automation

DESCRIPTION

@@ -6,7 +6,7 @@ Depends: R (>= 3.0.0)
 Imports: glmnet, palasso, cornet
 Suggests: knitr, testthat, MASS
 Enhances: spls, SiER, MRCE
-Authors@R: person("Armin","Rauschenberger",email="a.rauschenberger@vumc.nl",role=c("aut","cre"))
+Authors@R: person("Armin","Rauschenberger",email="armin.rauschenberger@uni.lu",role=c("aut","cre"))
 VignetteBuilder: knitr
 License: GPL-3
 LazyData: true

R/functions.R

 
-#.loss <- get(".loss",envir=asNamespace("palasso"))
-#.folds <- get(".folds",envir=asNamespace("palasso"))
-#.check <- get(".check",envir=asNamespace("cornet"))
+# import unexported functions:
+# FUNCTION <- get("FUNCTION",envir=asNamespace("PACKAGE"))
 
 #--- Main function -------------------------------------------------------------
 
 #' @export
-#' @aliases joinet-package
 #' @title
 #' Multivariate Elastic Net Regression
 #' 

R/pkgname.R

+
+#' @name joinet-package
+#' @keywords documentation
+#' @docType package
+#' 
+#' @title
+#' Multivariate Elastic Net Regression
+#' 
+#' @description
+#' The R package \code{joinet} implements multivariate
+#' ridge and lasso regression using stacked generalisation.
+#' This multivariate regression typically outperforms
+#' univariate regression at predicting correlated outcomes.
+#' It provides predictive and interpretable models
+#' in high-dimensional settings.
+#' 
+#' @details
+#' Use function \code{\link{joinet}} for model fitting.
+#' Type \code{library(joinet)} and then \code{?joinet} or
+#' \code{help("joinet)"} to open its help file.
+#' 
+#' See the vignette for further examples.
+#' Type \code{vignette("joinet")} or \code{browseVignettes("joinet")}
+#' to open the vignette.
+#' 
+#' @references
+#' Armin Rauschenberger and Enrico Glaab (2019).
+#' "joinet: predicting correlated outcomes jointly to improve clinical prognosis".
+#' \emph{Manuscript in preparation}.
+#' 
+#' \email{armin.rauschenberger@uni.lu}
+#'
+#' @examples
+#' #--- data simulation ---
+#' n <- 50; p <- 100; q <- 3
+#' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
+#' Y <- replicate(n=q,expr=rnorm(n=n,mean=rowSums(X[,1:5])))
+#' # n samples, p inputs, q outputs
+#' 
+#' #--- model fitting ---
+#' object <- joinet(Y=Y,X=X)
+#' # slot "base": univariate
+#' # slot "meta": multivariate
+#' 
+#' #--- make predictions ---
+#' y_hat <- predict(object,newx=X)
+#' # n x q matrix "base": univariate
+#' # n x q matrix "meta": multivariate 
+#' 
+#' #--- extract coefficients ---
+#' coef <- coef(object)
+#' # effects of inputs on outputs
+#' # q vector "alpha": intercepts
+#' # p x q matrix "beta": slopes
+#' 
+#' #--- model comparison ---
+#' loss <- cv.joinet(Y=Y,X=X)
+#' # cross-validated loss
+#' # row "base": univariate
+#' # row "meta": multivariate
+#' 
+NULL
+

_pkgdown.yml

@@ -17,7 +17,7 @@ navbar:
     - text: "functions"
       href: reference/index.html
     - text: "vignette"
-      href: articles/vignette.html
+      href: articles/joinet.html
     - text: "article"
       href: articles/article.html
     - text: "news"
@@ -29,12 +29,11 @@ navbar:
       href: https://cran.r-project.org/package=joinet
 
 reference:
-  - title: "User functions"
+  - title: "Functions"
     contents:
       - joinet
       - predict.joinet
       - coef.joinet
       - weights.joinet
-  - title: "Internal functions"
-    contents:
       - cv.joinet
+      - joinet-package

cran-comments.md

 
 # Notes
 
-- Early update because of manuscript submission (examples, vignettes).
-
-- The maintainer email will change to armin.rauschenberger@uni.lu.
\ No newline at end of file
+Please accept ::: calls to "palasso" and "cornet",
+as maintainer email changes for all packages.
\ No newline at end of file

docs/articles/article.html

@@ -40,7 +40,7 @@
   <a href="../reference/index.html">functions</a>
 </li>
 <li>
-  <a href="../articles/vignette.html">vignette</a>
+  <a href="../articles/joinet.html">vignette</a>
 </li>
 <li>
   <a href="../articles/article.html">article</a>

docs/articles/index.html

@@ -70,7 +70,7 @@
   <a href="../reference/index.html">functions</a>
 </li>
 <li>
-  <a href="../articles/vignette.html">vignette</a>
+  <a href="../articles/joinet.html">vignette</a>
 </li>
 <li>
   <a href="../articles/article.html">article</a>
@@ -114,7 +114,7 @@
 
       <ul>
         <li><a href="article.html">Multivariate Elastic Net Regression</a></li>
-        <li><a href="vignette.html">Multivariate Elastic Net Regression</a></li>
+        <li><a href="joinet.html">Multivariate Elastic Net Regression</a></li>
       </ul>
     </div>
   </div>

docs/articles/vignette.html → docs/articles/joinet.html

@@ -40,7 +40,7 @@
   <a href="../reference/index.html">functions</a>
 </li>
 <li>
-  <a href="../articles/vignette.html">vignette</a>
+  <a href="../articles/joinet.html">vignette</a>
 </li>
 <li>
   <a href="../articles/article.html">article</a>
@@ -77,8 +77,8 @@
       <h1>Multivariate Elastic Net Regression</h1>
             
       
-      <small class="dont-index">Source: <a href="https://github.com/rauschenberger/joinet/blob/master/vignettes/vignette.Rmd"><code>vignettes/vignette.Rmd</code></a></small>
-      <div class="hidden name"><code>vignette.Rmd</code></div>
+      <small class="dont-index">Source: <a href="https://github.com/rauschenberger/joinet/blob/master/vignettes/joinet.Rmd"><code>vignettes/joinet.Rmd</code></a></small>
+      <div class="hidden name"><code>joinet.Rmd</code></div>
 
     </div>
 

docs/authors.html

@@ -70,7 +70,7 @@
   <a href="reference/index.html">functions</a>
 </li>
 <li>
-  <a href="articles/vignette.html">vignette</a>
+  <a href="articles/joinet.html">vignette</a>
 </li>
 <li>
   <a href="articles/article.html">article</a>

docs/index.html

@@ -40,7 +40,7 @@
   <a href="reference/index.html">functions</a>
 </li>
 <li>
-  <a href="articles/vignette.html">vignette</a>
+  <a href="articles/joinet.html">vignette</a>
 </li>
 <li>
   <a href="articles/article.html">article</a>

docs/news/index.html

@@ -70,7 +70,7 @@
   <a href="../reference/index.html">functions</a>
 </li>
 <li>
-  <a href="../articles/vignette.html">vignette</a>
+  <a href="../articles/joinet.html">vignette</a>
 </li>
 <li>
   <a href="../articles/article.html">article</a>

docs/pkgdown.yml

@@ -3,5 +3,5 @@ pkgdown: 1.3.0
 pkgdown_sha: ~
 articles:
   article: article.html
-  vignette: vignette.html
+  joinet: joinet.html
 

docs/reference/coef.joinet.html

@@ -75,7 +75,7 @@ the coefficients from the base learners.)" />
   <a href="../reference/index.html">functions</a>
 </li>
 <li>
-  <a href="../articles/vignette.html">vignette</a>
+  <a href="../articles/joinet.html">vignette</a>
 </li>
 <li>
   <a href="../articles/article.html">article</a>

docs/reference/cv.joinet.html

@@ -73,7 +73,7 @@
   <a href="../reference/index.html">functions</a>
 </li>
 <li>
-  <a href="../articles/vignette.html">vignette</a>
+  <a href="../articles/joinet.html">vignette</a>
 </li>
 <li>
   <a href="../articles/article.html">article</a>

docs/reference/index.html

@@ -70,7 +70,7 @@
   <a href="../reference/index.html">functions</a>
 </li>
 <li>
-  <a href="../articles/vignette.html">vignette</a>
+  <a href="../articles/joinet.html">vignette</a>
 </li>
 <li>
   <a href="../articles/article.html">article</a>
@@ -119,7 +119,7 @@
     <tbody>
       <tr>
         <th colspan="2">
-          <h2 id="section-user-functions" class="hasAnchor"><a href="#section-user-functions" class="anchor"></a>User functions</h2>
+          <h2 id="section-functions" class="hasAnchor"><a href="#section-functions" class="anchor"></a>Functions</h2>
           <p class="section-desc"></p>
         </th>
       </tr>
@@ -147,20 +147,18 @@
           <p><code><a href="weights.joinet.html">weights(<i>&lt;joinet&gt;</i>)</a></code> </p>
         </td>
         <td><p>Extract Weights</p></td>
-      </tr>
-    </tbody><tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-internal-functions" class="hasAnchor"><a href="#section-internal-functions" class="anchor"></a>Internal functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
+      </tr><tr>
         
         <td>
           <p><code><a href="cv.joinet.html">cv.joinet()</a></code> </p>
         </td>
         <td><p>Model comparison</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="joinet-package.html">joinet-package</a></code> </p>
+        </td>
+        <td><p>Multivariate Elastic Net Regression</p></td>
       </tr>
     </tbody>
     </table>
@@ -169,8 +167,7 @@
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
     <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-user-functions">User functions</a></li>
-      <li><a href="#section-internal-functions">Internal functions</a></li>
+      <li><a href="#section-functions">Functions</a></li>
     </ul>
   </div>
 </div>

docs/reference/joinet-package.html

+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+  <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Multivariate Elastic Net Regression — joinet-package • joinet</title>
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+<meta property="og:title" content="Multivariate Elastic Net Regression — joinet-package" />
+
+<meta property="og:description" content="The R package joinet implements multivariate
+ridge and lasso regression using stacked generalisation.
+This multivariate regression typically outperforms
+univariate regression at predicting correlated outcomes.
+It provides predictive and interpretable models
+in high-dimensional settings." />
+<meta name="twitter:card" content="summary" />
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+  </head>
+
+  <body>
+    <div class="container template-reference-topic">
+      <header>
+      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">joinet</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
+      </span>
+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav">
+        <li>
+  <a href="../reference/index.html">functions</a>
+</li>
+<li>
+  <a href="../articles/joinet.html">vignette</a>
+</li>
+<li>
+  <a href="../articles/article.html">article</a>
+</li>
+<li>
+  <a href="../news/index.html">news</a>
+</li>
+      </ul>
+      
+      <ul class="nav navbar-nav navbar-right">
+        <li>
+  <a href="https://github.com/rauschenberger/joinet">
+    <span class="fa fa-github"></span>
+     
+  </a>
+</li>
+<li>
+  <a href="https://cran.r-project.org/package=joinet">
+    <span class="fa fa-download"></span>
+     
+  </a>
+</li>
+      </ul>
+      
+    </div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+      </header>
+
+<div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Multivariate Elastic Net Regression</h1>
+    <small class="dont-index">Source: <a href='https://github.com/rauschenberger/joinet/blob/master/R/pkgname.R'><code>R/pkgname.R</code></a></small>
+    <div class="hidden name"><code>joinet-package.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    
+    <p>The R package <code>joinet</code> implements multivariate
+ridge and lasso regression using stacked generalisation.
+This multivariate regression typically outperforms
+univariate regression at predicting correlated outcomes.
+It provides predictive and interpretable models
+in high-dimensional settings.</p>
+    
+    </div>
+
+        
+    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+    <p>Use function <code><a href='joinet.html'>joinet</a></code> for model fitting.
+Type <code><a href='https://www.rdocumentation.org/packages/base/topics/library'>library(joinet)</a></code> and then <code><a href='joinet.html'>?joinet</a></code> or
+<code>help("joinet)"</code> to open its help file.</p>
+<p>See the vignette for further examples.
+Type <code><a href='../articles/joinet.html'>vignette("joinet")</a></code> or <code><a href='https://www.rdocumentation.org/packages/utils/topics/browseVignettes'>browseVignettes("joinet")</a></code>
+to open the vignette.</p>
+    
+    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+    <p>Armin Rauschenberger and Enrico Glaab (2019).
+"joinet: predicting correlated outcomes jointly to improve clinical prognosis".
+<em>Manuscript in preparation</em>.</p>
+<p><a href='mailto:armin.rauschenberger@uni.lu'>armin.rauschenberger@uni.lu</a></p>
+    
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'><span class='co'>#--- data simulation ---</span>
+<span class='no'>n</span> <span class='kw'>&lt;-</span> <span class='fl'>50</span>; <span class='no'>p</span> <span class='kw'>&lt;-</span> <span class='fl'>100</span>; <span class='no'>q</span> <span class='kw'>&lt;-</span> <span class='fl'>3</span>
+<span class='no'>X</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/matrix'>matrix</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/Normal'>rnorm</a></span>(<span class='no'>n</span>*<span class='no'>p</span>),<span class='kw'>nrow</span><span class='kw'>=</span><span class='no'>n</span>,<span class='kw'>ncol</span><span class='kw'>=</span><span class='no'>p</span>)
+<span class='no'>Y</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/lapply'>replicate</a></span>(<span class='kw'>n</span><span class='kw'>=</span><span class='no'>q</span>,<span class='kw'>expr</span><span class='kw'>=</span><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/Normal'>rnorm</a></span>(<span class='kw'>n</span><span class='kw'>=</span><span class='no'>n</span>,<span class='kw'>mean</span><span class='kw'>=</span><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/colSums'>rowSums</a></span>(<span class='no'>X</span>[,<span class='fl'>1</span>:<span class='fl'>5</span>])))
+<span class='co'># n samples, p inputs, q outputs</span>
+
+<span class='co'>#--- model fitting ---</span>
+<span class='no'>object</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='joinet.html'>joinet</a></span>(<span class='kw'>Y</span><span class='kw'>=</span><span class='no'>Y</span>,<span class='kw'>X</span><span class='kw'>=</span><span class='no'>X</span>)
+<span class='co'># slot "base": univariate</span>
+<span class='co'># slot "meta": multivariate</span>
+
+<span class='co'>#--- make predictions ---</span>
+<span class='no'>y_hat</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/predict'>predict</a></span>(<span class='no'>object</span>,<span class='kw'>newx</span><span class='kw'>=</span><span class='no'>X</span>)
+<span class='co'># n x q matrix "base": univariate</span>
+<span class='co'># n x q matrix "meta": multivariate </span>
+
+<span class='co'>#--- extract coefficients ---</span>
+<span class='no'>coef</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>object</span>)
+<span class='co'># effects of inputs on outputs</span>
+<span class='co'># q vector "alpha": intercepts</span>
+<span class='co'># p x q matrix "beta": slopes</span>
+
+<span class='co'>#--- model comparison ---</span>
+<span class='no'>loss</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='cv.joinet.html'>cv.joinet</a></span>(<span class='kw'>Y</span><span class='kw'>=</span><span class='no'>Y</span>,<span class='kw'>X</span><span class='kw'>=</span><span class='no'>X</span>)
+<span class='co'># cross-validated loss</span>
+<span class='co'># row "base": univariate</span>
+<span class='co'># row "meta": multivariate</span></div></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+    <h2>Contents</h2>
+    <ul class="nav nav-pills nav-stacked">
+      
+      <li><a href="#details">Details</a></li>
+
+      <li><a href="#references">References</a></li>
+      
+      <li><a href="#examples">Examples</a></li>
+    </ul>
+
+  </div>
+</div>
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by <a href='https://rauschenberger.github.io'>Armin Rauschenberger</a>.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+</div>
+      </footer>
+   </div>
+
+  
+
+  </body>
+</html>
+

docs/reference/joinet.html

@@ -73,7 +73,7 @@
   <a href="../reference/index.html">functions</a>
 </li>
 <li>
-  <a href="../articles/vignette.html">vignette</a>
+  <a href="../articles/joinet.html">vignette</a>
 </li>
 <li>
   <a href="../articles/article.html">article</a>

docs/reference/predict.joinet.html

@@ -73,7 +73,7 @@
   <a href="../reference/index.html">functions</a>
 </li>
 <li>
-  <a href="../articles/vignette.html">vignette</a>
+  <a href="../articles/joinet.html">vignette</a>
 </li>
 <li>
   <a href="../articles/article.html">article</a>
@@ -158,110 +158,110 @@ with \(n\) rows (samples) and \(q\) columns (variables).</p>
 <span class='no'>Y</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/lapply'>replicate</a></span>(<span class='kw'>n</span><span class='kw'>=</span><span class='no'>q</span>,<span class='kw'>expr</span><span class='kw'>=</span><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/Normal'>rnorm</a></span>(<span class='kw'>n</span><span class='kw'>=</span><span class='no'>n</span>,<span class='kw'>mean</span><span class='kw'>=</span><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/colSums'>rowSums</a></span>(<span class='no'>X</span>[,<span class='fl'>1</span>:<span class='fl'>5</span>])))
 <span class='no'>object</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='joinet.html'>joinet</a></span>(<span class='kw'>Y</span><span class='kw'>=</span><span class='no'>Y</span>,<span class='kw'>X</span><span class='kw'>=</span><span class='no'>X</span>)
 <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/predict'>predict</a></span>(<span class='no'>object</span>,<span class='kw'>newx</span><span class='kw'>=</span><span class='no'>X</span>)</div><div class='output co'>#&gt; $base
-#&gt;             [,1]        [,2]         [,3]
-#&gt;  [1,] -0.6800725 -1.21872520 -0.310657961
-#&gt;  [2,]  2.5231822  2.01759432  2.319092565
-#&gt;  [3,]  3.0147246  2.95961835  3.071353923
-#&gt;  [4,] -2.0321731 -1.16697865 -1.131585864
-#&gt;  [5,]  1.1989575  1.94542159  1.205214655
-#&gt;  [6,] -5.2181676 -4.73651108 -5.106512539
-#&gt;  [7,]  2.6630929  2.28298777  1.837353182
-#&gt;  [8,]  4.1517740  3.68154548  2.859426063
-#&gt;  [9,]  2.2255938  2.62966728  2.209039320
-#&gt; [10,] -0.1976240 -0.26331544 -0.084736597
-#&gt; [11,] -2.2848625 -2.88205673 -3.371158126
-#&gt; [12,]  0.1395562  0.12678281  1.952331938
-#&gt; [13,]  0.5319628  1.08030034  0.877379283
-#&gt; [14,] -3.2092512 -3.20808021 -5.574818243
-#&gt; [15,]  2.1373104  1.54594741  0.792750994
-#&gt; [16,]  1.3677467  0.24229789  1.303661371
-#&gt; [17,]  2.4203610  1.97149218  2.164521950
-#&gt; [18,] -1.6439085 -1.13752492 -0.148270982
-#&gt; [19,] -2.6971069 -3.21077918 -3.448781770
-#&gt; [20,]  0.4847756  1.32920669  1.045263833
-#&gt; [21,]  1.0580634  1.41141884  0.487897356
-#&gt; [22,] -0.1159397  0.33252059  1.764586212
-#&gt; [23,] -2.4576322 -2.61545228 -1.960495924
-#&gt; [24,] -2.8963417 -2.86185997 -3.306570648
-#&gt; [25,]  1.0818188  1.14369892  2.186762596
-#&gt; [26,] -3.9271814 -3.84456309 -5.731322146
-#&gt; [27,] -2.3652352 -2.86340632 -3.227402032
-#&gt; [28,] -2.1800217 -1.48891855 -2.572985868
-#&gt; [29,]  0.7460273 -0.27982198 -0.506445835
-#&gt; [30,] -0.8429611  0.13194537 -0.737426505
-#&gt; [31,] -0.7316201 -1.51707620 -1.153890045
-#&gt; [32,] -2.5021179 -1.84304055 -3.478808874
-#&gt; [33,]  0.8250113 -0.21440315  0.524465823
-#&gt; [34,]  3.0831834  2.23039182  3.727105270
-#&gt; [35,]  0.4993630 -1.34134635 -1.164539640
-#&gt; [36,]  1.6239756  0.78835676  0.528243360
-#&gt; [37,]  2.1683663  0.91851657  1.521169026
-#&gt; [38,] -0.9397605  0.08426956 -0.751842377
-#&gt; [39,] -0.2803268 -1.20184123 -0.560565492
-#&gt; [40,]  1.9729289  3.26803044  2.090648484
-#&gt; [41,]  0.7398532 -0.83577871  1.020203057
-#&gt; [42,] -1.7847439 -2.02797038 -3.409427348
-#&gt; [43,]  0.9128885  1.60609986  2.616774138
-#&gt; [44,]  1.1536491  2.16601146 -0.015506128
-#&gt; [45,]  0.6315267  0.22276528  0.985103241
-#&gt; [46,]  5.4299519  5.38132076  6.438669837
-#&gt; [47,]  1.3572642 -0.09607223 -1.249216010
-#&gt; [48,]  0.3873464  0.41138065 -0.001234302
-#&gt; [49,]  2.9278013  2.67791507  3.629988512
-#&gt; [50,] -2.4898856 -2.53479214 -3.853167277
+#&gt;             [,1]       [,2]         [,3]
+#&gt;  [1,] -2.6382210 -2.9659453 -2.306391444
+#&gt;  [2,]  2.6552680  1.4525574  2.505892331
+#&gt;  [3,]  1.1295699  1.4181935  1.024506708
+#&gt;  [4,]  0.2566896 -1.1868062  0.770974904
+#&gt;  [5,]  0.9235359  2.1951153  1.435281993
+#&gt;  [6,]  0.7376982  1.7955112  1.613380715
+#&gt;  [7,] -0.3904051 -0.9624476 -1.305940614
+#&gt;  [8,] -4.8823206 -5.1329853 -5.632617590
+#&gt;  [9,] -2.8826967 -4.2866886 -3.319082823
+#&gt; [10,]  2.4610522  1.7177360  2.029169444
+#&gt; [11,]  0.9047337  1.7704820  0.138986055
+#&gt; [12,] -3.4383168 -3.4492442 -4.077404028
+#&gt; [13,]  0.3573390  1.0892937  0.751307437
+#&gt; [14,]  2.6856775  4.1461204  4.109918838
+#&gt; [15,] -2.5859515 -3.0620775 -3.039261367
+#&gt; [16,]  1.7188957  1.1177316  2.666496452
+#&gt; [17,] -2.8405784 -4.3156935 -3.265928842
+#&gt; [18,]  2.5205082  3.2674372  4.021626346
+#&gt; [19,]  2.4668067  2.2547918  1.521037026
+#&gt; [20,] -3.2163874 -5.1967661 -3.914674437
+#&gt; [21,] -1.8090909 -2.4841106 -2.800940136
+#&gt; [22,]  0.1219993 -0.4755235 -1.346081912
+#&gt; [23,]  0.5620446  2.9490435  0.834109773
+#&gt; [24,]  0.7231336 -0.8008719  0.006685054
+#&gt; [25,]  0.3882856 -0.4834631 -0.389710153
+#&gt; [26,]  0.8986010  0.3555128  0.582610989
+#&gt; [27,]  0.9810074  0.5822080 -0.083507593
+#&gt; [28,]  1.3495727  0.2573044  0.950629861
+#&gt; [29,]  1.5941948  1.6883281  2.610167833
+#&gt; [30,]  0.5201647 -0.4452296 -1.053437483
+#&gt; [31,]  2.5336520  3.9861323  3.091867020
+#&gt; [32,]  1.2177945  0.4127256  1.337044870
+#&gt; [33,]  2.3160903  2.8285159  2.868384803
+#&gt; [34,] -0.9393410 -0.3716184  0.146997363
+#&gt; [35,]  2.0302346  2.9987535  2.602339175
+#&gt; [36,]  2.5560019  4.2112428  2.946193469
+#&gt; [37,]  1.5872347  0.8023620  2.234054545
+#&gt; [38,]  1.1985388  1.9795947  1.730649774
+#&gt; [39,] -0.2143121  1.3476443 -0.594151486
+#&gt; [40,]  1.1493740  0.7250426  0.991941924