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Plot method for Orthogonalizing EM fitted objects" />
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<h1>Plot method for Orthogonalizing EM fitted objects</h1>
<small class="dont-index">Source: <a href='https://github.com/jaredhuling/oem/blob/master/R/methods.R'><code>R/methods.R</code></a></small>
<div class="hidden name"><code>plot.Rd</code></div>
</div>
<div class="ref-description">
<p>Plot method for Orthogonalizing EM fitted objects</p>
<p>Plot method for Orthogonalizing EM fitted objects</p>
</div>
<pre class="usage"><span class='co'># S3 method for oem</span>
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(
<span class='no'>x</span>,
<span class='kw'>which.model</span> <span class='kw'>=</span> <span class='fl'>1</span>,
<span class='kw'>xvar</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"norm"</span>, <span class='st'>"lambda"</span>, <span class='st'>"loglambda"</span>, <span class='st'>"dev"</span>),
<span class='kw'>labsize</span> <span class='kw'>=</span> <span class='fl'>0.6</span>,
<span class='kw'>xlab</span> <span class='kw'>=</span> <span class='no'>iname</span>,
<span class='kw'>ylab</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>main</span> <span class='kw'>=</span> <span class='no'>x</span>$<span class='no'>penalty</span>[<span class='no'>which.model</span>],
<span class='no'>...</span>
)
<span class='co'># S3 method for cv.oem</span>
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>which.model</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>sign.lambda</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>...</span>)
<span class='co'># S3 method for xval.oem</span>
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(
<span class='no'>x</span>,
<span class='kw'>which.model</span> <span class='kw'>=</span> <span class='fl'>1</span>,
<span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"cv"</span>, <span class='st'>"coefficients"</span>),
<span class='kw'>xvar</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"norm"</span>, <span class='st'>"lambda"</span>, <span class='st'>"loglambda"</span>, <span class='st'>"dev"</span>),
<span class='kw'>labsize</span> <span class='kw'>=</span> <span class='fl'>0.6</span>,
<span class='kw'>xlab</span> <span class='kw'>=</span> <span class='no'>iname</span>,
<span class='kw'>ylab</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>main</span> <span class='kw'>=</span> <span class='no'>x</span>$<span class='no'>penalty</span>[<span class='no'>which.model</span>],
<span class='kw'>sign.lambda</span> <span class='kw'>=</span> <span class='fl'>1</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>x</th>
<td><p>fitted "oem" model object</p></td>
</tr>
<tr>
<th>which.model</th>
<td><p>If multiple penalties are fit and returned in the same oem object, the which.model argument is used to
specify which model to plot. For example, if the oem object <code>"oemobj"</code> was fit with argument
<code>penalty = c("lasso", "grp.lasso")</code>, then <code>which.model = 2</code> provides a plot for the group lasso model.</p></td>
</tr>
<tr>
<th>xvar</th>
<td><p>What is on the X-axis. <code>"norm"</code> plots against the L1-norm of the coefficients, <code>"lambda"</code> against the log-lambda sequence, and <code>"dev"</code>
against the percent deviance explained.</p></td>
</tr>
<tr>
<th>labsize</th>
<td><p>size of labels for variable names. If labsize = 0, then no variable names will be plotted</p></td>
</tr>
<tr>
<th>xlab</th>
<td><p>label for x-axis</p></td>
</tr>
<tr>
<th>ylab</th>
<td><p>label for y-axis</p></td>
</tr>
<tr>
<th>main</th>
<td><p>main title for plot</p></td>
</tr>
<tr>
<th>...</th>
<td><p>other graphical parameters for the plot</p></td>
</tr>
<tr>
<th>sign.lambda</th>
<td><p>Either plot against log(lambda) (default) or its negative if <code>sign.lambda = -1</code>.</p></td>
</tr>
<tr>
<th>type</th>
<td><p>one of <code>"cv"</code> or <code>"coefficients"</code>. <code>type = "cv"</code> will produce a plot of cross validation results like plot.cv.oem.
<code>type = "coefficients"</code> will produce a coefficient path plot like <code>plot.oem()</code></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='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span>(<span class='fl'>123</span>)
<span class='no'>n.obs</span> <span class='kw'><-</span> <span class='fl'>1e4</span>
<span class='no'>n.vars</span> <span class='kw'><-</span> <span class='fl'>100</span>
<span class='no'>n.obs.test</span> <span class='kw'><-</span> <span class='fl'>1e3</span>
<span class='no'>true.beta</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fu'><a href='https://rdrr.io/r/stats/Uniform.html'>runif</a></span>(<span class='fl'>15</span>, -<span class='fl'>0.5</span>, <span class='fl'>0.5</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0</span>, <span class='no'>n.vars</span> - <span class='fl'>15</span>))
<span class='no'>x</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span>(<span class='no'>n.obs</span> * <span class='no'>n.vars</span>), <span class='no'>n.obs</span>, <span class='no'>n.vars</span>)
<span class='no'>y</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span>(<span class='no'>n.obs</span>, <span class='kw'>sd</span> <span class='kw'>=</span> <span class='fl'>3</span>) + <span class='no'>x</span> <span class='kw'>%*%</span> <span class='no'>true.beta</span>
<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='oem.html'>oem</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>x</span>, <span class='kw'>y</span> <span class='kw'>=</span> <span class='no'>y</span>, <span class='kw'>penalty</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"lasso"</span>, <span class='st'>"grp.lasso"</span>), <span class='kw'>groups</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>1</span>:<span class='fl'>10</span>, <span class='kw'>each</span> <span class='kw'>=</span> <span class='fl'>10</span>))
<span class='fu'><a href='https://rdrr.io/r/graphics/layout.html'>layout</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='fl'>1</span>:<span class='fl'>2</span>, <span class='kw'>ncol</span> <span class='kw'>=</span> <span class='fl'>2</span>))
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>which.model</span> <span class='kw'>=</span> <span class='fl'>1</span>)
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>which.model</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='output co'>#> <span class='warning'>Warning: collapsing to unique 'x' values</span></div><div class='img'><img src='plot-1.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span>(<span class='fl'>123</span>)
<span class='no'>n.obs</span> <span class='kw'><-</span> <span class='fl'>1e4</span>
<span class='no'>n.vars</span> <span class='kw'><-</span> <span class='fl'>100</span>
<span class='no'>n.obs.test</span> <span class='kw'><-</span> <span class='fl'>1e3</span>
<span class='no'>true.beta</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fu'><a href='https://rdrr.io/r/stats/Uniform.html'>runif</a></span>(<span class='fl'>15</span>, -<span class='fl'>0.5</span>, <span class='fl'>0.5</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0</span>, <span class='no'>n.vars</span> - <span class='fl'>15</span>))
<span class='no'>x</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span>(<span class='no'>n.obs</span> * <span class='no'>n.vars</span>), <span class='no'>n.obs</span>, <span class='no'>n.vars</span>)
<span class='no'>y</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span>(<span class='no'>n.obs</span>, <span class='kw'>sd</span> <span class='kw'>=</span> <span class='fl'>3</span>) + <span class='no'>x</span> <span class='kw'>%*%</span> <span class='no'>true.beta</span>
<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='cv.oem.html'>cv.oem</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>x</span>, <span class='kw'>y</span> <span class='kw'>=</span> <span class='no'>y</span>, <span class='kw'>penalty</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"lasso"</span>, <span class='st'>"grp.lasso"</span>), <span class='kw'>groups</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>1</span>:<span class='fl'>10</span>, <span class='kw'>each</span> <span class='kw'>=</span> <span class='fl'>10</span>))
<span class='fu'><a href='https://rdrr.io/r/graphics/layout.html'>layout</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='fl'>1</span>:<span class='fl'>2</span>, <span class='kw'>ncol</span> <span class='kw'>=</span> <span class='fl'>2</span>))
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>which.model</span> <span class='kw'>=</span> <span class='fl'>1</span>)
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>which.model</span> <span class='kw'>=</span> <span class='st'>"grp.lasso"</span>)</div><div class='img'><img src='plot-2.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span>(<span class='fl'>123</span>)
<span class='no'>n.obs</span> <span class='kw'><-</span> <span class='fl'>1e4</span>
<span class='no'>n.vars</span> <span class='kw'><-</span> <span class='fl'>100</span>
<span class='no'>n.obs.test</span> <span class='kw'><-</span> <span class='fl'>1e3</span>
<span class='no'>true.beta</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fu'><a href='https://rdrr.io/r/stats/Uniform.html'>runif</a></span>(<span class='fl'>15</span>, -<span class='fl'>0.5</span>, <span class='fl'>0.5</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0</span>, <span class='no'>n.vars</span> - <span class='fl'>15</span>))
<span class='no'>x</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span>(<span class='no'>n.obs</span> * <span class='no'>n.vars</span>), <span class='no'>n.obs</span>, <span class='no'>n.vars</span>)
<span class='no'>y</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span>(<span class='no'>n.obs</span>, <span class='kw'>sd</span> <span class='kw'>=</span> <span class='fl'>3</span>) + <span class='no'>x</span> <span class='kw'>%*%</span> <span class='no'>true.beta</span>
<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='xval.oem.html'>xval.oem</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>x</span>, <span class='kw'>y</span> <span class='kw'>=</span> <span class='no'>y</span>, <span class='kw'>penalty</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"lasso"</span>, <span class='st'>"grp.lasso"</span>), <span class='kw'>groups</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>1</span>:<span class='fl'>10</span>, <span class='kw'>each</span> <span class='kw'>=</span> <span class='fl'>10</span>))
<span class='fu'><a href='https://rdrr.io/r/graphics/layout.html'>layout</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='fl'>1</span>:<span class='fl'>4</span>, <span class='kw'>ncol</span> <span class='kw'>=</span> <span class='fl'>2</span>))
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>which.model</span> <span class='kw'>=</span> <span class='fl'>1</span>)
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>which.model</span> <span class='kw'>=</span> <span class='fl'>2</span>)
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>which.model</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"coef"</span>)
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>which.model</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"coef"</span>)</div><div class='output co'>#> <span class='warning'>Warning: collapsing to unique 'x' values</span></div><div class='img'><img src='plot-3.png' alt='' width='700' height='433' /></div><div class='input'>
</div></pre>
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