Commit 79c29efc authored by Armin Rauschenberger's avatar Armin Rauschenberger

automation

parent c6f42461
Package: starnet
Version: 0.0.1
Version: 0.0.2
Title: Stacked Elastic Net
Description: Implements stacked elastic net regression (Rauschenberger 2020, <doi:10.1093/bioinformatics/btaa535>). The elastic net generalises ridge and lasso regularisation (Zou 2005, <doi:10.1111/j.1467-9868.2005.00503.x>). Instead of fixing or tuning the mixing parameter alpha, we combine multiple alpha by stacked generalisation (Wolpert 1992 <doi:10.1016/S0893-6080(05)80023-1>).
Depends: R (>= 3.0.0)
......
## starnet 0.0.1 (2020-05-26)
## starnet 0.0.1 (2020-06-04)
* submission to CRAN
\ No newline at end of file
......@@ -84,7 +84,7 @@
#'
#' @examples
#' set.seed(1)
#' n <- 30; p <- 50
#' n <- 40; p <- 50
#' y <- rnorm(n=n)
#' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
#' object <- starnet(y=y,X=X,family="gaussian")
......@@ -317,7 +317,7 @@ starnet <- function(y,X,family="gaussian",nalpha=21,alpha=NULL,nfolds=10,foldid=
#'
#' @examples
#' set.seed(1)
#' n <- 30; p <- 50
#' n <- 40; p <- 50
#' y <- rnorm(n=n)
#' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
#' object <- starnet(y=y,X=X)
......@@ -385,7 +385,7 @@ predict.starnet <- function(object,newx,type="response",nzero=NULL,...){
#'
#' @examples
#' set.seed(1)
#' n <- 30; p <- 50
#' n <- 40; p <- 50
#' y <- rnorm(n=n)
#' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
#' object <- starnet(y=y,X=X)
......@@ -447,7 +447,7 @@ coef.starnet <- function(object,nzero=NULL,...){
#'
#' @examples
#' set.seed(1)
#' n <- 30; p <- 50
#' n <- 40; p <- 50
#' y <- rnorm(n=n)
#' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
#' object <- starnet(y=y,X=X)
......@@ -481,7 +481,7 @@ weights.starnet <- function(object,...){
#'
#' @examples
#' set.seed(1)
#' n <- 30; p <- 20
#' n <- 40; p <- 50
#' y <- rnorm(n=n)
#' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
#' object <- starnet(y=y,X=X)
......
Thanks. The vignette does not save files any more.
\ No newline at end of file
Reason for resubmission: error on r-patched-solaris-x86.
\ No newline at end of file
......@@ -71,7 +71,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
</span>
</div>
......
......@@ -31,7 +31,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
</span>
</div>
......@@ -90,10 +90,15 @@
<p>The <code>starnet</code> manuscript is in preparation. Click <a href="https://CRAN.R-project.org/package=starnet">here</a> for the R package.</p>
<p>Click <a href="https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaa535/33263777/btaa535.pdf">here</a> to download article.</p>
<div>
<object data="https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaa535/33263777/btaa535.pdf" type="application/pdf" width="100%" height="500px">
</object>
</div>
<div id="reference" class="section level2">
<h2 class="hasAnchor">
<a href="#reference" class="anchor"></a>Reference</h2>
<p>A Rauschenberger, E Glaab, and MA van de Wiel (2020). “Predictive and interpretable models via the stacked elastic net”. <em>Manuscript in preparation.</em></p>
<p>A Rauschenberger, E Glaab, and MA van de Wiel (2020). “Predictive and interpretable models via the stacked elastic net”. <em>Bioinformatics.</em> <a href="https://doi.org/10.1093/bioinformatics/btaa535">doi: 10.1093/bioinformatics/btaa535</a></p>
</div>
</div>
......
......@@ -71,7 +71,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
</span>
</div>
......
......@@ -31,7 +31,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
</span>
</div>
......@@ -82,7 +82,7 @@
<h1 data-toc-skip>Stacked Elastic Net</h1>
<h4 class="author">Armin Rauschenberger</h4>
<h4 class="date">03 June 2020</h4>
<h4 class="date">08 June 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/rauschenberger/starnet/blob/master/vignettes/script.Rmd"><code>vignettes/script.Rmd</code></a></small>
<div class="hidden name"><code>script.Rmd</code></div>
......
......@@ -31,7 +31,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
</span>
</div>
......@@ -97,7 +97,7 @@
<p>or the latest development version from <a href="https://github.com/rauschenberger/starnet">GitHub</a>:</p>
<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="co">#install.packages("devtools")</span>
<span class="kw pkg">devtools</span><span class="kw ns">::</span><span class="fu"><a href="https://devtools.r-lib.org//reference/remote-reexports.html">install_github</a></span>(<span class="st">"rauschenberger/starnet"</span>)</pre></body></html></div>
<p>A Rauschenberger, E Glaab, and MA van de Wiel (2020). “Predictive and interpretable models via the stacked elastic net”. <em>Bioinformatics.</em> In press.</p>
<p>A Rauschenberger, E Glaab, and MA van de Wiel (2020). “Predictive and interpretable models via the stacked elastic net”. <em>Bioinformatics.</em> <a href="https://doi.org/10.1093/bioinformatics/btaa535">doi: 10.1093/bioinformatics/btaa535</a></p>
</div>
</div>
......
......@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Authors • starnet</title>
<title>Citation and Authors • starnet</title>
<!-- jquery -->
......@@ -39,7 +39,7 @@
<meta property="og:title" content="Authors" />
<meta property="og:title" content="Citation and Authors" />
......@@ -58,7 +58,7 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-authors">
<div class="container template-citation-authors">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
......@@ -71,7 +71,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
</span>
</div>
......@@ -118,6 +118,21 @@
<div class="row">
<div class="contents col-md-9">
<div class="page-header">
<h1>Citation</h1>
<small class="dont-index">Source: <a href='https://github.com/rauschenberger/starnet/blob/master/inst/CITATION'><code>inst/CITATION</code></a></small>
</div>
<p>Armin Rauschenberger, Enrico Glaab, and Mark A. van de Wiel (2020). "Predictive and interpretable models via the stacked elastic net", Bioinformatics, In press. https://doi.org/10.1093/bioinformatics/btaa535</p>
<pre>@Article{,
title = {Predictive and interpretable models via the stacked elastic net},
author = {Armin Rauschenberger and Enrico Glaab and Mark A. {van de Wiel}},
journal = {Bioinformatics},
volume = {In press},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa535},
}</pre>
<div class="page-header">
<h1>Authors</h1>
</div>
......
......@@ -31,7 +31,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
</span>
</div>
......@@ -106,6 +106,8 @@
<div class="links">
<h2>Links</h2>
<ul class="list-unstyled">
<li>Download from CRAN at <br><a href="https://cloud.r-project.org/package=starnet">https://​cloud.r-project.org/​package=starnet</a>
</li>
<li>Browse source code at <br><a href="https://github.com/rauschenberger/starnet/">https://​github.com/​rauschenberger/​starnet/​</a>
</li>
<li>Report a bug at <br><a href="https://github.com/rauschenberger/starnet/issues">https://​github.com/​rauschenberger/​starnet/​issues</a>
......@@ -120,6 +122,12 @@
<li><a href="https://www.r-project.org/Licenses/GPL-3">GPL-3</a></li>
</ul>
</div>
<div class="citation">
<h2>Citation</h2>
<ul class="list-unstyled">
<li><a href="authors.html">Citing starnet</a></li>
</ul>
</div>
<div class="developers">
<h2>Developers</h2>
<ul class="list-unstyled">
......
......@@ -71,7 +71,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
</span>
</div>
......@@ -123,9 +123,9 @@
<small>Source: <a href='https://github.com/rauschenberger/starnet/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="starnet-001-2020-05-26" class="section level2">
<div id="starnet-001-2020-06-04" class="section level2">
<h2 class="hasAnchor">
<a href="#starnet-001-2020-05-26" class="anchor"></a>starnet 0.0.1 (2020-05-26)</h2>
<a href="#starnet-001-2020-06-04" class="anchor"></a>starnet 0.0.1 (2020-06-04)</h2>
<ul>
<li>submission to CRAN</li>
</ul>
......
......@@ -5,5 +5,5 @@ articles:
article: article.html
script: script.html
starnet: starnet.html
last_built: 2020-06-03T16:19Z
last_built: 2020-06-08T06:25Z
......@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
</span>
</div>
......@@ -160,7 +160,7 @@ respectively.</p>
<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'>1</span>)
<span class='no'>n</span> <span class='kw'>&lt;-</span> <span class='fl'>30</span>; <span class='no'>p</span> <span class='kw'>&lt;-</span> <span class='fl'>50</span>
<span class='no'>n</span> <span class='kw'>&lt;-</span> <span class='fl'>40</span>; <span class='no'>p</span> <span class='kw'>&lt;-</span> <span class='fl'>50</span>
<span class='no'>y</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span>(<span class='kw'>n</span><span class='kw'>=</span><span class='no'>n</span>)
<span class='no'>X</span> <span class='kw'>&lt;-</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</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'>object</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='starnet.html'>starnet</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>)
......
......@@ -72,7 +72,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
</span>
</div>
......
......@@ -73,7 +73,7 @@ with different handling of sparsity constraints." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
</span>
</div>
......
......@@ -72,7 +72,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
</span>
</div>
......
......@@ -72,7 +72,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
</span>
</div>
......
......@@ -72,7 +72,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
</span>
</div>
......
......@@ -71,7 +71,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
</span>
</div>
......
......@@ -72,7 +72,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
</span>
</div>
......@@ -173,7 +173,7 @@ and <code>none</code> (intercept-only model).</p>
<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'>1</span>)
<span class='no'>n</span> <span class='kw'>&lt;-</span> <span class='fl'>30</span>; <span class='no'>p</span> <span class='kw'>&lt;-</span> <span class='fl'>50</span>
<span class='no'>n</span> <span class='kw'>&lt;-</span> <span class='fl'>40</span>; <span class='no'>p</span> <span class='kw'>&lt;-</span> <span class='fl'>50</span>
<span class='no'>y</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span>(<span class='kw'>n</span><span class='kw'>=</span><span class='no'>n</span>)
<span class='no'>X</span> <span class='kw'>&lt;-</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</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'>object</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='starnet.html'>starnet</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>)
......
......@@ -72,7 +72,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
</span>
</div>
......@@ -151,7 +151,7 @@
<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'>1</span>)
<span class='no'>n</span> <span class='kw'>&lt;-</span> <span class='fl'>30</span>; <span class='no'>p</span> <span class='kw'>&lt;-</span> <span class='fl'>20</span>
<span class='no'>n</span> <span class='kw'>&lt;-</span> <span class='fl'>40</span>; <span class='no'>p</span> <span class='kw'>&lt;-</span> <span class='fl'>50</span>
<span class='no'>y</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span>(<span class='kw'>n</span><span class='kw'>=</span><span class='no'>n</span>)
<span class='no'>X</span> <span class='kw'>&lt;-</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</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'>object</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='starnet.html'>starnet</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>)
......
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  • 2-up
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......@@ -75,7 +75,7 @@ we combine multiple alphas by stacked generalisation." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
</span>
</div>
......
......@@ -72,7 +72,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
</span>
</div>
......@@ -241,7 +241,7 @@ doi: <a href='https://doi.org/10.1093/bioinformatics/btaa535'>10.1093/bioinforma
<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'>1</span>)
<span class='no'>n</span> <span class='kw'>&lt;-</span> <span class='fl'>30</span>; <span class='no'>p</span> <span class='kw'>&lt;-</span> <span class='fl'>50</span>
<span class='no'>n</span> <span class='kw'>&lt;-</span> <span class='fl'>40</span>; <span class='no'>p</span> <span class='kw'>&lt;-</span> <span class='fl'>50</span>
<span class='no'>y</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span>(<span class='kw'>n</span><span class='kw'>=</span><span class='no'>n</span>)
<span class='no'>X</span> <span class='kw'>&lt;-</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</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'>object</span> <span class='kw'>&lt;-</span> <span class='fu'>starnet</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='kw'>family</span><span class='kw'>=</span><span class='st'>"gaussian"</span>)</div></pre>
......
......@@ -73,7 +73,7 @@ i.e. the weights for the base learners." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
</span>
</div>
......@@ -153,12 +153,12 @@ i.e. the weights for the base learners.</p>
<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'>1</span>)
<span class='no'>n</span> <span class='kw'>&lt;-</span> <span class='fl'>30</span>; <span class='no'>p</span> <span class='kw'>&lt;-</span> <span class='fl'>50</span>
<span class='no'>n</span> <span class='kw'>&lt;-</span> <span class='fl'>40</span>; <span class='no'>p</span> <span class='kw'>&lt;-</span> <span class='fl'>50</span>
<span class='no'>y</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span>(<span class='kw'>n</span><span class='kw'>=</span><span class='no'>n</span>)
<span class='no'>X</span> <span class='kw'>&lt;-</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</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'>object</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='starnet.html'>starnet</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://rdrr.io/r/stats/weights.html'>weights</a></span>(<span class='no'>object</span>)</div><div class='output co'>#&gt; (Intercept) V1 V2 V3 V4 V5
#&gt; 0.08245817 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#&gt; 0.06032819 0.00000000 0.23525906 0.15396683 0.00000000 0.00000000
#&gt; V6 V7 V8 V9 V10 V11
#&gt; 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#&gt; V12 V13 V14 V15 V16 V17
......
citHeader("To cite starnet in publications use:")
citEntry(entry="Article",
title = "Predictive and interpretable models via the stacked elastic net",
author = personList(as.person("Armin Rauschenberger"),
as.person("Enrico Glaab"),
as.person("Mark A. van de Wiel")),
journal = "Bioinformatics",
volume= "In press",
year = 2020,
url = "https://doi.org/10.1093/bioinformatics/btaa535",
textVersion = paste("Armin Rauschenberger, Enrico Glaab, and Mark A. van de Wiel (2020).",
"\"Predictive and interpretable models via the stacked elastic net\",",
"Bioinformatics, In press.",
"https://doi.org/10.1093/bioinformatics/btaa535")
)
\ No newline at end of file
......@@ -25,7 +25,7 @@ Extracts pooled coefficients.
}
\examples{
set.seed(1)
n <- 30; p <- 50
n <- 40; p <- 50
y <- rnorm(n=n)
X <- matrix(rnorm(n*p),nrow=n,ncol=p)
object <- starnet(y=y,X=X)
......
......@@ -35,7 +35,7 @@ Predicts outcome from features with stacked model.
}
\examples{
set.seed(1)
n <- 30; p <- 50
n <- 40; p <- 50
y <- rnorm(n=n)
X <- matrix(rnorm(n*p),nrow=n,ncol=p)
object <- starnet(y=y,X=X)
......
......@@ -19,7 +19,7 @@ Prints object of class \link[starnet]{starnet}.
}
\examples{
set.seed(1)
n <- 30; p <- 20
n <- 40; p <- 50
y <- rnorm(n=n)
X <- matrix(rnorm(n*p),nrow=n,ncol=p)
object <- starnet(y=y,X=X)
......
......@@ -82,7 +82,7 @@ argument \code{nzero} in functions
}
\examples{
set.seed(1)
n <- 30; p <- 50
n <- 40; p <- 50
y <- rnorm(n=n)
X <- matrix(rnorm(n*p),nrow=n,ncol=p)
object <- starnet(y=y,X=X,family="gaussian")
......
......@@ -20,7 +20,7 @@ i.e. the weights for the base learners.
}
\examples{
set.seed(1)
n <- 30; p <- 50
n <- 40; p <- 50
y <- rnorm(n=n)
X <- matrix(rnorm(n*p),nrow=n,ncol=p)
object <- starnet(y=y,X=X)
......
tempdir()
grDevices::dev.off()
grDevices::dev.off()
This diff is collapsed.
......@@ -7,10 +7,15 @@ vignette: >
%\VignetteEncoding{UTF-8}
---
The `starnet` manuscript is in preparation. Click [here](https://CRAN.R-project.org/package=starnet) for the R package.
Click [here](https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaa535/33263777/btaa535.pdf) to download article.
<div>
<object data="https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaa535/33263777/btaa535.pdf" type="application/pdf" width="100%" height="500px">
</object>
</div>
## Reference
A Rauschenberger, E Glaab, and MA van de Wiel (2020).
"Predictive and interpretable models via the stacked elastic net".
*Manuscript in preparation.*
*Bioinformatics.* [doi: 10.1093/bioinformatics/btaa535](https://doi.org/10.1093/bioinformatics/btaa535)
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