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Commit 0c348ca3 authored by Armin Rauschenberger's avatar Armin Rauschenberger
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This package was submitted to CRAN on 2020-06-10.
Once it is accepted, delete this file and tag the release (commit 3841a5faed).
DESCRIPTION
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...@@ -11,6 +11,6 @@ VignetteBuilder: knitr ...@@ -11,6 +11,6 @@ VignetteBuilder: knitr
License: GPL-3 License: GPL-3
LazyData: true LazyData: true
Language: en-GB Language: en-GB
RoxygenNote: 7.1.0 RoxygenNote: 7.1.1
URL: https://github.com/rauschenberger/starnet URL: https://github.com/rauschenberger/starnet
BugReports: https://github.com/rauschenberger/starnet/issues BugReports: https://github.com/rauschenberger/starnet/issues
README.Rmd
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## Reference ## Reference
A Rauschenberger, E Glaab, MA van de Wiel (2020). "Predictive and interpretable models via the stacked elastic net". *Bioinformatics*, btaa535. [doi: 10.1093/bioinformatics/btaa535](https://doi.org/10.1093/bioinformatics/btaa535). A Rauschenberger, E Glaab, MA van de Wiel (2020). "Predictive and interpretable models via the stacked elastic net". *Bioinformatics*, btaa535. [doi: 10.1093/bioinformatics/btaa535](https://doi.org/10.1093/bioinformatics/btaa535).
[![CRAN version](https://www.r-pkg.org/badges/version/starnet)](https://CRAN.R-project.org/package=starnet)
[![CRAN RStudio mirror downloads](https://cranlogs.r-pkg.org/badges/starnet)](https://CRAN.R-project.org/package=starnet)
[![Total CRAN downloads](https://cranlogs.r-pkg.org/badges/grand-total/starnet)](https://CRAN.R-project.org/package=starnet)
README.md
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...@@ -36,3 +36,10 @@ A Rauschenberger, E Glaab, MA van de Wiel (2020). “Predictive and ...@@ -36,3 +36,10 @@ A Rauschenberger, E Glaab, MA van de Wiel (2020). “Predictive and
interpretable models via the stacked elastic net”. *Bioinformatics*, interpretable models via the stacked elastic net”. *Bioinformatics*,
btaa535. btaa535.
[doi: 10.1093/bioinformatics/btaa535](https://doi.org/10.1093/bioinformatics/btaa535). [doi: 10.1093/bioinformatics/btaa535](https://doi.org/10.1093/bioinformatics/btaa535).
[![CRAN
version](https://www.r-pkg.org/badges/version/starnet)](https://CRAN.R-project.org/package=starnet)
[![CRAN RStudio mirror
downloads](https://cranlogs.r-pkg.org/badges/starnet)](https://CRAN.R-project.org/package=starnet)
[![Total CRAN
downloads](https://cranlogs.r-pkg.org/badges/grand-total/starnet)](https://CRAN.R-project.org/package=starnet)
docs/404.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">starnet</a> <a class="navbar-link" href="index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
</span> </span>
</div> </div>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a> <a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
</span> </span>
</div> </div>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a> <a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
</span> </span>
</div> </div>
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docs/articles/script.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a> <a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
</span> </span>
</div> </div>
...@@ -82,7 +82,7 @@ ...@@ -82,7 +82,7 @@
<h1 data-toc-skip>Stacked Elastic Net</h1> <h1 data-toc-skip>Stacked Elastic Net</h1>
<h4 class="author">Armin Rauschenberger</h4> <h4 class="author">Armin Rauschenberger</h4>
<h4 class="date">10 June 2020</h4> <h4 class="date">21 October 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> <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> <div class="hidden name"><code>script.Rmd</code></div>
...@@ -491,7 +491,7 @@ ...@@ -491,7 +491,7 @@
<span class="fu"><a href="https://rdrr.io/r/base/cat.html">cat</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"-"</span>,<span class="no">type</span>[<span class="no">i</span>],<span class="st">"-"</span>),<span class="kw">times</span><span class="kw">=</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">10</span>,<span class="fl">1</span>,<span class="fl">10</span>)),<span class="st">"\n"</span>) <span class="fu"><a href="https://rdrr.io/r/base/cat.html">cat</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"-"</span>,<span class="no">type</span>[<span class="no">i</span>],<span class="st">"-"</span>),<span class="kw">times</span><span class="kw">=</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">10</span>,<span class="fl">1</span>,<span class="fl">10</span>)),<span class="st">"\n"</span>)
<span class="no">data</span> <span class="kw">&lt;-</span> <span class="kw pkg">curatedTCGAData</span><span class="kw ns">::</span><span class="fu">curatedTCGAData</span>(<span class="kw">diseaseCode</span><span class="kw">=</span><span class="no">type</span>[<span class="no">i</span>],<span class="kw">assays</span><span class="kw">=</span> <span class="st">"RNASeq2GeneNorm"</span>,<span class="kw">dry.run</span><span class="kw">=</span><span class="fl">FALSE</span>) <span class="no">data</span> <span class="kw">&lt;-</span> <span class="kw pkg">curatedTCGAData</span><span class="kw ns">::</span><span class="fu">curatedTCGAData</span>(<span class="kw">diseaseCode</span><span class="kw">=</span><span class="no">type</span>[<span class="no">i</span>],<span class="kw">assays</span><span class="kw">=</span> <span class="st">"RNASeq2GeneNorm"</span>,<span class="kw">dry.run</span><span class="kw">=</span><span class="fl">FALSE</span>)
<span class="no">data</span> <span class="kw">&lt;-</span> <span class="kw pkg">MultiAssayExperiment</span><span class="kw ns">::</span><span class="fu">mergeReplicates</span>(<span class="no">data</span>) <span class="no">data</span> <span class="kw">&lt;-</span> <span class="kw pkg">MultiAssayExperiment</span><span class="kw ns">::</span><span class="fu">mergeReplicates</span>(<span class="no">data</span>)
<span class="no">X</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/t.html">t</a></span>(<span class="kw pkg">SummarizedExperiment</span><span class="kw ns">::</span><span class="fu">assay</span>(<span class="no">data</span>)) <span class="no">X</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/t.html">t</a></span>(<span class="kw pkg">SummarizedExperiment</span><span class="kw ns">::</span><span class="fu"><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html">assay</a></span>(<span class="no">data</span>))
<span class="no">Y</span> <span class="kw">&lt;-</span> <span class="kw pkg">TCGAutils</span><span class="kw ns">::</span><span class="fu">TCGAbiospec</span>(<span class="fu"><a href="https://rdrr.io/r/base/colnames.html">rownames</a></span>(<span class="no">X</span>))$<span class="no">sample_definition</span> <span class="no">Y</span> <span class="kw">&lt;-</span> <span class="kw pkg">TCGAutils</span><span class="kw ns">::</span><span class="fu">TCGAbiospec</span>(<span class="fu"><a href="https://rdrr.io/r/base/colnames.html">rownames</a></span>(<span class="no">X</span>))$<span class="no">sample_definition</span>
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/table.html">table</a></span>(<span class="no">Y</span>)) <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/table.html">table</a></span>(<span class="no">Y</span>))
<span class="no">cond</span> <span class="kw">&lt;-</span> <span class="no">Y</span> <span class="kw">%in%</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Solid Tissue Normal"</span>,<span class="st">"Primary Solid Tumor"</span>) <span class="no">cond</span> <span class="kw">&lt;-</span> <span class="no">Y</span> <span class="kw">%in%</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Solid Tissue Normal"</span>,<span class="st">"Primary Solid Tumor"</span>)
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a> <a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
</span> </span>
</div> </div>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">starnet</a> <a class="navbar-link" href="index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
</span> </span>
</div> </div>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">starnet</a> <a class="navbar-link" href="index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
</span> </span>
</div> </div>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a> <a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
</span> </span>
</div> </div>
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article: article.html article: article.html
script: script.html script: script.html
starnet: starnet.html starnet: starnet.html
last_built: 2020-06-10T10:11Z last_built: 2020-10-21T05:34Z
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a> <a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
</span> </span>
</div> </div>
...@@ -163,8 +163,8 @@ respectively.</p> ...@@ -163,8 +163,8 @@ respectively.</p>
<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'>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'>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'>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'>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='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>)</div><div class='output co'>#&gt; <span class='error'>Error in loadNamespace(name): there is no package called 'joinet'</span></div><div class='input'><span class='no'>coef</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>object</span>)</div><div class='output co'>#&gt; <span class='error'>Error in coef(object): object 'object' not found</span></div><div class='input'>
<span class='no'>coef</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>object</span>)</div></pre> </div></pre>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top"> <nav id="toc" data-toggle="toc" class="sticky-top">
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a> <a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
</span> </span>
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...@@ -73,7 +73,7 @@ with different handling of sparsity constraints." /> ...@@ -73,7 +73,7 @@ with different handling of sparsity constraints." />
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a> <a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
</span> </span>
</div> </div>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a> <a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
</span> </span>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a> <a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a> <a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
</span> </span>
</div> </div>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a> <a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
</span> </span>
</div> </div>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a> <a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
</span> </span>
</div> </div>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a> <a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
</span> </span>
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...@@ -75,7 +75,7 @@ we combine multiple alphas by stacked generalisation." /> ...@@ -75,7 +75,7 @@ we combine multiple alphas by stacked generalisation." />
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a> <a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
</span> </span>
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docs/reference/starnet.html
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...@@ -72,7 +72,7 @@ ...@@ -72,7 +72,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a> <a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
</span> </span>
</div> </div>
......
docs/reference/weights.starnet.html
View file @ 0c348ca3
...@@ -73,7 +73,7 @@ i.e. the weights for the base learners." /> ...@@ -73,7 +73,7 @@ i.e. the weights for the base learners." />
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">starnet</a> <a class="navbar-link" href="../index.html">starnet</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
</span> </span>
</div> </div>
......
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