso 0.0.0 (2019-01-08)</h2>
<ul> <ul>
<li>Added functions</li> <li>Added functions</li>
</ul> </ul>
...@@ -114,7 +114,7 @@ ...@@ -114,7 +114,7 @@
<div id="tocnav"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#spliceqtl-0-0-0-2018-06-12">0.0.0</a></li> <li><a href="#colasso-0-0-0-2019-01-08">0.0.0</a></li>
</ul> </ul>
</div> </div>
</div> </div>
......
...@@ -111,9 +111,9 @@ ...@@ -111,9 +111,9 @@
</div> </div>
<pre class="usage"><span class='fu'>bilasso</span>(<span class='no'>y</span>, <span class='no'>cutoff</span>, <span class='no'>X</span>, <span class='kw'>npi</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>nsigma</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>sigma</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <pre class="usage"><span class='fu'>bilasso</span>(<span class='no'>y</span>, <span class='no'>cutoff</span>, <span class='no'>X</span>, <span class='kw'>npi</span> <span class='kw'>=</span> <span class='fl'>101</span>, <span class='kw'>pi</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>nsigma</span> <span class='kw'>=</span> <span class='fl'>99</span>,
<span class='kw'>nfolds</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>foldid</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>type.measure</span> <span class='kw'>=</span> <span class='st'>"deviance"</span>, <span class='kw'>sigma</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>nfolds</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>foldid</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>logistic</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre> <span class='kw'>type.measure</span> <span class='kw'>=</span> <span class='st'>"deviance"</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments"> <table class="ref-arguments">
...@@ -133,6 +133,16 @@ value between <code>min(y)</code> and <code>max(y)</code></p></td> ...@@ -133,6 +133,16 @@ value between <code>min(y)</code> and <code>max(y)</code></p></td>
<td><p>covariates<strong>:</strong> <td><p>covariates<strong>:</strong>
numeric matrix with \(n\) rows (samples) numeric matrix with \(n\) rows (samples)
and \(p\) columns (variables)</p></td> and \(p\) columns (variables)</p></td>
</tr>
<tr>
<th>npi</th>
<td><p>number of <code>pi</code> values</p></td>
</tr>
<tr>
<th>pi</th>
<td><p>pi sequence<strong>:</strong>
vector of values in the unit interval;
or <code>NULL</code> (default sequence)</p></td>
</tr> </tr>
<tr> <tr>
<th>nsigma</th> <th>nsigma</th>
...@@ -158,12 +168,6 @@ or <code>NULL</code> (balance)</p></td> ...@@ -158,12 +168,6 @@ or <code>NULL</code> (balance)</p></td>
<th>type.measure</th> <th>type.measure</th>
<td><p>loss function for binary classification <td><p>loss function for binary classification
(linear regression uses the deviance)</p></td> (linear regression uses the deviance)</p></td>
</tr>
<tr>
<th>logistic</th>
<td><p>fit logistic regression for comparison<strong>:</strong>
logical
(currently all methods require <code>TRUE</code>)</p></td>
</tr> </tr>
<tr> <tr>
<th>...</th> <th>...</th>
......
...@@ -111,7 +111,8 @@ ...@@ -111,7 +111,8 @@
</div> </div>
<pre class="usage"><span class='fu'>bilasso_compare</span>(<span class='no'>y</span>, <span class='no'>cutoff</span>, <span class='no'>X</span>, <span class='kw'>nfolds</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>type.measure</span> <span class='kw'>=</span> <span class='st'>"deviance"</span>)</pre> <pre class="usage"><span class='fu'>bilasso_compare</span>(<span class='no'>y</span>, <span class='no'>cutoff</span>, <span class='no'>X</span>, <span class='kw'>nfolds</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>foldid</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>type.measure</span> <span class='kw'>=</span> <span class='st'>"deviance"</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments"> <table class="ref-arguments">
...@@ -136,6 +137,12 @@ and \(p\) columns (variables)</p></td> ...@@ -136,6 +137,12 @@ and \(p\) columns (variables)</p></td>
<th>nfolds</th> <th>nfolds</th>
<td><p>number of folds</p></td> <td><p>number of folds</p></td>
</tr> </tr>
<tr>
<th>foldid</th>
<td><p>fold identifiers<strong>:</strong>
vector with entries between \(1\) and <code>nfolds</code>;
or <code>NULL</code> (balance)</p></td>
</tr>
<tr> <tr>
<th>type.measure</th> <th>type.measure</th>
<td><p>loss function for binary classification <td><p>loss function for binary classification
......
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<h1>to do</h1>
<small class="dont-index">Source: <a href='https://github.com/rauschenberger/colasso/blob/master/R/bilasso.R'><code>R/bilasso.R</code></a></small>
<div class="hidden name"><code>coef.bilasso.Rd</code></div>
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<div class="ref-description">
<p>to do</p>
</div>
<pre class="usage"><span class='co'># S3 method for bilasso</span>
<span class='fu'>coef</span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>object</th>
<td><p>bilasso object</p></td>
</tr>
<tr>
<th>...</th>
<td><p>to do</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='fl'>NA</span></div><div class='output co'>#&gt; [1] NA</div><div class='input'>
</div></pre>
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<h2>Contents</h2>
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<li><a href="#arguments">Arguments</a></li>
<li><a href="#examples">Examples</a></li>
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<h1>Arguments</h1>
<small class="dont-index">Source: <a href='https://github.com/rauschenberger/colasso/blob/master/R/bilasso.R'><code>R/bilasso.R</code></a></small>
<div class="hidden name"><code>dot-equal.Rd</code></div>
</div>
<div class="ref-description">
<p>Verifies whether two or more arguments are identical.</p>
</div>
<pre class="usage"><span class='fu'>.equal</span>(<span class='no'>...</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>...</th>
<td><p>scalars, vectors, or matrices of equal dimensions</p></td>
</tr>
<tr>
<th>na.rm</th>
<td><p>remove missing values<strong>:</strong>
logical</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='fl'>NA</span></div><div class='output co'>#&gt; [1] NA</div><div class='input'>
</div></pre>
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<h2>Contents</h2>
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<li><a href="#examples">Examples</a></li>
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...@@ -129,6 +129,12 @@ ...@@ -129,6 +129,12 @@
<td><p>Comparison</p></td> <td><p>Comparison</p></td>
</tr><tr> </tr><tr>
<td>
<p><code><a href="coef.bilasso.html">coef(<i>&lt;bilasso&gt;</i>)</a></code> </p>
</td>
<td><p>to do</p></td>
</tr><tr>
<td> <td>
<p><code><a href="colasso.html">colasso()</a></code> </p> <p><code><a href="colasso.html">colasso()</a></code> </p>
</td> </td>
...@@ -159,10 +165,28 @@ ...@@ -159,10 +165,28 @@
<td><p>Arguments</p></td> <td><p>Arguments</p></td>
</tr><tr> </tr><tr>
<td>
<p><code><a href="dot-equal.html">.equal()</a></code> </p>
</td>
<td><p>Arguments</p></td>
</tr><tr>
<td> <td>
<p><code><a href="moderate.html">moderate()</a></code> </p> <p><code><a href="moderate.html">moderate()</a></code> </p>
</td> </td>
<td><p>moderated response (trial)</p></td> <td><p>moderated response (trial)</p></td>
</tr><tr>
<td>
<p><code><a href="plot.bilasso.html">plot(<i>&lt;bilasso&gt;</i>)</a></code> </p>
</td>
<td><p>to do</p></td>
</tr><tr>
<td>
<p><code><a href="predict.bilasso.html">predict(<i>&lt;bilasso&gt;</i>)</a></code> </p>
</td>
<td><p>to do</p></td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
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